[Gate-users] optical and traditional Singles.

venialgo at cae.cnea.gov.ar venialgo at cae.cnea.gov.ar
Tue May 26 20:59:34 CEST 2009

Hi Uwe,

I checked the files you've sent me, and I think that in your macro file
you've defined only the optical adder because the Z position of the
singles in the file test.datSingles.dat are all the same ( I think the
photocatode position). For this reason, I think that in your singles file
you're not getting the tradictional singles, but only the optical singles.

What I want to know is the position of the scintillation event inside the
crystal, and the amount of light received in each photocatode.

A colleague is working with a delayed coincidence window to calculate the
random coincidence ratio. He advised me to use the same structure for the
commands to define a parallel chain, in the same way as it's defined for a
delayed coincidence sorter.

And finally it's working using the next commands:

# first of all, attach the photocatodes to store the amount of light
received in each PMT:
/gate/systems/SPECThead/pixel/attach PMTwindow

# second of all, attach the NaI crystal to store the gamma interaction
/gate/systems/SPECThead/crystal/attach cristalIoduro

# Also I defined two chains in parallel, one for the optical singles,
another one for the traditional singles inside the crystal.

/gate/digitizer/Singles/insert adder
/gate/digitizer/name OpticalSingles
/gate/digitizer/insert singleChain
/gate/digitizer/OpticalSingles/insert opticaladder

# And finally, enable the single output for each chain.
/gate/output/ascii/setOutFileSinglesFlag 1
/gate/output/ascii/setOutFileOpticalSinglesFlag 1

It's working, and I have one file of singles for each chain, one with the
traditional and other one with optical.


..I read your e-mail, and you recommend to run the "standard analysis"..
I'm using "fast analysis" because I want to speed up the simulation, but
in the manual says that the compton interaction in the crystal is missing.
And,  what does missing mean ??
1) Simulated but not stored, or
2) Not simulated, so not stored,

it is not same for me, because I'm studying the crystal resolution, and
the compton iteraction into the crystal is a factor which degrades it, so
I want to simulate it.

thanks for your help. Bye, Esteban.

> Dear  Esteban,
> recently one of our students came across the same problem / question.
> I looked into it and found the following concept, which I hope is
> correct
> (and experts, please, should correct me!!!).
> Unfortunately, I could not find any example root module for a combined
> analysis of standard and optical photons.
> All remarks refer to gate_v4.0.0!!
> Using the "opticaladder" adds the optical photons to the standard and
> does not replace the standard information! For a comprehensive
> analysis it is also recommended to run the standard "analysis"
> and not the "fastanalysis".
> The information concerning the gamma and the optical photons
> created by the incident gamma through photoeffect, comptoneffect, ...
> are stored in root files under
> gamma  >>  singles-tree
> optical photons  >>  hits-tree
> and also in the singles and hits ascii files, once you have switched
> on the ascii output option.
> Note, that the acscii files can get quite large, especially the "hits".
> For my tests I modified the materials.xml file reducing the number
> of photons per MeV in LSO from 26000 to 1000.
> In the attached file you find a simple example for a root source code
> reading root file and checking its contents.
> I also included the ascii files for comparison.
> Maybe this is helpful for you. I cannot warrant, that my understanding
> of handling the optical photons in GATE is correct, but it looked
> consistent to me.
> Kind regards,
> Uwe Pietrzyk
> On 20.05.2009, at 15:52, venialgo at cae.cnea.gov.ar wrote:
>> Hello Gate Users
>> I'm simulating the optical photons, I've defined a continuous
>> crystal of
>> NaI(Tl) coupled to an array of 6x8 PMTs. I have defined also the
>> optical
>> adder and I have the information of the amount of light received in
>> each
>> PMT, but also I want to know the position of the singles calculated
>> as the
>> energy-weighted centroid of the different hit positions produced by
>> the
>> gamma interaction into the crystal.
>> In the section 12.4 of the Gate Users guide v3.1.2 says it's to
>> possible
>> to create two chains in parallel one containing the traditional
>> singles
>> and one containing the singles generated by the optical photons.
>> In the macro I've just written:
>> /gate/digitizer/Singles/insert adder
>> /gate/digitizer/Singles/insert opticaladder
>> And the gateSingles.dat is completely empty.
>> but, when I comment out the optical adder ..
>> /gate/digitizer/Singles/insert adder
>> # /gate/digitizer/Singles/insert opticaladder
>> The  gateSingles.dat has the information of the traditional singles.
>> even more,  when I comment out the adder
>> # /gate/digitizer/Singles/insert adder
>> /gate/digitizer/Singles/insert opticaladder
>> The  gateSingles.dat has the information of the optical singles.
>> And finally I ran the simulation 7 days with the optical adder
>> commented
>> out, and 7 days more with the adder commented out. Obviously using the
>> same seed file in each run.
>> I want simulate only once, with two digitizer chains in parallel,
>> which
>> takes only 7 days, if it's possible off course.
>> P.S: I'm not using the last version of Gate, My configuration is :
>> Plataforma/Gate:  ROOT 5.14 / CLHEP / GEANT 4.9.0 (PATCH) /
>> 3.1.2                                            O.S.: Debian 4.0r1
>> AMD64
>> Kernel 2.6.24-etchnhalf.1-amd64
>> Thanks for your help,
>> Bye, Esteban Venialgo
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.healthgrid.org
>> http://lists.healthgrid.org/mailman/listinfo/gate-users
> /----------------------------------------------------------------------
> Prof. Dr. Uwe Pietrzyk
> Diplom-Physiker
> Institut für Neurowissenschaften und Medizin / INM-1
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