[Gate-users] benchSPECT run errors
Didier Benoit
benoit at imnc.in2p3.fr
Tue Apr 12 14:32:14 CEST 2011
Hi xuer,
You can visualize photon by photon try this:
/vis/open OGL 800x600-0+0
/vis/ogl/set/displayListLimit 8000000
/vis/viewer/set/viewpointThetaPhi 45 45
/vis/viewer/set/lightsMove camera
/vis/viewer/set/edge 1
/vis/viewer/set/hiddenEdge 1
/vis/drawVolume
/tracking/storeTrajectory 1
/vis/scene/add/trajectories
/vis/scene/add/trajectories smooth
Tell me if it works for you
Kind Regards,
Didier
On Apr 12, 2011, at 2:29 PM, xcao wrote:
> hi, Didier
>
> I know what the problem is, It is ok. I just found the display is not like the old Gate version(Gate5.0),
> so I think it have some problems. I think Gate6.1 have display all gammas, so it is ok!
> Thank you very much for your kindly help!
>
> Best wishes!
>
> xuer
>
>
> 2011-04-12
> xcao
> 发件人： Didier Benoit
> 发送时间： 2011-04-12 20:00:59
> 收件人： xcao
> 抄送： gate-users
> 主题： Re: [Gate-users] benchSPECT run errors
> Hi,
>
> If you want to use the visualization you can, it's just slow. In your first e-mail, your visualization was good.
>
> Kind Regards,
> Didier
>
> On Apr 12, 2011, at 1:56 PM, xcao wrote:
>
>> Hi，Didier
>>
>> I know it and I have tested it, it is ok!
>> But if I want to use visualization, how can I do with it.
>>
>> Best Regards
>> xuer
>>
>> 2011-04-12
>> xcao
>> 发件人： Didier Benoit
>> 发送时间： 2011-04-12 17:44:42
>> 收件人： xcao
>> 抄送： gate-users
>> 主题： Re: [Gate-users] benchSPECT run errors
>> Cao,
>>
>> You have a command:
>> /vis/disable
>>
>> Or just you delete the line about the visualization
>>
>> Kind Regards,
>> Didier
>>
>> On Apr 12, 2011, at 11:41 AM, xcao wrote:
>>
>>> Hi，Didier
>>>
>>> Ok，Ｉknow, thank you!
>>> Do you have any suggestion about visualization?
>>>
>>> Best Regards,
>>>
>>>
>>> 2011-04-12
>>> xcao
>>> 发件人： Didier Benoit
>>> 发送时间： 2011-04-12 17:27:12
>>> 收件人： xcao
>>> 抄送： gate-users
>>> 主题： Re: [Gate-users] benchSPECT run errors
>>> Hi Cao,
>>>
>>> If you don't want the Bremsstrahlung for the e+ it's not important. It's just a warning in this case.
>>>
>>> Kind Regards,
>>> Didier
>>>
>>> On Apr 12, 2011, at 10:53 AM, xcao wrote:
>>>
>>>> hi, Didier
>>>>
>>>> Thank you for your help, I think you conclusion is right, I check diable the visualization, it can run properly and the results is reasonable.
>>>> But there is a warning of e+:
>>>>
>>>> Particle: e+
>>>> * Model(s):
>>>> - <!> *** Warning *** <!> No model selected!
>>>>
>>>> I don't know if it will effect the programs.
>>>>
>>>> I checked the run informations with visualization, there is no obvious mistake(also have the ablove warning information)
>>>>
>>>> [G4]
>>>> [G4] *************************************************************
>>>> [G4] Geant4 version Name: geant4-09-03-patch-02 (17-September-2010)
>>>> [G4] Copyright : Geant4 Collaboration
>>>> [G4] Reference : NIM A 506 (2003), 250-303
>>>> [G4] WWW : http://cern.ch/geant4
>>>> [G4] *************************************************************
>>>> [G4]
>>>> [Core-0] Initialization of geometry
>>>> [Core-0] Initialization of physics
>>>> [Core-0] Initialization of actors
>>>> [Core-0]
>>>> [Core-0] **********************************************************************
>>>> [Core-0] GATE version name: gate_v6.1
>>>> [Core-0] Copyright : OpenGATE Collaboration
>>>> [Core-0] Reference : Phys. Med. Biol. 49 (2004) 4543-4561
>>>> [Core-0] Reference : Phys. Med. Biol. 56 (2011) 881-901
>>>> [Core-0] WWW : http://www.opengatecollaboration.org/
>>>> [Core-0] **********************************************************************
>>>> [Core-0]
>>>> [Core-0] Starting macro benchSPECT.mac
>>>> [G4] Got standard cmap
>>>> [G4] Window name: viewer-0 (OpenGLStoredX)
>>>> [G4] /tracking/storeTrajectory 1
>>>> [G4] GateDetectorConstruction::insertARFSD entered
>>>> [G4] created a ARF Sensivitive Detector
>>>> [G4] created command /gate/systems/SPECThead/arf/setARFStage
>>>> [G4] GetDirectoryName()+ setHeight = /gate/hole/geometry/setHeight
>>>> [G4] Translation speed = 0 0 0.04 cm/s
>>>> [G4] Translation speed = 0 0 0.04 cm/s
>>>> [G4]
>>>> [G4] GATE object: 'systems/SPECThead'
>>>> [G4] Components:
>>>> [G4]
>>>> [G4] GATE object: 'systems/SPECThead/base'
>>>> [G4] Attached to volume: SPECThead
>>>> [G4] Nb of children: 1
>>>> [G4] GATE object: 'systems/SPECThead/crystal'
>>>> [G4] Attached to volume: crystal
>>>> [G4] Nb of children: 1
>>>> [G4] GATE object: 'systems/SPECThead/pixel'
>>>> [G4] Attached to volume: ---
>>>> List of Enabled processes:
>>>> === Process: RayleighScattering ===
>>>> Particle: gamma
>>>> * Model(s):
>>>> - PenelopeModel
>>>> === Process: PhotoElectric ===
>>>> Particle: gamma
>>>> * Model(s):
>>>> - StandardModel
>>>> === Process: MultipleScattering ===
>>>> Particle: e-
>>>> === Process: ElectronIonisation ===
>>>> Particle: e+
>>>> * Model(s):
>>>> - <!> *** Warning *** <!> No model selected!
>>>> Particle: e-
>>>> * Model(s):
>>>> - StandardModel
>>>> === Process: Compton ===
>>>> Particle: gamma
>>>> * Model(s):
>>>> - PenelopeModel
>>>> === Process: Bremsstrahlung ===
>>>> Particle: e+
>>>> * Model(s):
>>>> - <!> *** Warning *** <!> No model selected!
>>>> Particle: e-
>>>> * Model(s):
>>>> - StandardModel
>>>> List of initialized processes:
>>>> [Core-0] Initialization of geometry
>>>> [Core-0] Initialization of physics
>>>> [Core-0] Initialization of actors
>>>> [G4] Nb of children: 0
>>>> Confirming confinement to volume 'movsource_phys'...
>>>> [Acquisition-0]
>>>> [Acquisition-0] ============= Source initialization =============
>>>> [Acquisition-0]
>>>> [Acquisition-0] ============= Acquisition starts! =============
>>>> [Acquisition-0] Simulation start time = 0 sec
>>>> [Acquisition-0] Simulation end time = 600 sec
>>>> [Acquisition-0] Simulation will have = 16 run(s)
>>>> --------- Ranlux engine status ---------
>>>> Initial seed = 123456789
>>>> randoms[] = 0.366829
>>>> 0.959976
>>>> 0.382801
>>>> 0.71216
>>>> 0.91131
>>>> 0.29693
>>>> 0.806733
>>>> 0.788568
>>>> 0.684343
>>>> 0.334206
>>>> 0.0928262
>>>> 0.66146
>>>> carry = 0, index = 11
>>>> luxury = 1 pDiscard = 87
>>>> ----------------------------------------
>>>> [Acquisition-0]
>>>> [Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final stop at 600 s.
>>>> [G4]
>>>> [G4] RayleighScattering: for gamma SubType= 11
>>>> [G4] Lambda tables from 100 eV to 10 TeV in 200 bins, spline: 1
>>>> [G4] ===== EM models for the G4Region DefaultRegionForTheWorld ======
>>>> [G4] PenRayleigh : Emin= 0 eV Emax= 100 GeV
>>>> [G4]
>>>> [G4] PhotoElectric: for gamma SubType= 12
>>>> [G4] ===== EM models for the G4Region DefaultRegionForTheWorld ======
>>>> [G4] PhotoElectric : Emin= 0 eV Emax= 10 TeV
>>>> [G4]
>>>> [G4] Compton: for gamma SubType= 13
>>>> [G4] Lambda tables from 100 eV to 10 TeV in 77 bins, spline: 1
>>>> [G4] ===== EM models for the G4Region DefaultRegionForTheWorld ======
>>>> [G4] PenCompton : Emin= 0 eV Emax= 10 TeV
>>>> [G4]
>>>> [G4] MultipleScattering: for e- SubType= 10
>>>> [G4] Lambda tables from 100 eV to 10 TeV in 77 bins, spline: 1
>>>> [G4] RangeFactor= 0.2, stepLimitType: 0, latDisplacement: 1, skin= 3, geomFactor= 2.5
>>>> [G4] ===== EM models for the G4Region DefaultRegionForTheWorld ======
>>>> [G4] UrbanMsc90 : Emin= 0 eV Emax= 10 TeV
>>>> [G4]
>>>> [G4] ElectronIonisation: for e- SubType= 2
>>>> [G4] dE/dx and range tables from 100 eV to 10 TeV in 77 bins
>>>> [G4] Lambda tables from threshold to 10 TeV in 77 bins, spline: 1
>>>> [G4] finalRange(mm)= 1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
>>>> [G4] ===== EM models for the G4Region DefaultRegionForTheWorld ======
>>>> [G4] MollerBhabha : Emin= 0 eV Emax= 10 TeV
>>>> [G4]
>>>> [G4] Bremsstrahlung: for e- SubType= 3
>>>> [G4] dE/dx and range tables from 100 eV to 10 TeV in 77 bins
>>>> [G4] Lambda tables from threshold to 10 TeV in 77 bins, spline: 1
>>>> [G4] LPM flag: 1 for E > 1 GeV
>>>> [G4] ===== EM models for the G4Region DefaultRegionForTheWorld ======
>>>> [G4] eBrem : Emin= 0 eV Emax= 1 GeV
>>>> [G4] eBremRel : Emin= 1 GeV Emax= 10 TeV
>>>> [G4]
>>>> [G4] ElectronIonisation: for e+ SubType= 2
>>>> [G4] dE/dx and range tables from 100 eV to 10 TeV in 77 bins
>>>> [G4] Lambda tables from threshold to 10 TeV in 77 bins, spline: 1
>>>> [G4] finalRange(mm)= 1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
>>>> [G4] ===== EM models for the G4Region DefaultRegionForTheWorld ======
>>>> [G4] MollerBhabha : Emin= 0 eV Emax= 10 TeV
>>>> [G4]
>>>> [G4] Bremsstrahlung: for e+ SubType= 3
>>>> [G4] dE/dx and range tables from 100 eV to 10 TeV in 77 bins
>>>> [G4] Lambda tables from threshold to 10 TeV in 77 bins, spline: 1
>>>> [G4] LPM flag: 1 for E > 1 GeV
>>>> [G4] ===== EM models for the G4Region DefaultRegionForTheWorld ======
>>>> [G4] eBrem : Emin= 0 eV Emax= 1 GeV
>>>> [G4] eBremRel : Emin= 1 GeV Emax= 10 TeV
>>>> [G4] clearing up the projection data matrices ... done
>>>>
>>>>
>>>> But I found when I run Geant4 examples, there are output information about visualization of these:
>>>>
>>>> You have successfully registered the following graphics systems.
>>>> Current available graphics systems are:
>>>> ASCIITree (ATree)
>>>> DAWNFILE (DAWNFILE)
>>>> G4HepRep (HepRepXML)
>>>> G4HepRepFile (HepRepFile)
>>>> RayTracer (RayTracer)
>>>> VRML1FILE (VRML1FILE)
>>>> VRML2FILE (VRML2FILE)
>>>> gMocrenFile (gMocrenFile)
>>>> FukuiRenderer (DAWN)
>>>> OpenGLImmediateX (OGLIX)
>>>> OpenGLStoredX (OGLSX)
>>>> RayTracerX (RayTracerX)
>>>> Registering model factories...
>>>> You have successfully registered the following model factories.
>>>> Registered model factories:
>>>> generic
>>>> drawByCharge
>>>> drawByParticleID
>>>> drawByOriginVolume
>>>> drawByAttribute
>>>> Registered filter factories:
>>>> chargeFilter
>>>> particleFilter
>>>> originVolumeFilter
>>>> attributeFilter
>>>>
>>>> But Gate programs do not have, does it matter?
>>>>
>>>>
>>>> 2011-04-12
>>>> xcao
>>>> 发件人： Didier Benoit
>>>> 发送时间： 2011-04-11 18:13:20
>>>> 收件人： xcao
>>>> 抄送： gate-users
>>>> 主题： Re: [Gate-users] benchSPECT run errors
>>>> Hi Cao,
>>>>
>>>> Your detector seems good on your screenshot, and it's normal for your gammas. You have to disable the visualization. The visualization is just to check the position of your detector and source.
>>>> Do you have some errors when you launch GATE?
>>>>
>>>> Kind Regards,
>>>> Didier
>>>>
>>>> On 04/06/2011 05:19 AM, xcao wrote:
>>>>>
>>>>> hi, gate users!
>>>>>
>>>>> I have installed Gate6.1 on Scientific Linux CERN 5.6 (SLC5.6) with geant4.9.3.p02 and root-5.26、clhep-2.0.4.5.
>>>>> and everything goes well, but when I run benchSPECT for test, it returns unproper results:
>>>>> 1. The detector is not constructed completely
>>>>> 2. There are so many gammas, and it will not stop.
>>>>> just like this :
>>>>>
>>>>>
>>>>> I run Geant4 examples as test, and it runs ok, no errors return, and the results is correct.
>>>>> My PATH and LD_LIBRARY_PATH is :
>>>>> $echo $PATH
>>>>> /opt/software_simulation/ROOT/root/bin:/opt/software_simulation/Gate/gate_v6.1/bin/Linuxg++:
>>>>> /opt/software_simulation/Dawn/dawn_3_90b:/opt/software_simulation/ROOT/root/bin:/usr/sue/sbin:
>>>>> /usr/sue/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:
>>>>> /usr/X11R6/bin:/root/bin:/opt/software_simulation/Geant4/g4work/bin/Linux-g++
>>>>>
>>>>> $echo $LD_LIBRARY_PATH
>>>>> /opt/software_simulation/Gate/gate_v6.1/tmp/Linux-g++/Gate:/opt/software_simulation/ROOT/root/lib:
>>>>> /opt/software_simulation/CLHEP/lib:/opt/software_simulation/CLHEP/lib/:
>>>>> /opt/software_simulation/ROOT/root/lib::/opt/software_simulation/Geant4/geant4.9.3.p02/lib/Linux-g++:
>>>>> /opt/software_simulation/CLHEP/lib:/opt/software_simulation/lmf/lib
>>>>>
>>>>> Can anyone give me some helps or any suggestion.
>>>>> Thank you!
>>>>>
>>>>>
>>>>> 2011-04-06
>>>>>
>>>>>
>>>>>
>>>>> xcao
>>>>>
>>>>> _______________________________________________
>>>>> Gate-users mailing list
>>>>> Gate-users at lists.opengatecollaboration.org
>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>
>>>>
>>>> --
>>>> ----------------------------------------------------------------
>>>> Didier BENOIT, GATE Engineer
>>>>
>>>> Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
>>>> IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
>>>> Campus d’Orsay
>>>> Bâtiment 440
>>>> 91405 ORSAY Cedex
>>>>
>>>> Tél : (33) 1 69 15 68 76
>>>> E-mail : benoit at imnc.in2p3.fr
>>>> http://www.imnc.in2p3.fr
>>>> ----------------------------------------------------------------
>>>
>>> ----------------------------------------------------------------
>>> Didier BENOIT, GATE Engineer
>>> Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
>>> IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
>>> Campus d’Orsay
>>> Bâtiment 440
>>> 91406 ORSAY Cedex
>>>
>>> Tél : (33) 1 69 15 68 76
>>> E-mail : benoit at imnc.in2p3.fr
>>> http://www.imnc.in2p3.fr
>>> ----------------------------------------------------------------
>>>
>>>
>>>
>>
>> ----------------------------------------------------------------
>> Didier BENOIT, GATE Engineer
>> Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
>> IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
>> Campus d’Orsay
>> Bâtiment 440
>> 91406 ORSAY Cedex
>>
>> Tél : (33) 1 69 15 68 76
>> E-mail : benoit at imnc.in2p3.fr
>> http://www.imnc.in2p3.fr
>> ----------------------------------------------------------------
>>
>>
>>
>
> ----------------------------------------------------------------
> Didier BENOIT, GATE Engineer
> Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
> IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
> Campus d’Orsay
> Bâtiment 440
> 91406 ORSAY Cedex
>
> Tél : (33) 1 69 15 68 76
> E-mail : benoit at imnc.in2p3.fr
> http://www.imnc.in2p3.fr
> ----------------------------------------------------------------
>
>
>
----------------------------------------------------------------
Didier BENOIT, GATE Engineer
Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
Campus d’Orsay
Bâtiment 440
91406 ORSAY Cedex
Tél : (33) 1 69 15 68 76
E-mail : benoit at imnc.in2p3.fr
http://www.imnc.in2p3.fr
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