[Gate-users] Running simulations on gatelab

Panagiotis Papadimitroulas panpap_5 at hotmail.com
Fri Feb 10 18:46:23 CET 2012 

Well, yes
Normally you should have a number of you TotatlPrimaries = Activity (in Bq) x Time (in sec).
So 20 microCuries are 740000 Bq, and 10h are (10x60x60=36000sec).
Yes, GATE should be able to handle these large numbers. 

Regards,
Panagiotis

##########################################
###   Panagiotis Papadimitroulas, Msc                                        
###   PhD candidate, Department of Medical Physics      
###   University of Patras                                                    
###   Greece                                                                           
###                                                                                           
###   email:        panpap_5 at hotmail.com       
###   web page: http://www.teiath.gr/stef/tio/ni/
###                       http://www.kagadis.gr

> From: slee91 at utk.edu
> To: panpap_5 at hotmail.com; gate-users at lists.opengatecollaboration.org
> Subject: RE: [Gate-users] Running simulations on gatelab
> Date: Fri, 10 Feb 2012 17:30:44 +0000
> 
> Thanks!
> 
> I manually converted every decimals to integers, and everything is working fine now. ;) It seems that gatelab parser can't handle floating numbers yet. 
> It would be great if the parser can't automatically convert floating point numbers to integer numbers.
> 
> I have one more question. My background is computer science so this might be a silly question. ;)
> 
> I am trying to run a simulation where I have a Cobalt-57 point source with 20 micro-curie activity. I want to run the simulation for 10 hours.
> 
> In this case, what value should I set /gate/application/setTotalNumberOfPrimaries to be? is it 10 * 60 * 60 * 3.7 × 10^10 * 0.0002? Is gate able to handle this large number?
> 
> Thank you very much for your help
> 
> Sanghyeb(Sam) Lee
> 
> PhD Candidate
> Department of Electrical Engineering and Computer Science
> University of Tennessee, Knoxville
> ________________________________________
> From: Panagiotis Papadimitroulas [panpap_5 at hotmail.com]
> Sent: 10 February 2012 11:54
> To: Lee, Sam (SAM LEE); gate-users at lists.opengatecollaboration.org
> Subject: RE: [Gate-users] Running simulations on gatelab
> 
> Dear Lee,
> Yes exactly. In GateLab when you define the time start/stop/slice you should define an integer number, and not a decimal. In your case 37.5 sec is wrong. you should remove the dots (.). And maybe you can try to write lets say in ms (37500 ms instead of 37.5 s ). Hope it helps.
> 
> Best regards,
> Panagiotis
> 
> ##########################################
> ###   Panagiotis Papadimitroulas, Msc
> ###   PhD candidate, Department of Medical Physics
> ###   University of Patras
> ###   Greece
> ###
> ###   email:        panpap_5 at hotmail.com
> ###   web page: http://www.teiath.gr/stef/tio/ni/
> ###                       http://www.kagadis.gr<http://www.kagadis.gr/>
> 
> > From: slee91 at utk.edu
> > To: gate-users at lists.opengatecollaboration.org
> > Date: Fri, 10 Feb 2012 16:29:51 +0000
> > Subject: Re: [Gate-users] Running simulations on gatelab
> >
> > Moreover, this is the error message I received from gateLab applet. It seems like there is something with its parser. It can't handle a floating number such as '37.5'?
> >
> > MacroParser COnstructor 2, dirname is mac
> > **************Processing macro file /home/slee91/Downloads/example_SPECT/mac/SPECT.mac
> > I've just added /home/slee91/Downloads/example_SPECT/data/GateMaterials.db to the inputs
> > Detected output *** output/root ***
> > Detected output *** output/ascii ***
> > Detected output *** output/projection ***
> > *** Found /gate/application/SetTotalNumberOfPrimaries 999999 ***
> > this.nseconds 37.5 ***
> > this.nstart 0. ***
> > this.nstop 600. ***
> > All time patterns found
> > Feb 10, 2012 11:25:16 AM fr.insalyon.creatis.vip.gatelab.applet.loadmac.LoadMac jFileChooserActionPerformed
> > SEVERE: null
> > java.lang.NumberFormatException: For input string: "37.5"
> > at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
> > at java.lang.Integer.parseInt(Integer.java:481)
> > at java.lang.Integer.parseInt(Integer.java:514)
> > at fr.insalyon.creatis.vip.gatelab.applet.loadmac.MacroParser.handleSeconds(MacroParser.java:283)
> > at fr.insalyon.creatis.vip.gatelab.applet.loadmac.MacroParser.processLineByLine(MacroParser.java:378)
> > at fr.insalyon.creatis.vip.gatelab.applet.loadmac.MacroParser.parseMacroFiles(MacroParser.java:84)
> > at fr.insalyon.creatis.vip.gatelab.applet.loadmac.LoadMac.jFileChooserActionPerformed(LoadMac.java:166)
> > at fr.insalyon.creatis.vip.gatelab.applet.loadmac.LoadMac.access$100(LoadMac.java:58)
> > at fr.insalyon.creatis.vip.gatelab.applet.loadmac.LoadMac$2.actionPerformed(LoadMac.java:110)
> > at javax.swing.JFileChooser.fireActionPerformed(JFileChooser.java:1736)
> > at javax.swing.JFileChooser.approveSelection(JFileChooser.java:1646)
> > at javax.swing.plaf.basic.BasicFileChooserUI$Handler.mouseClicked(BasicFileChooserUI.java:448)
> > at sun.swing.FilePane$Handler.mouseClicked(FilePane.java:1835)
> > at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:270)
> > at java.awt.Component.processMouseEvent(Component.java:6206)
> > at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
> > at java.awt.Component.processEvent(Component.java:5968)
> > at java.awt.Container.processEvent(Container.java:2105)
> > at java.awt.Component.dispatchEventImpl(Component.java:4564)
> > at java.awt.Container.dispatchEventImpl(Container.java:2163)
> > at java.awt.Component.dispatchEvent(Component.java:4390)
> > at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4461)
> > at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4134)
> > at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4055)
> > at java.awt.Container.dispatchEventImpl(Container.java:2149)
> > at java.awt.Component.dispatchEvent(Component.java:4390)
> > at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:649)
> > at java.awt.EventQueue.access$000(EventQueue.java:96)
> > at java.awt.EventQueue$1.run(EventQueue.java:608)
> > at java.awt.EventQueue$1.run(EventQueue.java:606)
> > at java.security.AccessController.doPrivileged(Native Method)
> > at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
> > at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:116)
> > at java.awt.EventQueue$2.run(EventQueue.java:622)
> > at java.awt.EventQueue$2.run(EventQueue.java:620)
> > at java.security.AccessController.doPrivileged(Native Method)
> > at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
> > at java.awt.EventQueue.dispatchEvent(EventQueue.java:619)
> > at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
> > at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
> > at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
> > at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
> > at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
> > at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
> >
> >
> > This is where the number 37.5 comes from.
> >
> > /gate/timing/setTime 0. s
> > /gate/timing/setTime 37.5 s
> > /gate/timing/setTime 75 s
> >
> > Sanghyeb(Sam) Lee
> >
> > PhD Candidate
> > Department of Electrical Engineering and Computer Science
> > University of Tennessee, Knoxville
> >
> > ________________________________________
> > From: gate-users-bounces at lists.opengatecollaboration.org [gate-users-bounces at lists.opengatecollaboration.org] on behalf of Lee, Sam (SAM LEE) [slee91 at utk.edu]
> > Sent: 10 February 2012 11:20
> > To: gate-users
> > Subject: [Gate-users] Running simulations on gatelab
> >
> > Hey,
> >
> > I have been trying to run the example_SPECT script on the gatelab simulation. However, i am having trouble loading the script in the first place.
> >
> > 1) I have organized my files as below
> >
> > data/GateMaterials.db
> > mac/SPECT.mac
> > output/
> >
> > 2) I have merged all the macro files into one file, SPECT.mac
> > 3) I have added /gate/application/setTotalNumberOfPrimaries to SPECT.mac
> >
> > I am able to run this simulation on my desktop. However, I cannot load SPECT.mac script into gatelab.
> > When I click "open" button, it does not do anything.
> >
> > Can anyone tell me what I am doing wrong? Am i missing something?
> >
> > Thanks,
> >
> > Sanghyeb(Sam) Lee
> > Department of Electrical Engineering and Computer Science
> > University of Tennessee, Knoxville
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >
> >
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>

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