[Gate-users] Parallel Hole Collimator

Carlos Uribe carluri at phas.ubc.ca
Wed Mar 13 18:39:29 CET 2013 

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> 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> 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>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> 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>
>>>> To: "gate-users at lists.opengatecollaboration.org"
>>>>         <gate-users at lists.opengatecollaboration.org>
>>>> Subject: [Gate-users] Parallel hole Collimator
>>>> Message-ID:
>>>>         <CAPJy_1TcFTKwiEpu_Zicc=+
>>>> UKYN3hfHMjvhumfzWL6AxyZ+1Sg at mail.gmail.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> 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
>>>> -------------- next part --------------
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>>>> >
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Mon, 11 Mar 2013 12:40:11 -0700
>>>> From: Carlos Uribe <carluri at phas.ubc.ca>
>>>> To: samira nezhad <sn90113 at gmail.com>
>>>> Cc: "gate-users at lists.opengatecollaboration.org"
>>>>         <gate-users at lists.opengatecollaboration.org>
>>>> Subject: Re: [Gate-users] ASCII output
>>>> Message-ID:
>>>>         <CAPJy_1QZT9uYF1VmobA3Mk2xMfS_2MRTmQfv41x=
>>>> 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/> 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>
>>>> 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
>>>> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>> >
>>>> > --
>>>> > Carlos F Uribe
>>>> >
>>>> -------------- next part --------------
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>>>> >
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 3
>>>> Date: Tue, 12 Mar 2013 10:11:10 +0100
>>>> From: Hermann Fuchs <hermann.fuchs at meduniwien.ac.at>
>>>> To: Carlos Uribe <carluri at phas.ubc.ca>
>>>> Cc: "gate-users at lists.opengatecollaboration.org"
>>>>         <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>
>>>> 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
>>>> > 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<%2B%2043%20%2F%201%20%2F%2040%20400%207271>
>>>> Mail. hermann.fuchs at meduniwien.ac.at
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>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> Gate-users mailing list
>>>> Gate-users at lists.opengatecollaboration.org
>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>
>>>> End of Gate-users Digest, Vol 82, Issue 20
>>>> ******************************************
>>>>
>>>
>>>
>>> _______________________________________________
>>> Gate-users mailing list
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>>>
>>>  --
>>> Carlos F Uribe
>>> <http://lists.opengatecollaboration.org/mailman/listinfo/gate-users>
>>
>>
>>
>> _______________________________________________
>> Gate-users mailing listGate-users at lists.opengatecollaboration.orghttp://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>>
>>
>
>
>  --
> Carlos F Uribe
>
> --
> Carlos F Uribe
>
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