[Gate-users] Re: Gate-users Digest, Vol 24, Issue 31
Nicolas Karakatsanis
knicolas at mail.ntua.gr
Tue May 27 23:56:47 CEST 2008
Dear Sonal
thanks for sending me the macro.
By checking the commands I spotted that your macro contains two comment
lines which include the character "_".
As we had discussed recently in this mailing list the presence of the
character "_" inside comment lines is causing an error and the abortion
of the simulation at the current version of GATE (3.1.2)
The most common case is the presence of this character at the comment
lines preceding the section of the GATE macro code that is referring to
the ROOT and ASCII output.
By removing the character "_" from these comment lines the error
messages will no longer be printed.
Unfortunately this is a common mistake when someone uses the example or
benchmark macros provided with the latest GATE distribution. So keep in
mind to check these two particular comment lines at all the above
mentioned macros and remove these characters. This will be corrected in
the next version of GATE.
However in you macro I observed that, despite the above corrections,
your simulation was still exiting with an error status.
Another possible source for these errors are hidden characters inside
your macro.
These hidden characters are usually added by text editors of non-Linux
operating systems and represent the EOL (end of line) or EOF (end of
text file) characters.
Unfortunately most Linux text editors use a different character to
signal the end of line compared to some popular windows text editors
such as Notepad.
My suggestion is to avoid using Notepad to edit files that you are going
later to use in Linux to run applications (e.g. Gate macro files)
In order to quickly deal with this problem I used the following Unix
command "tr" that is designed to perform some basic operations at the
ASCII characters of a text file.
tr -d '\r' <PET_Ecat_System.mac> PET_Ecat_System1.mac
Thus, I removed the EOL "\r" character (added by another text editor,
probably windows Notepad) and left only the EOL character "\n" which is
actually used by Linux to signal end of line in a text file. A new macro
file was created with the filename: PET_Ecat_System1.mac.
After that GATE was able to correctly read all the command and comment
lines of the new macro file and proceed with the execution of the GATE
simulation without aborting!
If you would like to learn more about the hidden characters added by
text editors and the purpose of the Unix command "tr" I have posted a
more detailed text at the GATE-user mailing list
Please try these two suggestions and let us know about the outcome!
Best regards
Nicolas
___________________________________________________
Nicolas Karakatsanis, PhD Candidate
Biomedical Simulations and Imaging Technologies Laboratory
School of Electrical and Computer Engineering
National Technical University of Athens, Greece
Sonal Ambwani wrote:
> Sure.
>
> The macro is attached.
> The latest update on my problem is that no matter whether I turn root
> on or off....the digitizer module is not being recognized by Gate.
> I performed a simple check after re-compiling GATE
> [sonal at master gate_v3.1.2]$ Gate
>
> *************************************************************
> Geant4 version Name: geant4-09-01-patch-01 (25-January-2008)
> Copyright : Geant4 Collaboration
> Reference : NIM A 506 (2003), 250-303
> WWW : http://cern.ch/geant4
> *************************************************************
>
> Visualization Manager instantiating...
> Visualization Manager initialising...
> Registering graphics systems...
>
> 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)
> 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
>
> /control/saveHistory
> /run/verbose 2
> /event/verbose 1
> /tracking/verbose 1
> /gate/timing/setTime 0. s
> /gate/application/setTimeSlice 1. s
> PreInit> /gate/digitizer/Singles/insert adder
> /gate/digitizer/Singles/insert adder
> command </gate/digitizer/Singles/insert adder> not found
>
> Anyway, please look at the macro. I would really appreciate any help
> with fixing this.
> Best,
> Sonal
>
> Quoting Nicolas Karakatsanis <knicolas at mail.ntua.gr>:
>
>> Ok Sonal,
>>
>> can you please send me your macro file so that i can check it at my
>> system?
>> There might be some hidden characters inside your macro causing that
>> error message, for example.
>>
>> Best regards
>> Nicolas
>>
>>
>>
>> Sonal Ambwani wrote:
>>> Hi Nicolas,
>>>
>>> Yes, I have now tried the process of uninstalling root-then
>>> installing and configuring root-then doing make clean in the
>>> $GATEHOME-then recompiling gate several times with no luck!
>>>
>>> I get the same error of "***** COMMAND NOT FOUND
>>> </gate/digitizer/Singles/insert adder>" for the digitizer module no
>>> matter what macro I use.
>>>
>>> I'm quite stumped.
>>>
>>>
>>> Quoting Nicolas Karakatsanis <knicolas at mail.ntua.gr>:
>>>
>>>> Hi Sonal
>>>>
>>>> did you re-compile GATE after installing the ROOT 5.14 version.
>>>> If the problem remains please send me your macro file so that i can
>>>> test
>>>> it with my set-up as well!
>>>>
>>>> Best regards
>>>> Nicolas
>>>>
>>>>
>>>>
>>>> Sonal Ambwani wrote:
>>>>> Hi Nicolas and Susana,
>>>>>
>>>>> Thanks for the reply and the clarification. However, even with
>>>>> root 5.14 installed I am getting the same error on running
>>>>> benchmark.mac as I had with 5.18
>>>>>
>>>>> The strangest thing is that Gate works fine with root disabled. I
>>>>> am going to investigate further.
>>>>> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
>>>>>
>>>>> ***** Batch is interupted!! *****
>>>>> Ignoring confine condition
>>>>> Ignoring confine condition
>>>>> GateSourceMgr::ListSources: List of the sources in the source
>>>>> managaer
>>>>> Source --------------> F18LineSource
>>>>> ID : 0
>>>>> type :
>>>>> activity (Bq) : 100000
>>>>> startTime (s) : 0
>>>>> time (s) : 0
>>>>> forcedUnstable : 1
>>>>> forcedHalfLife (s) : 6586.2
>>>>> verboseLevel : 0
>>>>> ----------------------
>>>>>
>>>>> Source --------------> O15LineSource
>>>>> ID : 1
>>>>> type :
>>>>> activity (Bq) : 100000
>>>>> startTime (s) : 0
>>>>> time (s) : 0
>>>>> forcedUnstable : 1
>>>>> forcedHalfLife (s) : 122.24
>>>>> verboseLevel : 0
>>>>> ----------------------
>>>>>
>>>>> ***** COMMAND NOT FOUND </gate/output/ascii/setOutFileHitsFlag 1>
>>>>> *****
>>>>>
>>>>> ***** Batch is interupted!! *****
>>>>> Idle> exit
>>>>>
>>>>>
>>>>> I'd appreciate any inputs at this point. I'm working on a 64 bit
>>>>> linux machine.
>>>>>
>>>>> Thanks again.
>>>>> Sonal
>>>>>
>>>>> Quoting Nicolas Karakatsanis <knicolas at mail.ntua.gr>:
>>>>>
>>>>>> Hi Sonal,
>>>>>>
>>>>>>
>>>>>> for the current version of GATE (3.1.2), the recommended version
>>>>>> of ROOT
>>>>>> is 5.14. You can find this ROOT distribution at the following link
>>>>>> http://root.cern.ch/root/Version514.html
>>>>>>
>>>>>>
>>>>>> The error message generated by GATE suggests that the problem is
>>>>>> caused
>>>>>> by an incompatibility between the GATE and the ROOT versions that
>>>>>> are
>>>>>> installed on your system.
>>>>>> Therefore it is most likely that the problem will be solved when you
>>>>>> install this particular ROOT distribution.
>>>>>> GATE had been tested with this version and no error messages of this
>>>>>> nature were reported.
>>>>>>
>>>>>> Please let us know about the outcome of your GATE simulations after
>>>>>> installing ROOT 5.14
>>>>>>
>>>>>> Best regards
>>>>>> Nicolas
>>>>>>
>>>>>>
>>>>>>
>>>>>> _____________________________________________________
>>>>>> Nicolas Karakatsanis
>>>>>> PhD Candidate
>>>>>> Biomedical Simulations and Imaging Technologies Laboratory
>>>>>> School of Electrical and Computer Engineer
>>>>>> National Technical University of Athens, Greece
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Sonal Ambwani wrote:
>>>>>>> Thanks Jose,
>>>>>>> The thought of reinstalling root occured to me too. Could you
>>>>>>> tell me which version of root you are using? I have 5.18 right
>>>>>>> now and it is causing issues with the digitizer module it seems.
>>>>>>>
>>>>>>> Quoting José Ramos <joserm84 at gmail.com>:
>>>>>>>
>>>>>>>> Hi Sonal
>>>>>>>> I had a similar problem, I solved it, "reinstalling root" and
>>>>>>>> recompile
>>>>>>>> Gate
>>>>>>>> I hope this help
>>>>>>>> Best regards
>>>>>>>> 2008/5/24 <gate-users-request at lists.healthgrid.org>:
>>>>>>>>
>>>>>>>>> Send Gate-users mailing list submissions to
>>>>>>>>> gate-users at lists.healthgrid.org
>>>>>>>>>
>>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>>>>>> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>>>>>>>> or, via email, send a message with subject or body 'help' to
>>>>>>>>> gate-users-request at lists.healthgrid.org
>>>>>>>>>
>>>>>>>>> You can reach the person managing the list at
>>>>>>>>> gate-users-owner at lists.healthgrid.org
>>>>>>>>>
>>>>>>>>> When replying, please edit your Subject line so it is more
>>>>>>>>> specific
>>>>>>>>> than "Re: Contents of Gate-users digest..."
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Today's Topics:
>>>>>>>>>
>>>>>>>>> 1. Gate digitizer error (Sonal Ambwani)
>>>>>>>>> 2. Re: Gate digitizer error (Sonal Ambwani)
>>>>>>>>> 3. Re: Gate digitizer error---update (Sonal Ambwani)
>>>>>>>>> 4. Re: Transmission tomography (Javier Serrano)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>> Message: 1
>>>>>>>>> Date: Fri, 23 May 2008 12:04:26 -0400
>>>>>>>>> From: Sonal Ambwani <ambwani at bu.edu>
>>>>>>>>> Subject: [Gate-users] Gate digitizer error
>>>>>>>>> To: gate-users at lists.healthgrid.org
>>>>>>>>> Message-ID: <20080523120426.q8daye1hws4k4ckw at www.bu.edu>
>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1;
>>>>>>>>> format="flowed"
>>>>>>>>>
>>>>>>>>> Dear Gate-users,
>>>>>>>>>
>>>>>>>>> I am suddenly getting the following error while running
>>>>>>>>> benchmarkSPECT :
>>>>>>>>>
>>>>>>>>> /gate/physics/setXRayCut 200. keV
>>>>>>>>> /gate/physics/setElectronCut 1. km
>>>>>>>>> /gate/physics/setDeltaRayCut 1. GeV
>>>>>>>>> /run/initialize
>>>>>>>>> WARNING !
>>>>>>>>> SetCutValueForOthers became obsolete.
>>>>>>>>> It is harmless to remove this invokation without any side
>>>>>>>>> effects.
>>>>>>>>> This dummy method implementation will be removed soon.
>>>>>>>>> /gate/digitizer/Singles/insert adder
>>>>>>>>> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder>
>>>>>>>>> *****
>>>>>>>>>
>>>>>>>>> ***** Batch is interupted!! *****
>>>>>>>>> Idle>
>>>>>>>>>
>>>>>>>>> Can someone please point out what might be wrong. This was
>>>>>>>>> working till
>>>>>>>>> a few days ago.
>>>>>>>>>
>>>>>>>>> Sonal Ambwani
>>>>>>>>>
>>>>>>>>> Dept. of Electrical and Computer Engineering
>>>>>>>>> Boston University
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>>
>>>>>>>>> Message: 2
>>>>>>>>> Date: Fri, 23 May 2008 12:34:14 -0400
>>>>>>>>> From: Sonal Ambwani <ambwani at bu.edu>
>>>>>>>>> Subject: Re: [Gate-users] Gate digitizer error
>>>>>>>>> To: gate-users at lists.healthgrid.org
>>>>>>>>> Message-ID: <20080523123414.rtnx27xw0c04sog0 at www.bu.edu>
>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1;
>>>>>>>>> format="flowed"
>>>>>>>>>
>>>>>>>>> Hi again,
>>>>>>>>>
>>>>>>>>> I am getting the same error for benchmarkPET. I guess it might
>>>>>>>>> help to
>>>>>>>>> mention the macro here:
>>>>>>>>>
>>>>>>>>> ###GATE : benchmarkPET.mac
>>>>>>>>> /gate/world/geometry/setXLength 150. cm
>>>>>>>>> /gate/world/geometry/setYLength 150. cm
>>>>>>>>> /gate/world/geometry/setZLength 150. cm
>>>>>>>>>
>>>>>>>>> /control/execute camera.mac
>>>>>>>>>
>>>>>>>>> /control/execute phantom.mac
>>>>>>>>>
>>>>>>>>> /control/execute physics.mac
>>>>>>>>>
>>>>>>>>> # I N I T I A L I Z E
>>>>>>>>> /gate/systems/cylindricalPET/verbose 0
>>>>>>>>> /gate/geometry/enableAutoUpdate
>>>>>>>>> /run/initialize
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> /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 0.26
>>>>>>>>> /gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
>>>>>>>>> /gate/digitizer/Singles/insert thresholder
>>>>>>>>> /gate/digitizer/Singles/thresholder/setThreshold 350. keV
>>>>>>>>> /gate/digitizer/Singles/insert upholder
>>>>>>>>> /gate/digitizer/Singles/upholder/setUphold 650. keV
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> # C O I N C I S O R T E R
>>>>>>>>> /gate/digitizer/Coincidences/setWindow 120. ns
>>>>>>>>> /gate/digitizer/Coincidences/MultiplesPolicy takeWinnerOfGoods
>>>>>>>>>
>>>>>>>>> /gate/digitizer/name delay
>>>>>>>>> /gate/digitizer/insert coincidenceSorter
>>>>>>>>> /gate/digitizer/delay/setWindow 120. ns
>>>>>>>>> /gate/digitizer/delay/setOffset 500. ns
>>>>>>>>> /gate/digitizer/delay/MultiplesPolicy takeWinnerOfGoods
>>>>>>>>>
>>>>>>>>> /control/verbose 0
>>>>>>>>> /grdm/verbose 0
>>>>>>>>> /run/verbose 0
>>>>>>>>> /event/verbose 0
>>>>>>>>> /tracking/verbose 0
>>>>>>>>> /gate/application/verbose 0
>>>>>>>>> /gate/generator/verbose 0
>>>>>>>>> /gate/stacking/verbose 0
>>>>>>>>> /gate/event/verbose 0
>>>>>>>>> /gate/source/verbose 0
>>>>>>>>>
>>>>>>>>> /control/execute sources.mac
>>>>>>>>>
>>>>>>>>> # O U T P U T
>>>>>>>>>
>>>>>>>>> /gate/output/verbose 0
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> /gate/output/ascii/setOutFileHitsFlag 1
>>>>>>>>> /gate/output/ascii/setOutFileSinglesFlag 1
>>>>>>>>> /gate/output/ascii/setOutFileCoincidencesFlag 1
>>>>>>>>> /gate/output/ascii/setOutFiledelayFlag 1
>>>>>>>>>
>>>>>>>>> /gate/output/root/setFileName benchmarkPET
>>>>>>>>> /gate/output/root/setRootHitFlag 0
>>>>>>>>> /gate/output/root/setRootSinglesFlag 0
>>>>>>>>> /gate/output/root/setRootCoincidencesFlag 1
>>>>>>>>> /gate/output/root/setRootdelayFlag 1
>>>>>>>>> /gate/output/root/setRootNtupleFlag 0
>>>>>>>>> /gate/output/root/setSaveRndmFlag 0
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> # S T A R T
>>>>>>>>> /gate/application/setTimeSlice 120. s
>>>>>>>>> /gate/application/setTimeStart 0. s
>>>>>>>>> /gate/application/setTimeStop 240. s
>>>>>>>>> /gate/application/startDAQ
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Quoting Sonal Ambwani <ambwani at bu.edu>:
>>>>>>>>>
>>>>>>>>> > Dear Gate-users,
>>>>>>>>> >
>>>>>>>>> > I am suddenly getting the following error while running
>>>>>>>>> benchmarkSPECT :
>>>>>>>>> >
>>>>>>>>> > /gate/physics/setXRayCut 200. keV
>>>>>>>>> > /gate/physics/setElectronCut 1. km
>>>>>>>>> > /gate/physics/setDeltaRayCut 1. GeV
>>>>>>>>> > /run/initialize
>>>>>>>>> > WARNING !
>>>>>>>>> > SetCutValueForOthers became obsolete.
>>>>>>>>> > It is harmless to remove this invokation without any side
>>>>>>>>> effects.
>>>>>>>>> > This dummy method implementation will be removed soon.
>>>>>>>>> > /gate/digitizer/Singles/insert adder
>>>>>>>>> > ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert
>>>>>>>>> adder> *****
>>>>>>>>> >
>>>>>>>>> > ***** Batch is interupted!! *****
>>>>>>>>> > Idle>
>>>>>>>>> >
>>>>>>>>> > Can someone please point out what might be wrong. This was
>>>>>>>>> working till
>>>>>>>>> > a few days ago.
>>>>>>>>> >
>>>>>>>>> > Sonal Ambwani
>>>>>>>>> >
>>>>>>>>> > Dept. of Electrical and Computer Engineering
>>>>>>>>> > Boston University
>>>>>>>>> >
>>>>>>>>> > _______________________________________________
>>>>>>>>> > Gate-users mailing list
>>>>>>>>> > Gate-users at lists.healthgrid.org
>>>>>>>>> > http://lists.healthgrid.org/mailman/listinfo/gate-users
>>>>>>>>> >
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Sonal Ambwani
>>>>>>>>>
>>>>>>>>> Dept. of Electrical and Computer Engineering
>>>>>>>>> Boston University
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>>
>>>>>>>>> Message: 3
>>>>>>>>> Date: Fri, 23 May 2008 13:53:17 -0400
>>>>>>>>> From: Sonal Ambwani <ambwani at bu.edu>
>>>>>>>>> Subject: Re: [Gate-users] Gate digitizer error---update
>>>>>>>>> To: gate-users at lists.healthgrid.org
>>>>>>>>> Message-ID: <20080523135317.uly9soqzc4c8s840 at www.bu.edu>
>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1;
>>>>>>>>> format="flowed"
>>>>>>>>>
>>>>>>>>> benchmarkPET.mac works after disabling the root output
>>>>>>>>> completely.
>>>>>>>>> Please help!
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Quoting Sonal Ambwani <ambwani at bu.edu>:
>>>>>>>>>
>>>>>>>>> > Hi again,
>>>>>>>>> >
>>>>>>>>> > I am getting the same error for benchmarkPET. I guess it
>>>>>>>>> might help to
>>>>>>>>> > mention the macro here:
>>>>>>>>> >
>>>>>>>>> > ###GATE : benchmarkPET.mac
>>>>>>>>> > /gate/world/geometry/setXLength 150. cm
>>>>>>>>> > /gate/world/geometry/setYLength 150. cm
>>>>>>>>> > /gate/world/geometry/setZLength 150. cm
>>>>>>>>> >
>>>>>>>>> > /control/execute camera.mac
>>>>>>>>> >
>>>>>>>>> > /control/execute phantom.mac
>>>>>>>>> >
>>>>>>>>> > /control/execute physics.mac
>>>>>>>>> >
>>>>>>>>> > # I N I T I A L I Z E
>>>>>>>>> > /gate/systems/cylindricalPET/verbose 0
>>>>>>>>> > /gate/geometry/enableAutoUpdate
>>>>>>>>> > /run/initialize
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > /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 0.26
>>>>>>>>> > /gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
>>>>>>>>> > /gate/digitizer/Singles/insert thresholder
>>>>>>>>> > /gate/digitizer/Singles/thresholder/setThreshold 350. keV
>>>>>>>>> > /gate/digitizer/Singles/insert upholder
>>>>>>>>> > /gate/digitizer/Singles/upholder/setUphold 650. keV
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > # C O I N C I S O R T E R
>>>>>>>>> > /gate/digitizer/Coincidences/setWindow 120. ns
>>>>>>>>> > /gate/digitizer/Coincidences/MultiplesPolicy takeWinnerOfGoods
>>>>>>>>> >
>>>>>>>>> > /gate/digitizer/name delay
>>>>>>>>> > /gate/digitizer/insert coincidenceSorter
>>>>>>>>> > /gate/digitizer/delay/setWindow 120. ns
>>>>>>>>> > /gate/digitizer/delay/setOffset 500. ns
>>>>>>>>> > /gate/digitizer/delay/MultiplesPolicy takeWinnerOfGoods
>>>>>>>>> >
>>>>>>>>> > /control/verbose 0
>>>>>>>>> > /grdm/verbose 0
>>>>>>>>> > /run/verbose 0
>>>>>>>>> > /event/verbose 0
>>>>>>>>> > /tracking/verbose 0
>>>>>>>>> > /gate/application/verbose 0
>>>>>>>>> > /gate/generator/verbose 0
>>>>>>>>> > /gate/stacking/verbose 0
>>>>>>>>> > /gate/event/verbose 0
>>>>>>>>> > /gate/source/verbose 0
>>>>>>>>> >
>>>>>>>>> > /control/execute sources.mac
>>>>>>>>> >
>>>>>>>>> > # O U T P U T
>>>>>>>>> >
>>>>>>>>> > /gate/output/verbose 0
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > /gate/output/ascii/setOutFileHitsFlag 1
>>>>>>>>> > /gate/output/ascii/setOutFileSinglesFlag 1
>>>>>>>>> > /gate/output/ascii/setOutFileCoincidencesFlag 1
>>>>>>>>> > /gate/output/ascii/setOutFiledelayFlag 1
>>>>>>>>> >
>>>>>>>>> > /gate/output/root/setFileName benchmarkPET
>>>>>>>>> > /gate/output/root/setRootHitFlag 0
>>>>>>>>> > /gate/output/root/setRootSinglesFlag 0
>>>>>>>>> > /gate/output/root/setRootCoincidencesFlag 1
>>>>>>>>> > /gate/output/root/setRootdelayFlag 1
>>>>>>>>> > /gate/output/root/setRootNtupleFlag 0
>>>>>>>>> > /gate/output/root/setSaveRndmFlag 0
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > # S T A R T
>>>>>>>>> > /gate/application/setTimeSlice 120. s
>>>>>>>>> > /gate/application/setTimeStart 0. s
>>>>>>>>> > /gate/application/setTimeStop 240. s
>>>>>>>>> > /gate/application/startDAQ
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > Quoting Sonal Ambwani <ambwani at bu.edu>:
>>>>>>>>> >
>>>>>>>>> >> Dear Gate-users,
>>>>>>>>> >>
>>>>>>>>> >> I am suddenly getting the following error while running
>>>>>>>>> benchmarkSPECT :
>>>>>>>>> >>
>>>>>>>>> >> /gate/physics/setXRayCut 200. keV
>>>>>>>>> >> /gate/physics/setElectronCut 1. km
>>>>>>>>> >> /gate/physics/setDeltaRayCut 1. GeV
>>>>>>>>> >> /run/initialize
>>>>>>>>> >> WARNING !
>>>>>>>>> >> SetCutValueForOthers became obsolete.
>>>>>>>>> >> It is harmless to remove this invokation without any side
>>>>>>>>> effects.
>>>>>>>>> >> This dummy method implementation will be removed soon.
>>>>>>>>> >> /gate/digitizer/Singles/insert adder
>>>>>>>>> >> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert
>>>>>>>>> adder> *****
>>>>>>>>> >>
>>>>>>>>> >> ***** Batch is interupted!! *****
>>>>>>>>> >> Idle>
>>>>>>>>> >>
>>>>>>>>> >> Can someone please point out what might be wrong. This was
>>>>>>>>> working till
>>>>>>>>> >> a few days ago.
>>>>>>>>> >>
>>>>>>>>> >> Sonal Ambwani
>>>>>>>>> >>
>>>>>>>>> >> Dept. of Electrical and Computer Engineering
>>>>>>>>> >> Boston University
>>>>>>>>> >>
>>>>>>>>> >> _______________________________________________
>>>>>>>>> >> Gate-users mailing list
>>>>>>>>> >> Gate-users at lists.healthgrid.org
>>>>>>>>> >> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>>>>>>>> >>
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > Sonal Ambwani
>>>>>>>>> >
>>>>>>>>> > Dept. of Electrical and Computer Engineering
>>>>>>>>> > Boston University
>>>>>>>>> >
>>>>>>>>> > _______________________________________________
>>>>>>>>> > Gate-users mailing list
>>>>>>>>> > Gate-users at lists.healthgrid.org
>>>>>>>>> > http://lists.healthgrid.org/mailman/listinfo/gate-users
>>>>>>>>> >
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Sonal Ambwani
>>>>>>>>>
>>>>>>>>> Dept. of Electrical and Computer Engineering
>>>>>>>>> Boston University
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>>
>>>>>>>>> Message: 4
>>>>>>>>> Date: Fri, 23 May 2008 19:51:50 +0200
>>>>>>>>> From: "Javier Serrano" <fjaviersr at usal.es>
>>>>>>>>> Subject: Re: [Gate-users] Transmission tomography
>>>>>>>>> To: gate-users at lists.healthgrid.org
>>>>>>>>> Message-ID:
>>>>>>>>>
>>>>>>>>> <89978e4d0805231051m2239f53ci102cb532b02309c3 at mail.gmail.com>
>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>>>>>>>
>>>>>>>>> > Richard Taschereau wrote:
>>>>>>>>> > While it is technically possible to simulate an x-ray CT,
>>>>>>>>> the amount of
>>>>>>>>> photons you would need is prohibitive.
>>>>>>>>>
>>>>>>>>> Yes, I think so too. I did try to simulate this with Geant4
>>>>>>>>> some time
>>>>>>>>> ago and I found this problem.
>>>>>>>>>
>>>>>>>>> > Franca Cassol-Brunner wrote:
>>>>>>>>> > this will be available in the next Gate release, where a CT
>>>>>>>>> system will
>>>>>>>>> be
>>>>>>>>> > added.
>>>>>>>>>
>>>>>>>>> This is very interesting for me, especially if the next
>>>>>>>>> release is
>>>>>>>>> coming soon. I would like to simulate a CT system with Gate
>>>>>>>>> even with
>>>>>>>>> a limited number of photons or projections. I will keep
>>>>>>>>> waiting for
>>>>>>>>> the next release.
>>>>>>>>>
>>>>>>>>> Thank you all.
>>>>>>>>> Greetings, Javi.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2008/5/22 Franca Cassol-Brunner <cassol at cppm.in2p3.fr>:
>>>>>>>>> > Javier Serrano wrote:
>>>>>>>>> >
>>>>>>>>> >> Is it possible to use Gate to simulate an x-ray scanner
>>>>>>>>> with an
>>>>>>>>> >> external cone-beam source?
>>>>>>>>> >
>>>>>>>>> > Hello Javier,
>>>>>>>>> >
>>>>>>>>> > this will be available in the next Gate release, where a CT
>>>>>>>>> system will
>>>>>>>>> be
>>>>>>>>> > added. With the present release you can simulate the cone
>>>>>>>>> beam source but
>>>>>>>>> > there is no adapted output for the CT images.
>>>>>>>>> >
>>>>>>>>> > Don't hesitate to contact me directly to get more details.
>>>>>>>>> >
>>>>>>>>> > Cheers
>>>>>>>>> >
>>>>>>>>> > Franca
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > ****************************************************
>>>>>>>>> > Dr. F. Cassol Brunner
>>>>>>>>> > CPPM/IN2P3 (CNRS) Office: 305
>>>>>>>>> > 163, Avenue de Luminy Phone : (+33) 491827248
>>>>>>>>> > 13288, Marseille Fax : (+33) 491827299
>>>>>>>>> > France
>>>>>>>>> > ****************************************************
>>>>>>>>> >
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Gate-users mailing list
>>>>>>>>> Gate-users at lists.healthgrid.org
>>>>>>>>> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> End of Gate-users Digest, Vol 24, Issue 31
>>>>>>>>> ******************************************
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> e- + e+ -> ~~>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Sonal Ambwani
>>>>>>>
>>>>>>> Dept. of Electrical and Computer Engineering
>>>>>>> Boston University
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Gate-users mailing list
>>>>>>> Gate-users at lists.healthgrid.org
>>>>>>> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>>>>>>
>>>>>>> __________ NOD32 3128 (20080523) Information __________
>>>>>>>
>>>>>>> This message was checked by NOD32 antivirus system.
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>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Sonal Ambwani
>>>>>
>>>>> Dept. of Electrical and Computer Engineering
>>>>> Boston University
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>> Sonal Ambwani
>>>
>>> Dept. of Electrical and Computer Engineering
>>> Boston University
>>>
>>>
>>> __________ NOD32 3134 (20080527) Information __________
>>>
>>> This message was checked by NOD32 antivirus system.
>>> http://www.eset.com
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>>>
>>
>
>
>
> Sonal Ambwani
>
> Dept. of Electrical and Computer Engineering
> Boston University
>
>
> __________ NOD32 3134 (20080527) Information __________
>
> This message was checked by NOD32 antivirus system.
> http://www.eset.com
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