[Gate-users] Movement of source with cold_area

Zhengzhi Liu zliu36 at stanford.edu
Thu Apr 2 19:32:53 CEST 2020


Hi Maxime,

Thank you very much for scrutinizing my code and providing suggestions.

You said I "didn't add the '_phys' part on the object name when using the
forbid command" and I "didn't follow that part of the wiki example". First,
which wiki example were you referring to? Secondly, it looks like '_phys'
is only used in the old way of moving source as stated here
<https://opengate.readthedocs.io/en/latest/source_and_particle_management.html#movement-of-a-source>
in the user manual. For creating a source with Forbid, I have not seen
people appending  '_phys' to their object name.

Yes, it looks like the GATE is capable of creating an annulus source
<https://opengate.readthedocs.io/en/latest/source_and_particle_management.html#defining-the-shape-of-the-source>,
however, literally, it is a ring source, as it does support adding *halfz*
to its definition. Thus it has no thickness. I also am not sure which wiki
example you were referring to.


What I am trying to achieve is to move the NEMA IEC Body Phantom
<http://www.spect.com/pub/NEMA_IEC_Body_Phantom_Set.pdf> with the source in
my simulated PET system along axial direction back and forth. The
definition of the source is a little bit complicated, it uses many
cold_area. Thus, I started with a simplistic case where there is only a
source created with cold_area. However, after the movement, the annulus
didn't maintain its shape. If I can't get this simple case work, I don't
see any chance to move the NEMA phantom and source correctly.

I think sincerely thank you for your great contribution to GATE development
and helping me and others.

Zhengzhi



On Thu, Apr 2, 2020 at 6:43 AM Maxime Toussaint <
Maxime.Toussaint at usherbrooke.ca> wrote:

> Greetings,
>
> I do not know why the approach you used did not work. The only difference
> I have found between your code and the example shown in the wiki, is that
> you didn't add the "_phys" part on the object name when using the forbid
> command. Is there a reason for why you didn't follow that part of the wiki
> example?
>
> Also, from my understanding, you want an annulus source. Why don't you
> directly define one as shown in the wiki? Is there a particularity in your
> case that make it invalid?
>
> Have a nice day,
> Maxime Toussaint
>
>
> ------------------------------
> *De :* Gate-users <gate-users-bounces at lists.opengatecollaboration.org> de
> la part de Zhengzhi Liu <zliu36 at stanford.edu>
> *Envoyé :* 1 avril 2020 18:23
> *À :* gate-users <gate-users at lists.opengatecollaboration.org>
> *Objet :* [Gate-users] Movement of source with cold_area
>
> Dear Gate users,
>
> I am trying to move NEMA IQ phantom with the source along the axial
> direction back and forth to simulate a real experiment that we have done. I
> started with a much simpler case where there is only an annulus phantom
> with an annulus source in the simulated PET system. Phantom as a volume is
> very easy to be translated. According to the user manual, to move a
> source,  the source had better be attached to a volume. For common source
> without cold_area, it works very well. However, I found it did not work in
> the case where the source is determined by a volume and a cold_area (which
> is also a volume), such as the annulus source. Could anyone teach me how to
> do so if it is possible?
>
> Following is my code, I moved the phantom and cold_area simultaneously,
> whether or not I attached the source to phantom, after the translation,
> GATE did not return an annulus source rather a cylindrical source same as
> the phantom as shown in the attached screenshot.
>
> phantom.mac
> #=====================================================
> # WATER PHANTOM
> #=====================================================
> /gate/world/daughters/name                            Normal_AP
> /gate/world/daughters/insert                          cylinder
> /gate/Normal_AP/geometry/setRmax                      30.051 cm
> /gate/Normal_AP/geometry/setRmin                      30.0 cm
> /gate/Normal_AP/geometry/setHeight                    6 cm
> /gate/Normal_AP/placement/setTranslation              0.0 0.0 0.0 cm
> /gate/Normal_AP/moves/insert                       genericMove
> /gate/Normal_AP/genericMove/setPlacementsFilename
>  ./macros/phantomMovement0.placements
> /gate/Normal_AP/setMaterial                           Water
> /gate/Normal_AP/vis/forceSolid
> /gate/Normal_AP/vis/setColor                          white
> /gate/Normal_AP/vis/setVisible                        1
>
> /gate/world/daughters/name                            cold_area
> /gate/world/daughters/insert                          cylinder
> /gate/cold_area/geometry/setRmax                      30.00 cm
> /gate/cold_area/geometry/setHeight                    6 cm
> /gate/cold_area/placement/setTranslation              0.0 0.0 0.0 cm
> /gate/cold_area/moves/insert                       genericMove
> /gate/cold_area/genericMove/setPlacementsFilename
>  ./macros/phantomMovement0.placements
> /gate/cold_area/setMaterial                           Air
> /gate/cold_area/vis/forceWireframe
> /gate/cold_area/vis/setColor white
>
>
> source.mac
> #=====================================================
> # FASTER PRODUCTION MODULE FOR GE-68 ISOTOPES
> #=====================================================
> /gate/source/addSource                                 Ge68
> /gate/source/Ge68/setActivity                          37000 Bq #1. uci
> /gate/source/Ge68/gps/particle                         gamma
> /gate/source/Ge68/setType                              backtoback
> /gate/source/Ge68/gps/type                             Volume
> /gate/source/Ge68/gps/shape                            Cylinder
> /gate/source/Ge68/gps/radius                           30.051  cm
> /gate/source/Ge68/gps/halfz                            3  cm
> /gate/source/Ge68/gps/centre                           0. 0. 0. cm
> #/gate/source/Ge68/attachTo                             Normal_AP
> /gate/source/Ge68/gps/energytype                       Mono
> /gate/source/Ge68/gps/monoenergy                       0.511 MeV
> /gate/source/Ge68/gps/angtype                          iso
> /gate/source/Ge68/setForcedUnstableFlag                false
>  #/gate/source/Ge68/setForcedHalfLife                  6586 s
> /gate/source/Ge68/gps/Forbid cold_area
> /gate/source/Ge68/dump  1
>
> /gate/source/list
>
>
> Thanks a lot for your reading and any help.
> Sincerely,
> Zhengzhi
>
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