[Gate-users] Regular Parameterization Error with Geant4 v10

Fri Feb 17 16:00:44 CET 2017

Hello,

I have proposed a fix for the ImageRegionalizedVolume bug (
https://github.com/OpenGATE/Gate/pull/101).

This problem will no longer appear in the upcoming version of Gate.

Sincerely,

Thomas

*Thomas DESCHLER*
Doctorant en Physique des Rayonnements
Institut Pluridisciplinaire Hubert Curien <http://www.iphc.cnrs.fr/>
Département Recherches Subatomiques
<http://www.iphc.cnrs.fr/spip.php?page=rubrique&id_rubrique=143> - Groupe
Ramses <http://www.iphc.cnrs.fr/-Ramses-.html>
Bâtiment 35, Bureau 208

Thomas.Deschler at iphc.cnrs.fr
<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=Thomas.Deschler@iphc.cnrs.fr>
(+33) 03 88 10 63 95 <+33388106395>
(+33) 06 20 96 07 49 <+33620960749>

2017-02-13 17:07 GMT+01:00 Maxime Chauvin <maxime.chauvin at inserm.fr>:

> Hello Nicolas,
>
> Yes I remember this. It is a bug I think.
> I just set min, max: -1,4 in my* data/waterbottle_HU2mat.txt*
> *And then it doesn’t complain.*
>
> *This is just a fix and hopefully this bug will be corrected soon.*
>
> *Cheers,*
> *  Maxime*
>
> On 13 Feb 2017, at 16:38, Triltsch, Nicolas <nicolas.triltsch at tum.de>
> wrote:
>
> Hey David & Maxime,
>
> Thanks for your advice. I tried to use the option ImageRegionalizedVolume
> (plus the distance map) instead of ImageNestedParametrisedVolume, but it
> gives the following error:
>
> "*[Physic-0] The following Geant4's physic-list is enabled :emlivermore*
> *GateVImageVolume.cc <http://gatevimagevolume.cc> (l.363): The image
> contains HU indices out of range of the HU range found in
> data/waterbottle_HU2mat.txt*
> *min, max:0, 4.*
> *min, max in image: -1, 3*
> *Abort.*
> "
>
> I am confused by this error as I am using the the same HU2mat.txt and
> .mhd+.raw files as before. Does the new Parameterization method require
> different material descriptors or what could be the reason? My image
> contains of 4 materials only: Air (index 0), water (index 1), plastic
> (index 2) and lead (index 3).
>
> Cheers,
>
> Nico
> On 02/10/2017 04:57 PM, David Sarrut wrote:
>
> Hello,
>
> To my knowledge, RegularParameterization with flag skipEqualMaterials is
> still buggy (it should be disabled: if someone know this code, please
> propose a pull request to correct or disable this option).
>
> Use either:
> - ImageNestedParametrisedVolume : simple conventional navigator, similar
> to regular, (slightly faster)
>
> - ImageRegionalizedVolume as proposed by Maxime. It could be 3-4 times
> faster in some cases but it depends on what you are storing during the
> simulation. If it is a dose map, take care to the statistical
> uncertainties. If you are only interested in particle outgoing the volume
> (for imaging for example), it is safe to use. Of course, the speed up
> depends on the voxelized volume (faster if lot of similar material).
>
> Doc is here: http://wiki.opengatecollaboration.org/index.php/Users_
> Guide_V8.0:Voxelized_Source_and_Phantom#Nested_parameterization_method
>
> David
>
>
> On Fri, Feb 10, 2017 at 4:45 PM, Maxime Chauvin <maxime.chauvin at inserm.fr>
> wrote:
>
>> Hello Nicolas,
>>
>> I had the same problem as you and couldn’t fix it. On the other hand
>> there is a even more efficient way  using
>> ImageRegionalizedVolume. It will further speed up the simulation
>> especially if your geometry has a lot of common voxel
>> and you will get rid of this warning.
>>
>> Cheers,
>>   Maxime
>>
>> On 10 Feb 2017, at 14:41, Triltsch, Nicolas <nicolas.triltsch at tum.de>
>> wrote:
>>
>> Hello,
>>
>> I tried to speed up my simulation by choosing Regular Parameterization
>> (with flag skipEqualMaterials to 1) instead of Nested Parameterization,
>> because my Volume got a lot of voxels with the same material. It did indeed
>> speed up the simulation by a factor of 15, but some projections of my CT
>> simulation failed (error: segmentation fault; crash).
>>
>> Now I saw that during the initialization phase of gate it states the
>> following:
>>
>> *### WARNING ### setSkipEqualMaterials at false !! The Geant4 method is
>> not safe since the release 9.5 - Need to be fixed*
>>
>> I am pretty sure that this warning is somehow connected to the warning.
>> Does anyone know if there had been a bug fix for Geant4 v10.2.2?
>>
>> In the appendix there is a screenshot of the error.
>>
>> Cheers,
>> Nico
>>
>> --
>> B.Sc. Nicolas Triltsch
>> Masterand
>>
>> Technische Universität München
>> Physik-Department
>> Lehrstuhl für Biomedizinische Physik E17
>>
>> James-Franck-Straße 1
>> 85748 Garching b. München
>>
>> Tel: +49 89 289 12591 <+49%2089%2028912591>
>> nicolas.triltsch at tum.dewww.e17.ph.tum.de
>>
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>
>
>
> --
> David Sarrut, Phd
> Directeur de recherche CNRS
> CREATIS, UMR CNRS 5220, Inserm U1206
> Centre de lutte contre le cancer Léon Bérard
> 28 rue Laënnec, 69373 Lyon cedex 08
> Tel : 04 78 78 51 51 / 06 74 72 05 42
> http://www.creatis.insa-lyon.fr/~dsarrut
> _________________________________
>  "2 + 2 = 5,  for extremely large values of 2"
> _________________________________
>
>
> --
> B.Sc. Nicolas Triltsch
> Masterand
>
> Technische Universität München
> Physik-Department
> Lehrstuhl für Biomedizinische Physik E17
>
> James-Franck-Straße 1
> 85748 Garching b. München
>
> Tel: +49 89 289 12591 <+49%2089%2028912591>
> nicolas.triltsch at tum.dewww.e17.ph.tum.de
>
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