[Gate-users] Σχετ: Σχετ: Energy spectrum

David Boersma david.boersma at igp.uu.se
Wed Sep 27 10:49:30 CEST 2017 

Hi Tony,

Unfortunately your macro depends on several items that I do not have. 
When I run (using the same Gate and ROOT releases) the 
mac/fluorescenceTest.mac example in 
{Gate_v7.2_srcdir}/examples/example_fluorescence/ (which has an energy 
spectrum actor) then I do not see the warnings/errors that you see.

Can you tell us what stdout/stderr you get when you run this example on 
your system?

Another basic check: could you completely comment out the energy 
spectrum actor and run your macro one more time?

* If you then still see the same ROOT errors/warnings then they are 
obviously not caused by the spectrum actor, maybe they are coming from 
the physics list or the phasespace instead.

* If the errors/warnings do disappear then we need to have another hard 
look at the spectrum actor. Increasing the verbosity of "Actor" might 
helpful for the localization the problem.

(I already stared at the GATE & ROOT code quite a bit yesterday and I 
can see which lines in the TH1 and TH2 code are giving the warnings you 
quote, but they are in methods that do not appear to be used in the 
energy spectrum code.)

The warnings might be completely harmless, but they could also be 
indicative of some subtle bug. That's the very reason for warnings to 
begin with. So it's good to report them (and even better to really 
understand them and fix the causes so that the warnings go away).

/DavidB



Den 26/09/2017 kl. 15:15, skrev tony youness:
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> #                     VERBOSE and VISUALISATION
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> /control/execute mac/verbose.mac
> #/control/execute mac/visu.mac
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> #         A specific material database is created
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> /gate/geometry/setMaterialDatabase data/Materials.db
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> #                     GEOMETRY
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> #                     WORLD
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> /gate/world/setMaterial Air
> /gate/world/geometry/setXLength 5.0 m
> /gate/world/geometry/setYLength 5.0 m
> /gate/world/geometry/setZLength 5.0 m
> /gate/world/vis/setVisible 0
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> #                 PATIENT/PHANTOM
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> /control/execute mac/Waterphantom_DSP95.mac
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> #                 Accelerator GEOMETRY
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> /control/execute mac/Linac.mac
> 
> 
> #=====================================================
> # OUTPUT ACTORS
> #=====================================================
> 
> /gate/actor/addActor          EnergySpectrumActor    spectrum
> /gate/actor/spectrum/attachTo                        layer3
> /gate/actor/spectrum/addFilter                       particleFilter
> /gate/actor/spectrum/particleFilter/addParticle      e-
> /gate/actor/spectrum/save                            output/WaterSpec.root
> /gate/actor/spectrum/energySpectrum/setEmin          0 eV
> /gate/actor/spectrum/energySpectrum/setEmax          6 MeV
> /gate/actor/spectrum/energySpectrum/setNumberOfBins  300
> 
> 
> 
> #=====================================================
> # PHYSICS
> #=====================================================
> 
> /gate/physics/addPhysicsList emlivermore
> /gate/physics/Gamma/SetCutInRegion      world 1 mm
> /gate/physics/Electron/SetCutInRegion   world 1 mm
> /gate/physics/Positron/SetCutInRegion   world 1 mm
> /gate/physics/Gamma/SetCutInRegion      patient 0.1 mm
> /gate/physics/Electron/SetCutInRegion   patient 0.1 mm
> /gate/physics/Positron/SetCutInRegion   patient 0.1 mm
> /gate/physics/Gamma/SetCutInRegion      mylinac 1 mm
> /gate/physics/Electron/SetCutInRegion   mylinac 1 mm
> /gate/physics/Positron/SetCutInRegion   mylinac 1 mm
> /gate/physics/displayCuts
> /gate/physics/print output/physics.txt
> 
> #=====================================================
> # INITIALISATION
> #=====================================================
> 
> 
> /gate/run/initialize
> 
> 
> #=====================================================
> # INPUT BEAM
> #=====================================================
> 
> /gate/source/addSource MyBeam phaseSpace
> /gate/source/MyBeam/addPhaseSpaceFile data/IAEA.IAEAphsp
> /gate/source/MyBeam/attachTo outPhSp
> 
> #=====================================================
> # START BEAMS
> #=====================================================
> 
> /gate/random/setEngineName MersenneTwister
> /gate/random/setEngineSeed auto
> /control/execute mac/timeslices.mac
> /gate/application/setTotalNumberOfPrimaries 10000000
> /gate/application/start
> 
> 
> On 26/09/17 3:03 pm, Konstantinos P. Chatzipapas, MSc wrote:
>> If you can, please attach the mac file that you use.
>> -----------------------------------------------------
>>  Konstantinos Chatzipapas
>>     Medical Physicist, MSc
>> University of Patras
>>
>>    web page:Physics Magazine <http://www.physicsmag.com/>
>>
>>
>> Στις 3:57 μ.μ. Τρίτη, 26 Σεπτεμβρίου 2017, ο/η tony youness 
>> <tony_youness at live.com> έγραψε:
>>
>>
>> Hi,
>> I just tried to stick with only basic commands and still getting the 
>> same error.
>>
>>
>> On 26/09/17 2:35 pm, Konstantinos P. Chatzipapas, MSc wrote:
>>> Hi,
>>>
>>> Have you try to only use the basic commands that are given by the 
>>> guide?? Do they work??
>>>
>>>
>>>       Energy spectrum
>>>
>>> This actor builds four histograms: the initial kinetic energy of each 
>>> track (energySpectrum), the energy deposition per event (edepHisto), 
>>> the energy deposition per track (edepTrackHisto), the energy loss per 
>>> track (eLossHisto). These histograms are stored in a root file. They 
>>> takes into account the weight of particles. They are three commands 
>>> to define the boundaries and the binning of the energy spectrum and 
>>> three commands to define the boundaries and the binning of the energy 
>>> loss histograms (edepHisto, edepTrackHisto, eLossHisto).
>>> /gate/actor/addActor  EnergySpectrumActor*MyActor*
>>> /gate/actor/*MyActor*/save  MyOutputFile.root
>>> /gate/actor/*MyActor*/energySpectrum/setEmin 0 eV
>>> /gate/actor/*MyActor*/energySpectrum/setEmax 10 GeV
>>> /gate/actor/*MyActor*/energySpectrum/setNumberOfBins 200
>>> /gate/actor/*MyActor*/energyLossHisto/setEmin 0 eV
>>> /gate/actor/*MyActor*/energyLossHisto/setEmax 15 MeV
>>> /gate/actor/*MyActor*/energyLossHisto/setNumberOfBins 120
>>>
>>> If you haven't try them, try. Because I see that you are trying with 
>>> extra commands, such as AttachTo, Filter etc.
>>> Regards,
>>> -----------------------------------------------------
>>>  Konstantinos Chatzipapas
>>>     Medical Physicist, MSc
>>> University of Patras
>>>
>>>    web page:Physics Magazine <http://www.physicsmag.com/>
>>>
>>>
>>> Στις 3:23 μ.μ. Τρίτη, 26 Σεπτεμβρίου 2017, ο/η tony youness 
>>> <tony_youness at live.com> <mailto:tony_youness at live.com> έγραψε:
>>>
>>>
>>> Dear David,
>>>
>>> -Gate v7.2
>>>
>>> -Root v5.34/30
>>>
>>> Tony
>>>
>>>
>>> On 26/09/17 2:17 pm, David Boersma wrote:
>>> > Dear Tony,
>>> >
>>> > For us to reproduce the error:
>>> > - Which version of GATE?
>>> > - Which version of ROOT?
>>> >
>>> > DavidB
>>> >
>>> > Den 26/09/2017 kl. 14:03, skrev tony youness:
>>> >> Dear Maxime,
>>> >>
>>> >> Thank you for your response.
>>> >>
>>> >> I just tried to increase the Emin to 1 MeV and reduced the number of
>>> >> bins to 100 (just for testing), and I still get the same error...
>>> >>
>>> >> Tony
>>> >>
>>> >>
>>> >> On 26/09/17 1:51 pm, Maxime Chauvin wrote:
>>> >>> Dear Tony,
>>> >>>
>>> >>> what I can tell is that the error seems to come from Root (TH1D).
>>> >>> I don’t know what cause the error but maybe the number of bins is
>>> >>> too high or the Emin is too small…
>>> >>>
>>> >>>    Maxime
>>> >>>
>>> >>>> On 26 Sep 2017, at 13:17, tony youness <tony_youness at live.com 
>>> <mailto:tony_youness at live.com>> wrote:
>>> >>>>
>>> >>>> Dear fellow Gate users,
>>> >>>>
>>> >>>> I am trying to generate the electrons energy spectrum at 10 cm in
>>> >>>> water
>>> >>>> phantom. I used the Energy spectrum actor as follow:
>>> >>>>
>>> >>>> /gate/actor/addActor          EnergySpectrumActor spectrum
>>> >>>> /gate/actor/spectrum/attachTo                        layer3
>>> >>>> /gate/actor/spectrum/addFilter particleFilter
>>> >>>> /gate/actor/spectrum/particleFilter/addParticle      e-
>>> >>>> /gate/actor/spectrum/save output/WaterSpec.root
>>> >>>> /gate/actor/spectrum/energySpectrum/setEmin          0 eV
>>> >>>> /gate/actor/spectrum/energySpectrum/setEmax          6 MeV
>>> >>>> /gate/actor/spectrum/energySpectrum/setNumberOfBins  300
>>> >>>>
>>> >>>> layer3 is a small water volume created in the water phantom at 
>>> 10 cm.
>>> >>>> When i launch the simulation i get the following error:
>>> >>>>
>>> >>>> Error in <TH1D::Rebin>: Illegal value of ngroup=10815379
>>> >>>> Error in <TH1D::Rebin>: Illegal value of ngroup=10815379
>>> >>>> Error in <TH2D::Rebin>: Illegal value of nxgroup=10815379
>>> >>>> Error in <TH1D::Rebin>: Illegal value of ngroup=10815379
>>> >>>> Error in <TH1D::Rebin>: Illegal value of ngroup=10815379
>>> >>>> WARNING: Scene "none" not found.
>>> >>>>    /vis/scene/list to see scenes.
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>> ### === G4UAtomicDeexcitation::InitialiseForNewRun()
>>> >>>> ### ===  PIXE model for hadrons: Empirical
>>> >>>> ### ===  PIXE model for e+-:    Livermore
>>> >>>> Error in <TH2D::Fill>: Invalid signature - do nothing
>>> >>>> Error in <TH2D::Fill>: Invalid signature - do nothing
>>> >>>> Error in <TH2D::Fill>: Invalid signature - do nothing
>>> >>>> Error in <TH2D::Fill>: Invalid signature - do nothing
>>> >>>> Error in <TH2D::Fill>: Invalid signature - do nothing
>>> >>>> Error in <TH2D::Fill>: Invalid signature - do nothing
>>> >>>> Error in <TH2D::Fill>: Invalid signature - do nothing
>>> >>>> ...
>>> >>>>
>>> >>>> Any ideas where this problem could come from?
>>> >>>>
>>> >>>> Regards,
>>> >>>>
>>> >>>> Tony Younes
>>> >>>>
>>> >>>> _______________________________________________
>>> >>>> Gate-users mailing list
>>> >>>> Gate-users at lists.opengatecollaboration.org 
>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>> >>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>
>>> >>
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>>>
>>
>>
>>
> 
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