[Gate-users] FW: Parallel Hole Collimator
Ferrer Ludovic
Ludovic.Ferrer at ico.unicancer.fr
Mon Mar 18 16:14:16 CET 2013
Hi,
Actually, "/gate/output/analysis/recordSeptalPenetration" and "/gate/output/analysis/setSeptalVolumeName" are commands that are not intended to work with "parallelebeam" command. Those 2 previous commands work with the "old classical" geometry. Moreover, I think that parallelbeam collimator is modelling a leaf collimator (not cast one that is to say that septal thichness is double in y direction that "oblique" direction ).
In order to record septal photons, you need to set to true "recordSeptalPenetration" flag and to explicitely name the volume you want to track the septal informations (usually the collimator but it may not). Additionnaly, you have to set output as ROOT file.
All the best.
Ludovic
De : Carlos Uribe <carluri at phas.ubc.ca<mailto:carluri at phas.ubc.ca>>
Date : Wed, 13 Mar 2013 14:35:37 -0700
À : Jonathan Moody <jbm139 at gmail.com<mailto:jbm139 at gmail.com>>
Cc : "gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>" <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Objet : Re: [Gate-users] Parallel Hole Collimator
I wasn't setting up a root file as an output...Thanks for letting me know now I guess that solves everything.
Carlos
On Wed, Mar 13, 2013 at 1:54 PM, Jonathan Moody <jbm139 at gmail.com<mailto:jbm139 at gmail.com>> wrote:
Carlos,
From the Gate source code it looks like setting "recordSeptalPenetration" to true should create new branches called "septalNb" in the Hit and Singles tree of the output root file. It does not look like this septal data is available with any other type of output. You don't see the "septalNb" branches in the root file?
--
Jon
On 3/13/2013 1:39 PM, Carlos Uribe wrote:
Hi Jon,
Yes the collimator is attached to the phantomSD.
When I run my code with the
/gate/output/analysis/recordSeptalPenetration true
/gate/output/analysis/setSeptalVolumeName collimator
I don't get errors or anything like that...the code works fine. I just don't get any output related to septal penetration information.
On Wed, Mar 13, 2013 at 7:44 AM, Jon Moody <jbmoody at umich.edu<mailto:jbmoody at umich.edu>> wrote:
I have not used this feature. When you said you tried it and it didn't work what happened?
Was the collimator attached to the phantomSD by the command
/gate/collimator/attachPhantomSD
--
Jon
On 3/12/2013 5:52 PM, Carlos Uribe wrote:
Thanks for the reply Jonathan..
Do you know then how can I use
/gate/output/analysis/recordSeptalPenetration true
/gate/output/analysis/setSeptalVolumeName collimator
with this way of specifying the collimator?
Carlos
On Tue, Mar 12, 2013 at 11:18 AM, Jonathan Moody <jbm139 at gmail.com<mailto:jbm139 at gmail.com>> wrote:
Hi Carlos,
I think "parallelbeam" collimator construction has not been working right since Gate v.5.0.0, so the other option is to use cubicArray and linear repeaters as Giuseppe mentioned. In this case, the septal thickness is defined implicitly in the two repeatVectors. For hexagonal shaped holes the second and third components of the cubicArray repeatVector are:
Ry = hole_diameter + septal_thickness
Rz = Ry * sqrt(3)
where hole_diameter is defined across the flat sides. The corresponding two components of the linear repeatVector are:
Ly = Ry / 2
Lz = Rz / 2
(the x-components of both repeatVectors are 0). Then the cubicArray repeatNumberY/Z determine the number of holes in each direction divided by 2.
--
Jon
On 3/12/2013 1:16 PM, Carlos Uribe wrote:
Hi Giuseppe,
Thanks for your reply...I tried it but it still doesn't solve the problem.
I know that I can use your specified macro to create a collimator step by step. However, I do want to use the option given in the guide using the
/gate/SPECThead/daughters/insert parallelbeam
This has a parameter that specifies the septal thickness
/gate/colli/geometry/setSeptalThickness 0.2 cm
I guess I will be able to track the septal penetration using
/gate/output/analysis/recordSeptalPenetration true
/gate/output/analysis/setSeptalVolumeName collimator
I've tried this using the macro that you suggested and it doesn't work. I assume that you need to set the septal thickness shown in the guide's example. If there's another way that someone knows to make it work please let me know.
Thanks,
Carlos
On Tue, Mar 12, 2013 at 5:26 AM, Giuseppe Magro <beppe.magro at gmail.com<mailto:beppe.magro at gmail.com>> wrote:
/gate/colli/setMaterial Lead
(instead of setMaterialName)
Example (shielding as mother volume):
#=====================================
# Collimator
#=====================================
/gate/shielding/daughters/name collimator
/gate/shielding/daughters/insert box
/gate/collimator/geometry/setXLength 3. cm
/gate/collimator/geometry/setYLength 19. cm
/gate/collimator/geometry/setZLength 28. cm
/gate/collimator/placement/setTranslation -2. 0. 0. cm
/gate/collimator/setMaterial Lead
/gate/collimator/vis/setColor red
/gate/collimator/vis/forceWireframe
/gate/collimator/describe
/gate/collimator/daughters/name hole
/gate/collimator/daughters/insert hexagone
/gate/hole/geometry/setHeight 3. cm
/gate/hole/geometry/setRadius .15 cm
/gate/hole/placement/setRotationAxis 0 1 0
/gate/hole/placement/setRotationAngle 90 deg
/gate/hole/placement/setTranslation 0. -0.25 -0.25 cm #
/gate/hole/setMaterial Air
/gate/hole/describe
/gate/hole/repeaters/insert cubicArray
/gate/hole/cubicArray/setRepeatNumberX 1
/gate/hole/cubicArray/setRepeatNumberY 18 #9
/gate/hole/cubicArray/setRepeatNumberZ 27 #9
/gate/hole/cubicArray/setRepeatVector 0. 1. 1. cm
/gate/hole/cubicArray/autoCenter true #false
/gate/hole/repeaters/insert linear
/gate/hole/linear/setRepeatNumber 2
/gate/hole/linear/setRepeatVector 0. 0.5 0.5 cm
/gate/hole/linear/autoCenter false
Regards,
Giuseppe M.
PhD Student - CNAO
On 12 March 2013 12:00, <gate-users-request at lists.opengatecollaboration.org<mailto:gate-users-request at lists.opengatecollaboration.org>> wrote:
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Today's Topics:
1. Parallel hole Collimator (Carlos Uribe)
2. Re: ASCII output (Carlos Uribe)
3. Re: Process for Photon Evaporation (Hermann Fuchs)
----------------------------------------------------------------------
Message: 1
Date: Mon, 11 Mar 2013 11:31:41 -0700
From: Carlos Uribe <carluri at phas.ubc.ca<mailto:carluri at phas.ubc.ca>>
To: "gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>"
<gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: [Gate-users] Parallel hole Collimator
Message-ID:
<CAPJy_1TcFTKwiEpu_Zicc=+UKYN3hfHMjvhumfzWL6AxyZ+1Sg at mail.gmail.com<mailto:UKYN3hfHMjvhumfzWL6AxyZ%2B1Sg at mail.gmail.com>>
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Hello everyone,
I'm following the user's guide
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Defining_a_system
trying to model a parallel hole collimator.
The guide shows the following example:
/gate/SPECThead/daughters/name colli
#specify that the parallel beam collimator setup must be used
/gate/SPECThead/daughters/insert parallelbeam
#set the collimator material
/gate/colli/setMaterialName Lead
#set the collimator dimensions
/gate/colli/geometry/setDimensionX 70 cm
/gate/colli/geometry/setDimensionY 80 cm
#set the thickness of the collimator
/gate/colli/geometry/setHeight 3 cm
#specify the hole radius
/gate/colli/geometry/setInnerRadius 0.5 cm
#set the septal thickness to the required distance between the holes
/gate/colli/geometry/setSeptalThickness 0.2 cm
/gate/colli/placement/alignToX
/gate/colli/placement/setRotationAxis 0 0 1
/gate/colli/placement/setRotationAngle -90 deg
I'm getting a problem as follows:
/opt/simulation/gate_v6.2/source/geometry/src/GateVVolume.cc (l.179): The
material of the volume side hole 1 is not defined.
Anyone knows how to fix this?
Thanks,
--
Carlos F Uribe
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Message: 2
Date: Mon, 11 Mar 2013 12:40:11 -0700
From: Carlos Uribe <carluri at phas.ubc.ca<mailto:carluri at phas.ubc.ca>>
To: samira nezhad <sn90113 at gmail.com<mailto:sn90113 at gmail.com>>
Cc: "gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>"
<gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: Re: [Gate-users] ASCII output
Message-ID:
<CAPJy_1QZT9uYF1VmobA3Mk2xMfS_2MRTmQfv41x=2nVvdJ2ssg at mail.gmail.com<mailto:2nVvdJ2ssg at mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"
I had the same problem and here is how I fixed it
In the GateConfiguration.h.in<http://GateConfiguration.h.in> <http://gateconfiguration.h.in/> file found
within the home folder of Gate, change this line:
#cmakedefine GATE_USE_FILE @GATE_USE_FILE@
to this:
#cmakedefine GATE_ANALYSIS_USE_FILE @GATE_ANALYSIS_USE_FILE@
Recompile Gate and it should now work!
Cheers,
Carlos
On Sun, Mar 10, 2013 at 3:10 AM, samira nezhad <sn90113 at gmail.com<mailto:sn90113 at gmail.com>> wrote:
> Dear all,
>
> I need to ASCII output but by gate6.2 i couldn't get it .
> when use this command
> /gate/output/ascii/enable
>
> It gives this error message:
>
> COMMAND NOT FOUND
>
> I appreciate if you guide me, thanks in advance
>
> Best regards,
>
>
>
> _______________________________________________
> 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
>
> --
> Carlos F Uribe
>
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Message: 3
Date: Tue, 12 Mar 2013 10:11:10 +0100
From: Hermann Fuchs <hermann.fuchs at meduniwien.ac.at<mailto:hermann.fuchs at meduniwien.ac.at>>
To: Carlos Uribe <carluri at phas.ubc.ca<mailto:carluri at phas.ubc.ca>>
Cc: "gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>"
<gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: Re: [Gate-users] Process for Photon Evaporation
Message-ID:
<1363079470.5371.3.camel at strahlen41.strahlen.meduniwien.ac.at<mailto:1363079470.5371.3.camel at strahlen41.strahlen.meduniwien.ac.at>>
Content-Type: text/plain; charset="utf-8"
That is an interesting question.
Could you keep me informed on your findings?
If it isn't already in Gate it should be easy to add.
Just contact me and I can help you with this or implement it for you.
Best reards,
Hermann
On Fri, 2013-03-08 at 12:22 -0800, Carlos Uribe wrote:
> Hello everybody,
>
>
>
> Can anyone please tell me which process to add to my Physics list in
> order to see the de-exitation of the metastable daughter?
>
>
> The parent follows a beta-minus decay which works great except I don't
> see the gammas generated by the metastable daughter.
>
>
> I am using
> /gate/physics/addProcess RadioactiveDecay
>
>
> but apparently, Geant4 handles the meta-stable states through the
> existing photo-evaporation code;
>
>
>
> How do I set the photon evaporation process?
>
>
> Thanks in advance,
> --
>
>
> Carlos F Uribe
>
> _______________________________________________
> 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
--
-------------
DI Hermann Fuchs
Christian Doppler Laboratory for Medical Radiation Research for Radiation Oncology
Department of Radiation Oncology
Medical University Vienna
W?hringer G?rtel 18-20
A-1090 Wien
Tel. + 43 / 1 / 40 400 7271<tel:%2B%2043%20%2F%201%20%2F%2040%20400%207271>
Mail. hermann.fuchs at meduniwien.ac.at<mailto:hermann.fuchs at meduniwien.ac.at>
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--
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Carlos F Uribe
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Carlos F Uribe
--
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