[Gate-users] ROOT tree is empty

jmmaratas at physics.msuiit.edu.ph jmmaratas at physics.msuiit.edu.ph
Tue Jul 29 23:54:21 CEST 2008

Dear Gate-users,

I am a new user of GATE and this is the first that I joined the Gate-talk.
I started studying, practicing, and using GATE now. I read some of the
thread and I was able to implement a voxelized phantom (zubal
cardiac/torso phantom) by converting the data to interfile format. I can
visualize it, modify its size and the materials. In other words, I believe
I succesfully installed ROOTv5.14, CLHEPv2.0.3.1, GEANT4.9.0.p02,
GATE3.1.2. In fact, I even tried the benchmarkPET and benchmarkSPECT
examples with no problem encountered.

However, when I implemented the voxelized zubal cardiac/torso phantom, I
am no longer sure what to do next. For example,
(1) The "Hits" of the ROOT output turns out to be empty. I mean I can see
the leaves (nPhantomCompton, nCrystalCompton, etc), however when I
double-click it, nothing happens. This the macro of the phantom that I

/gate/world/daughters/name     zubalphantom
/gate/world/daughters/insert   parameterizedBoxMatrix
/gate/zubalphantom/geometry/insertReader   interfile
/gate/zubalphantom/interfileReader/insertTranslator   range
/gate/zubalphantom/interfileReader/rangeTranslator/readTable   range.dat
/gate/zubalphantom/interfileReader/readFile   zubalphantom.h33

/gate/zubalphantom/addOutput   doseOutput
/gate/output/doseOutput/setFileName     zubalphantom_dose.bin

Prior to this, I used SPECThead as the system of my scanner. This is the
macro (scanner) file that I used,

/gate/world/daughters/name      SPECThead
/gate/world/daughters/insert    box
/gate/SPECThead/geometry/setXLength   60. cm
/gate/SPECThead/geometry/setYLength   5. cm
/gate/SPECThead/geometry/setXLength    5. cm
/gate/SPECThead/placement/setTranslation  0. 0. 57.5 cm
/gate/SPECThead/setMaterial     Water

/gate/SPECThead/daughters/name   crystal
/gate/SPECThead/daughters/insert box
/gate/SPECThead/geometry/setXLength   60. cm
/gate/SPECThead/geometry/setYLength   5. cm
/gate/SPECThead/geometry/setXLength    5. cm
/gate/SPECThead/setMaterial     Water

/gate/systems/SPECThead/crystal/attach   crystal

And the macro for data output and format is this,

/gate/output/root/setSaveRndmFlag    1
/gate/output/root/setRootHitFlag     1
/gate/output/root/setRootSinglesFlag 1
/gate/output/root/setRootNtupleFlag  1
/gate/output/root/setFileName        zubalphantom

(2) By the way, how should I open the output binary file
(zubalphantom_dose.bin)? I've read in the Gate-user's talk archive/s that
I can open it using Amide. But I need the numbers. :)

Or is it that the parameterizedBoxMatrix phantom not yet allowed/ready to
save its output in Root?

Any help is and will be much appreciated!

Sincerely yours,

Jan Mickelle V. Maratas

* @ Computational High Energy Physics, Physics Department, MSU - Iligan
Institute of Technology
* A. Bonifacio Ave., Tibanga, 9200 Iligan City, Philippines

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