Re: [fluka-discuss]: Conversion of ICRP No 110 Phantoms to .vxl?

From: Vittorio Boccone <dr.vittorio.boccone_at_ieee.org>
Date: Wed, 6 Jul 2016 23:38:09 +0200

Hi Alex, no problem. Apologies for the rough answer, I should have reread the mail before sending it.

Contrary of what I mentioned in the first mail the AM.dat is not ready for voxel…. so yes you need to pass also from fortran.
VOXEL conversion code is included in the manual and you have several example on the list.

I added the relevant files on a github repository (should be freely accessible) https://github.com/drbokko/fluka-snippets

Download the files and edit the relevant parameters filenames, NX,NY,NZ and DX,DY,DZ and data sorting and then compile with the makefile
> make
or by hand with
> $FLUPRO/flutil/fff writeVoxelFile.f
> $FLUPRO/flutil/lfluka writeVoxelFile.o writeVoxelFile

The organ number will reconverted in the VOXEL format, the correspondance list original_organ_number voxel_organ_number will be printed during the execution of the conversion script. At this stage you will have a valid voxel file to be imported in Fluka and you can proceed with the material definition.

About the scripting I cannot suggest you to go in detail using a specific scripting language instead of another in order to build the material you need. I would try rather to help you with a scripting/analysis language that is in your comfort zone. Do you have any preferred analysis/scripting language?

Best,
Vittorio


> On 06 Jul 2016, at 21:43, Ševčik Aleksandras <aleksandras.sevcik_at_ktu.edu> wrote:
>
> Dear Vittorio,
>
> It's the first time ever I'm trying to do this, and never tried anything similar before. What I understood, is that I can open .dat with VOXEL card as it is. I also know about generic Flair's dicom folder with predefined materials/compounds accordingly Hounsfield values. However I have no idea how to carry on "with the simple scripting" yet I understand and respect that this mailing list is for concrete issues but not for teaching basic things. But just in case you would like to share any link/tutorial, I would appreciate it very much. If there isn't available any, it's ok then, I'll try to learn this somehow.
>
> In any case, your attention is very appreciated,
>
> Regards
> Aleksandras
> From: Vittorio Boccone <dr.vittorio.boccone_at_ieee.org>
> Sent: Wednesday, July 6, 2016 9:27:53 PM
> To: Ševčik Aleksandras
> Cc: fluka-discuss_at_fluka.org
> Subject: Re: [fluka-discuss]: Conversion of ICRP No 110 Phantoms to .vxl?
>
> Dear Alex, yes I read the README files.
> Once more, the A[M/F].dat can be open with a VOXEL as it is. Perhaps theres some inversion in the coordinates but nothing that any matrix handling code can work out.
> What you need to do is to define the correct material for each organ. This is indeed obtained simple scripting and you are not bound to Fortran. As a matter of fact I approached similar problem both in bash and python. The technical knowledge required is not dramatic.
>
> There are very few simulation cases where one doesn’t need to get the hand a bit dirty with coding. The task can be also approached manually and will not require you more than a couple of hours for the material definition (definition of the compounds and the assignment of the organ to the correct material). It’s outside of the scopes of the list to solve the problem for you but we are more than happy to help you debugging your simulation in case you get a first draft of the input file.
>
> Best,
> Vittorio
>
>> On 06 Jul 2016, at 11:57, Ševčik Aleksandras <aleksandras.sevcik_at_ktu.edu <mailto:aleksandras.sevcik_at_ktu.edu>> wrote:
>>
>> Dear Vittorio,
>>
>> Thank you so much for your input. Hereby is that README file attached which most likely gives that necessary input you mentioned. However, I have no any practice with scripting/programming at all.
>>
>> So, as you mentioned, if someone on the list has a model to share, I would be eternally grateful, or maybe any step-by-step tutorial is available how to utilize the information given in Readme file.
>>
>> Regards,
>> Aleksandras
>> From: Vittorio Boccone <dr.vittorio.boccone_at_ieee.org <mailto:dr.vittorio.boccone_at_ieee.org>>
>> Sent: Tuesday, July 5, 2016 10:37:46 PM
>> To: Ševčik Aleksandras
>> Cc: fluka-discuss_at_fluka.org <mailto:fluka-discuss_at_fluka.org>
>> Subject: Re: [fluka-discuss]: Conversion of ICRP No 110 Phantoms to .vxl?
>>
>> Dear Alex,
>> as far as the organs A[M/F].dat are basically already in a voxel format, as the numbers in it correspond to the organ identifier. Next step is to define for you the material/composition of each organ id. Correspondence between ID and density can be found in A[M/F]_organs .dat, Material composition can be found in the A[M/F]_media.dat file.
>>
>> So being the voxel structures there, the rest of the input file needed is just about material and region definition. I think you are pretty much there already. As the organ and media definition are in a pseudo-nicely-formatted ASCII, one can obtain a decent input file with a few lines of python or another scripting language in about an hour or word or less. Alternatively the same results can be obtained in a few hours more by building the materials in the good ol’ way.
>>
>> Maybe someone on the list has a model to share?
>>
>> Best,
>> Vittorio
>>
>>
>>> On 05 Jul 2016, at 13:04, Ševčik Aleksandras <aleksandras.sevcik_at_ktu.edu <mailto:aleksandras.sevcik_at_ktu.edu>> wrote:
>>>
>>> Hello!
>>>
>>> Currently I am enjoying the FLUKA/FLAIR capabilities, especially DICOM conversion to .vxl and reviewing it with SimpleGeo/DaVis 3D.
>>> I am very interested in ICRP No 110 Adult Reference Computational Phantoms, however, they consists of several .dat files, and added Readme, unfortunately, is beyond my knowledge to understand ( it gives instructions for Fortran programming, etc.)
>>> http://www.icrp.org/publication.asp?id=ICRP%20Publication%20110 <http://www.icrp.org/publication.asp?id=ICRP%20Publication%20110>
>>>
>>> <http://www.icrp.org/publication.asp?id=ICRP%20Publication%20110>Question: is there any simpler way to transform these .dat files to .vxl and use it for internal dose calculations?
>>>
>>> I've read several articles describing use of FLUKA dose calculations with these phantoms, unfortunately only results were presented without internal details.
>>>
>>> Thank you very much,
>>>
>>> Alex
>>
>> <README.txt>



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Received on Thu Jul 07 2016 - 01:03:31 CEST

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