[Gate-users] Gate Root Output

[Marcin Balcerzyk]

Dear Yuri.

If I may suggest, first try to enable Singles in the root output (this should not affect the singles input to digitizer), and Hits output. Run simulation so that there is a few thousands decays expected and see in root viewer if there are hits. If you have hits and no singles, you may have problem with SetDepth. To check it out generate a very small ascii output and make sense at which level your hits appear and set proper depth (I think you can see that also in a root file in appropriate leaf). In asci file of hits have a look at the position of your hits if it is correctly located in the crystals.

If you have no hits, then probably something is wrong with your detection system, for example the material is wrongly defined or you rotate subsystem of your scanner, without rotating main cylinder of the PET. 

If you have hits but no singles, have a look how you group your hits to make a pulse. In ascii file, if you sum up manually the deposited energy of an event with particular number, and it is within the window of energy, but it does not appear as single, so maybe your setDepth is wrong. In doubtfull case, I would open the energy window for singles.

In still doubtfull case, run your simulation of benchmarkPET and see the generated root file. 

Kind regards
Marcin Balcerzyk

> Message: 3
> Date: Mon, 4 Jun 2012 14:06:22 -0300
> From: Yuri Jaeger Monti <yurijm at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Gate Root Output
> Message-ID:
> <CABbroOa_fRYsJiaTBgmgn38ZdWPGrmN7c6G63dtQcGnNAXii_w at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hello friends,
> 
> I'm trying to get Gate 6.1 to generate output for Root, but I'm having
> some problems (and looks like other users as well) with the digi
> collection modules.
> 
> I'm asking you guys in hope that you could at least give me a 
> hint on
> what this problem could be, because I'm stuck at this and don't know
> what to do anymore. :)
> 
> When running my simulation with verbose 2 set in root, Gate 
> would tell
> me that it could not find some "digi collections" and generates an
> empty root file output. The errors are like this:
> 
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'Singles' not found
> [GateToRoot::CoincidenceOutputChannel::RecordDigitizer]: digi
> collection 'Coincidences' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesAdder' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesReadout' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesBlurring' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesThresholder' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesUpholder' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'Singles' not found
> 
> Someone also got this same error and sent it to the mailing list last
> year, but no answer was given, I contacted him and he told me he had
> to downgrade to Gate version 5 to get it to work.
> 
> Below is his original thread with more detailed description 
> about the problem:
> 
> "
> From: Pieter Mollet <pieter.mollet at ...>
> Subject: gate2root in Gate 6.1
> Newsgroups: gmane.comp.science.opengate.user
> Date: 2011-08-26 13:27:53 GMT (38 weeks, 6 days, 5 hours and 51 
> minutes ago)
> 
> Hi,
> 
> I'm running PET simulations in Gate 6.1. My digitizer and output
> commands are shown below. Although the commands are right, there seems
> to be a problem with the gate2root module and the root-files are 
> empty.
> Error :
> 
>  [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi 
> collection'Singles' not found
> [GateToRoot::CoincidenceOutputChannel::RecordDigitizer]: digi 
> collection'Coincidences' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesAdder' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesReadout' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesBlurring' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesThresholder' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'SinglesUpholder' not found
> [GateToRoot::SingleOutputChannel::RecordDigitizer]: digi collection
> 'Singles' not found
> 
> Commands :
> 
> # D I G I T I Z E R
> /gate/digitizer/Singles/insert adder
> /gate/digitizer/Singles/insert readout
> /gate/digitizer/Singles/readout/setDepth 1
> /gate/digitizer/Singles/insert blurring
> /gate/digitizer/Singles/blurring/setResolution 0.115
> /gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
> /gate/digitizer/Singles/insert thresholder
> /gate/digitizer/Singles/thresholder/setThreshold 440. keV
> /gate/digitizer/Singles/insert upholder
> /gate/digitizer/Singles/upholder/setUphold 665. keV
> 
> # C O I N C I    S O R T E R
> /gate/digitizer/Coincidences/setWindow 3.8 ns
> /gate/digitizer/Coincidences/minSectorDifference 7
> /gate/digitizer/Coincidences/MultiplesPolicy  takeWinnerOfGoods
> 
> ####################################################
> #     ROOT 
> OUTPUT                                  #
> ####################################################
> /gate/output/root/enable
> /gate/output/root/setFileName GEMINI_NEMA
> /gate/output/root/setRootHitFlag 0
> /gate/output/root/setRootSinglesFlag 0
> /gate/output/root/setRootCoincidencesFlag 1
> /gate/output/root/setRootNtupleFlag 0
> /gate/output/root/verbose 2
> 
> "
> 
> If you could share some information of what this could be, it 
> would be awesome!
> 
> Thank you all for the attention!
> 
> Best regards,
> ---
> Yuri Jaeger Monti
> PUCRS University
> Porto Alegre - RS - Brazil
> 
>