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

From: Vittorio Boccone <dr.vittorio.boccone_at_ieee.org>
Date: Fri, 8 Jul 2016 22:14:07 +0200

Your modification of the file are working and for me on CentOS7 with gcc/gfotran 4.8.5 are able to read the file downloaded from the ICRP page.
The question is on which linux are you compiling, with which compiler. I would not share the AF files as they are protected by copyright (http://www.icrp.org/page.asp?id=11)

Second how do you compile it?

Best,
Vittorio

> On 08 Jul 2016, at 09:22, Ševčik Aleksandras <aleksandras.sevcik_at_ktu.edu> wrote:
>
> Ševčik Aleksandras has shared a OneDrive for Business file with you. To view it, click the link below.
>
> AF.dat
> <https://ktuedu-my.sharepoint.com/personal/alesev_ktu_lt/Documents/Email%20attachments/AF.dat> <https://ktuedu-my.sharepoint.com/personal/alesev_ktu_lt/Documents/Email%20attachments/AF.dat>
> AF.dat <https://ktuedu-my.sharepoint.com/personal/alesev_ktu_lt/Documents/Email%20attachments/AF.dat>
> Again - thank your for the whole complete lesson. Hopefully it will help for other beginners too as I saw many previous questions regarding voxel geometry in the mailing list.
>
> The whole picture is clear, just lack of programming skills most likely does not allow to see some miscellaneous things I am missing again. I modified writeVoxel.f file ( changed NX,NY,NZ and source file to 'AF.dat'. (attached). I compiled it, but when I trying execute ./writeVoxel, I get an error showing type mismatch or smth:
>
> incomprehensible list input
> apparent state: unit 30 named AF
> last format: list io
> lately reading direct formatted external IO
> Aborted (core dumped)
>
> Files are attached. Do not expect more of your time, but just in case someone else will have desire to give a basic lesson, you're more than welcome <OutlookEmoji-😊.png>
>
> Regards
> A.
>
>
> From: Vittorio Boccone <dr.vittorio.boccone_at_ieee.org>
> Sent: Friday, July 8, 2016 12:27:36 AM
> To: Ševčik Aleksandras
> Cc: Apple Inc.
> Subject: Re: [fluka-discuss]: Conversion of ICRP No 110 Phantoms to .vxl?
>
>
>> On 07 Jul 2016, at 21:10, Ševčik Aleksandras <aleksandras.sevcik_at_ktu.edu <mailto:aleksandras.sevcik_at_ktu.edu>> wrote:
>>
>> Thank you very much, Vittorio, I've reviewed all the relevant manual sections, tutorials and mailing list topics. However, still many miscellaneous question remain regarding some req
>
> Ok, that’s a good start.
>
>> So the pathway from ICRP 110 .dat to .vxl is kinda clear now. But could you elaborate maybe on how to assign materials to it using Python language?
>
> At this point one could create the compound by hand. Using python one could construct a part of the FLUKA input file with the information available in the media, organ, blow and bone file.
>
> One should parse the all the information from the ascii files and build the relevant materials, compounds and assignmat lines using the above parsed information.
> Technically is just parsing the files and printing out strings.
>
> I add a few python lines here that you can freely use as a guideline https://github.com/drbokko/fluka-snippets/tree/master/Geometry/DummyPhantomGeneration <https://github.com/drbokko/fluka-snippets/tree/master/Geometry/DummyPhantomGeneration>
>
> The script will fetch the infos from the media and organ files (not included in the repo for obvious licensing reasons) and build the relevant materials and compound, usage of bone/blood radio and assignment of the organ material to the voxel regions is left as an exercise.
>
> Hope it helps
>
> Best,
> Vittorio
>
>
>>
>> Regards
>> Aleksandras
>> From: Vittorio Boccone <dr.vittorio.boccone_at_ieee.org <mailto:dr.vittorio.boccone_at_ieee.org>>
>> Sent: Thursday, July 7, 2016 8:30:51 PM
>> To: Ševčik Aleksandras
>> Cc: Apple Inc.
>> Subject: Re: [fluka-discuss]: Conversion of ICRP No 110 Phantoms to .vxl?
>>
>> Dear Alex,
>> always keep the fluke-list in cc as more people might benefit of this discussion
>>
>>> On 07 Jul 2016, at 09:24, Ševčik Aleksandras <aleksandras.sevcik_at_ktu.edu <mailto:aleksandras.sevcik_at_ktu.edu>> wrote:
>>>
>>> Thank you, Vittorio. I'm a master student in Medical Physics; what we are taught it's doesn't cover any of these topics neither programming. We are seen more like users only while I don't like this and want to learn mc transport coding myself and get out of the black box effect, if I may say so. However, this means that I have poor or no skills in some of the areas which result in asking basic/obvious questions as manual or tutorials are not always clear for me. So any respond for experts are highly valuable to me. In the whole country we have only several dozens of medical physicists and not a single of them have experience in mc transport coding. In general, Lithuania only seeks to become an associated CERN member so there are so many areas to improve here..
>> You are right, university doesn’t teach much about the computing tools and programming. But every student in the STEM fields must get the hands on a scripting/analysis language which can help him/her in computational or analysis tasks and in general to solve more or less complex tasks
>>
>>> So far I understood the schematics. I have .dat file, with the help of writeVoxelFile.f I can convert it to .vxl as per your instructions ( I found it in the manual finally too). I also understand that I can open writeVoxelFile.f and edit PARAMETERS (DZ...NZ) if required. So now we have voxel geometry where similar voxels account for the same region. Let's say we get 3000 such regions.
>> If you are beginner. I would suggest you to go thought the manual introduction and the slides of the beginner course at first. A voxel is a regular 3D pixel structure with NX, NY, NZ pixels extension over the three dimensions. in the dat file you find a table of organ indexes which must be converted in a voxel structure. This is what the writeVoxelFile does. The dat file contain the ascii table with the organ index per each pixel.
>>
>> You need to pass from here in order to make the voxel file. All you need is in the repo, you just have to adapt the NX,NY,NZ, DX, DY, DZ variables to the values that mentioned in the Readme file, compile and run the conversion. 3000 different tissue regions are an overkill. Many people reduces them to a few hundreds at most.
>>
>>> So now we need to assign mat to these regions. I assume that definitions of the materials are encoded in the rest of .dat files and the scripting language like Python can be used. Unfortunately I have no any use or experience of any programming language before.
>>>
>>> The following questions arise:
>>>
>>> 1) You mentioned I could it manually. Would you be so kind to explain this? Or should I better go and learn Python and come back after 2-3 weeks when I learn the basics? I planned to do this sooner or earlier anyway.
>> IMO a python course is a good idea only if it contains hands-on exercises.
>>
>>> 2) Interesting : so in .vxl file we have voxels that are differentiated into the regions according levels of grey (HU units)? So we appoint materials(compounds) according HU values?
>> The voxel file contains the region/organ index for each pixel one after the other. What the organ/region is should be added in the input file with the user cards. You can use the flair interface to build and check your file.
>>
>>> One more 3) question. As I understand Flair has automatized all these actions when import DICOM and convert it to .vxl. , while using materials.inp where 47 compounds are described. However there is no automatic adding of corresponding material => voxel (region). In other words, I have predefined materials imported ("HU<1020", HU<"1000", etc.) and at least 3000 voxel regions (VOXEL001...VOXEL3000). But how should I choose for which region which "HU<1020" should be selected? I read some topics in the mailing list about this issue but no clear answer was given.
>> Did you already looked at this thread (and references therein)?
>> http://www.fluka.org/web_archive/earchive/new-fluka-discuss/8841.html <http://www.fluka.org/web_archive/earchive/new-fluka-discuss/8841.html>
>>
>>
>>
>> Best,
>> Vittorio
>
> <writeVoxel.f>



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Received on Fri Jul 08 2016 - 23:52:57 CEST

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