[Gate-users] Parallel Hole Collimator

Carlos Uribe carluri at phas.ubc.ca
Wed Mar 13 22:35:37 CET 2013 

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> 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> 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:
>>>>
>>>>> Send Gate-users mailing list submissions to
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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
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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
>>>>> >
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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
>>>> Gate-users at lists.opengatecollaboration.org
>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>
>>>>  --
>>>> 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
>>
>> --
>> Carlos F Uribe
>>
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