[Gate-users] Optical Photons Surfaces and Materials
ilker ozsahin
ilkerozsahin at gmail.com
Thu Jul 16 15:32:48 CEST 2015
Hi,
The optical photon simulation works with the Surfaces.xml file. The problem
was the position of the initialization. It must be defined after adding the
processes.
Thank you very much Vesna
Ilker
2015-07-16 9:19 GMT-04:00 ilker ozsahin <ilkerozsahin at gmail.com>:
> Ok, of course How can I add an answer on the mailing list? I thought this
> was in there already?
>
> Also, what about the Materials.xml? Do you have any idea?
>
> 2015-07-16 9:12 GMT-04:00 Vesna Cuplov <vesna.cuplov at gmail.com>:
>
>> Hi,
>>
>> Oh yes, sometimes it's a silly issue like the position of the
>> initialisation. I'm glad you figured this out.
>> Could you please add an answer on the mailing list so everyone knows that
>> it works :)
>>
>> thank you
>> vesna
>>
>>
>> Vesna Cuplov
>> Laboratoire Imagerie Moléculaire In Vivo (IMIV)
>> UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
>> CEA/I2BM/Service Hospitalier Frédéric Joliot
>> 4 place du Général Leclerc
>> 91400 Orsay
>> http://v-cuplov.net
>>
>> On Thu, Jul 16, 2015 at 3:08 PM, ilker ozsahin <ilkerozsahin at gmail.com>
>> wrote:
>>
>>> Please see the output attached, now it has optical processes and it
>>> seems it works.
>>> I enabled and initialized the processList after addProcess. That was the
>>> silly problem I guess, sorry. Thanks a lot, this conversation really helps
>>> to my understanding.
>>>
>>> The macro is little complicated actually, but path is correct, because
>>> when I put a material that is in GateMaterials.db but not in Materials.xml,
>>> it work. I have both material files in the same directory.
>>>
>>> I can send the macro anyway after arranging, if it will help for the
>>> Materials.xml
>>>
>>>
>>>
>>>
>>> 2015-07-16 8:55 GMT-04:00 Vesna Cuplov <vesna.cuplov at gmail.com>:
>>>
>>>> Do you give the right path of the GateMaterials.db ?
>>>>
>>>> If you have a simple macro, could you send it to me?
>>>>
>>>> Vesna Cuplov
>>>> Laboratoire Imagerie Moléculaire In Vivo (IMIV)
>>>> UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
>>>> CEA/I2BM/Service Hospitalier Frédéric Joliot
>>>> 4 place du Général Leclerc
>>>> 91400 Orsay
>>>> http://v-cuplov.net
>>>>
>>>> On Thu, Jul 16, 2015 at 2:37 PM, ilker ozsahin <ilkerozsahin at gmail.com>
>>>> wrote:
>>>>
>>>>> Well, maybe we can understand the problem through the Materials.xml.
>>>>> What can you say about Materials.xml? Since we see the output gives
>>>>> something like ABSLENGTH, RINDEX, FASTCOMPONENT, etc., maybe it means I use
>>>>> optical processes? Also when I use Epoxy as a material which is defined in
>>>>> the Materials.xml, it says:
>>>>>
>>>>> /usr/local/gate6.2/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc
>>>>> (l.132): GateMaterialDatabase: could not find the definition for material
>>>>> 'Epoxy' in material files
>>>>>
>>>>>
>>>>> but if I use BGO which is also defined in the Materials.xml, it works
>>>>> and gives its properties from that file.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 2015-07-16 1:52 GMT-04:00 Vesna Cuplov <vesna.cuplov at gmail.com>:
>>>>>
>>>>>> no. If you use optical processes the code knows that it needs to look
>>>>>> at these xml files.
>>>>>> I am sure that you do not actually use optical processes at all. Did
>>>>>> you see the output.txt? These processes are not enabled.
>>>>>>
>>>>>> Vesna Cuplov
>>>>>> Laboratoire Imagerie Moléculaire In Vivo (IMIV)
>>>>>> UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
>>>>>> CEA/I2BM/Service Hospitalier Frédéric Joliot
>>>>>> 4 place du Général Leclerc
>>>>>> 91400 Orsay
>>>>>> http://v-cuplov.net
>>>>>>
>>>>>> On Wed, Jul 15, 2015 at 6:48 PM, ilker ozsahin <
>>>>>> ilkerozsahin at gmail.com> wrote:
>>>>>>
>>>>>>> So, there is not any command to point the xml file, isnt there?
>>>>>>>
>>>>>>> 2015-07-15 12:32 GMT-04:00 ilker ozsahin <ilkerozsahin at gmail.com>:
>>>>>>>
>>>>>>>> I have
>>>>>>>>
>>>>>>>> /gate/physics/addProcess OpticalAbsorption
>>>>>>>>
>>>>>>>> /gate/physics/addProcess OpticalRayleigh
>>>>>>>>
>>>>>>>> /gate/physics/addProcess OpticalBoundary
>>>>>>>>
>>>>>>>> in my macro.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 2015-07-15 12:30 GMT-04:00 Vesna Cuplov <vesna.cuplov at gmail.com>:
>>>>>>>>
>>>>>>>>> I don't see any physics process related to optical photons?
>>>>>>>>>
>>>>>>>>> You need some of these otherwise you're not doing anything to the
>>>>>>>>> photons.... The OpticalBoundary process is important in case you look at
>>>>>>>>> physics of optical photons through surfaces.
>>>>>>>>>
>>>>>>>>> /gate/physics/addProcess OpticalAbsorption
>>>>>>>>> /gate/physics/addProcess OpticalRayleigh
>>>>>>>>> /gate/physics/addProcess OpticalBoundary
>>>>>>>>> /gate/physics/addProcess OpticalMie
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> vesna
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Vesna Cuplov
>>>>>>>>> Laboratoire Imagerie Moléculaire In Vivo (IMIV)
>>>>>>>>> UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
>>>>>>>>> CEA/I2BM/Service Hospitalier Frédéric Joliot
>>>>>>>>> 4 place du Général Leclerc
>>>>>>>>> 91400 Orsay
>>>>>>>>> http://v-cuplov.net
>>>>>>>>>
>>>>>>>>> On Wed, Jul 15, 2015 at 6:21 PM, ilker ozsahin <
>>>>>>>>> ilkerozsahin at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Attached please find the output. I also attached the one with
>>>>>>>>>> uncommented inserting the surface name and type, the output2
>>>>>>>>>>
>>>>>>>>>> 2015-07-15 12:11 GMT-04:00 Vesna Cuplov <vesna.cuplov at gmail.com>:
>>>>>>>>>>
>>>>>>>>>>> maybe your macro points to an other xml file, but not the one
>>>>>>>>>>> you are modifying?
>>>>>>>>>>> I usually point to the entire path in my macro.
>>>>>>>>>>>
>>>>>>>>>>> Could you run Gate like this:
>>>>>>>>>>>
>>>>>>>>>>> Gate yourmacro.mac &> output.txt
>>>>>>>>>>>
>>>>>>>>>>> and send me the output.txt ?
>>>>>>>>>>>
>>>>>>>>>>> vesna
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Vesna Cuplov
>>>>>>>>>>> Laboratoire Imagerie Moléculaire In Vivo (IMIV)
>>>>>>>>>>> UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
>>>>>>>>>>> CEA/I2BM/Service Hospitalier Frédéric Joliot
>>>>>>>>>>> 4 place du Général Leclerc
>>>>>>>>>>> 91400 Orsay
>>>>>>>>>>> http://v-cuplov.net
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Jul 15, 2015 at 5:59 PM, ilker ozsahin <
>>>>>>>>>>> ilkerozsahin at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> Yes, It is, as well.
>>>>>>>>>>>> Also, when I remove the Surface.xml file from the directory, it
>>>>>>>>>>>> works and I can see the optical photons anyway. Also even I put something
>>>>>>>>>>>> like
>>>>>>>>>>>>
>>>>>>>>>>>> /gate/coupling/surface/name teflonsurf
>>>>>>>>>>>> ......insert
>>>>>>>>>>>> ......rough
>>>>>>>>>>>>
>>>>>>>>>>>> it runs without any errors.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Ilker
>>>>>>>>>>>>
>>>>>>>>>>>> 2015-07-15 11:55 GMT-04:00 Vesna Cuplov <vesna.cuplov at gmail.com
>>>>>>>>>>>> >:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>> If you have no error then the Gate_use_optical is ON,
>>>>>>>>>>>>> otherwise it would have complained because without that boolean ON, you can
>>>>>>>>>>>>> not work with the optical photons.
>>>>>>>>>>>>> What do you mean by 'it doesn't recognize the files'? You
>>>>>>>>>>>>> change some values and it doesn't make any difference in the output?
>>>>>>>>>>>>>
>>>>>>>>>>>>> vesna
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, Jul 15, 2015 at 5:49 PM, ilker ozsahin <
>>>>>>>>>>>>> ilkerozsahin at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> There is no error. It just works without recognizing the
>>>>>>>>>>>>>> files.
>>>>>>>>>>>>>> How can I enable it? It says uncomment this line
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> export GATE_USE_OPTICAL=1 (in env_gate.sh)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Where can I find it?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 2015-07-15 11:36 GMT-04:00 Vesna Cuplov <
>>>>>>>>>>>>>> vesna.cuplov at gmail.com>:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Did you enable the use of optical photons in Gate:
>>>>>>>>>>>>>>> GATE_USE_OPTICAL = ON?
>>>>>>>>>>>>>>> Could you send your error message?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> vesna
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Vesna Cuplov
>>>>>>>>>>>>>>> Laboratoire Imagerie Moléculaire In Vivo (IMIV)
>>>>>>>>>>>>>>> UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
>>>>>>>>>>>>>>> CEA/I2BM/Service Hospitalier Frédéric Joliot
>>>>>>>>>>>>>>> 4 place du Général Leclerc
>>>>>>>>>>>>>>> 91400 Orsay
>>>>>>>>>>>>>>> http://v-cuplov.net
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Wed, Jul 15, 2015 at 5:23 PM, ilker ozsahin <
>>>>>>>>>>>>>>> ilkerozsahin at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I have both Surface.xml and Materials.xml files in the
>>>>>>>>>>>>>>>> directory where I run Gate but it does not recognize the files. Is there a
>>>>>>>>>>>>>>>> command to execute those files? Anyone has ever managed to use and modify
>>>>>>>>>>>>>>>> those files?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>>>> Ilker
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Gate-users mailing list
>>>>>>>>>>>>>>>> Gate-users at lists.opengatecollaboration.org
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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