[Gate-users] Running simulations on gatelab

Lee, Sam (SAM LEE) slee91 at utk.edu
Fri Feb 10 18:30:44 CET 2012 

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
>
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>
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