[Gate-users] Movement of source with cold_area

Zhengzhi Liu zliu36 at stanford.edu
Fri Apr 3 02:27:53 CEST 2020


Hi Maxime,

Thanks for your prompt reply. I see your point on "_phys". In the new
document for v9.0, there is a "_phys" appending to cold_area in
"*/gate/source/number1/gps/Forbid cold_area_phys*". However, in the
document for v8.0, there is no such a "_phys". I tried that, even though
the GATE did not throw any error, but it did not solve the problem either.

I also thought about the third hack you put forward. It works for simple
geometries, like the one, a single annulus source. However, I am
overwhelmed with moving NEMA body phantom. I wish there is someone who has
tried this before and could share their thoughts. The reason why I feel it
is hard to move NEMA body phantom and its sources is that some sources may
dump many volumes to form the desired shape. I try to break them into
pieces and see if I can successfully move them together.

Thank you very much.

Zhengzhi

On Thu, Apr 2, 2020 at 11:13 AM Maxime Toussaint <
Maxime.Toussaint at usherbrooke.ca> wrote:

> Greetings,
>
> No problemo about the (attempt to) help.
>
> For the first part, I was refering to section 6.1.8 in [1], named
> "Defining a cold source". I have no idea if the "_phys" is required or if
> it is an error in the wiki.
>
> For the second part, my bad. I assumed that an annulus was a 3D object
> from your message. I was wrong and it explains why you are not using it. We
> can define a hollowed cylinder geometry, so I had assumed that we could do
> the same with a source. You could stack a couple of annulus source but I
> hope you won't need to ressort to that!
>
> I still do not have an idea about the problem you highlighted, but another
> hack would be to create a voxelized version of that phantom.
>
> A third hack: if you are only doing one translation: extend, in the motion
> axis, your cold cylinder height to the full domain of position and do not
> apply motion on it. Thus, if the "forbid" command work but it cannot be
> moved, it should be okay.
>
> Well, let's hope that a Gate Master will have a more pratical answer than
> those 3 hacks!
>
> Have a nice day,
> Maxime Toussaint
>
> [1]
> https://opengate.readthedocs.io/en/latest/source_and_particle_management.html#id12
>
> ------------------------------
> *De :* Zhengzhi Liu <zliu36 at stanford.edu>
> *Envoyé :* 2 avril 2020 13:32
> *À :* Maxime Toussaint <Maxime.Toussaint at USherbrooke.ca>
> *Cc :* gate-users <gate-users at lists.opengatecollaboration.org>
> *Objet :* Re: [Gate-users] Movement of source with cold_area
>
> 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://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fsource_and_particle_management.html%23movement-of-a-source&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7C35185c3a8f24483b35ba08d7d72c097c%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637214457128673504&sdata=8ZrcE8%2BkKwESK9WZpKJddbbwZtrcX5kT0HfzGh4tOm0%3D&reserved=0>
> 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://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fsource_and_particle_management.html%23defining-the-shape-of-the-source&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7C35185c3a8f24483b35ba08d7d72c097c%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637214457128673504&sdata=q7R6sS30whSJ8vD7VIsiUxZGyt3h6xfvDD%2FPPz0gccI%3D&reserved=0>,
> 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
> <https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.spect.com%2Fpub%2FNEMA_IEC_Body_Phantom_Set.pdf&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7C35185c3a8f24483b35ba08d7d72c097c%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637214457128683499&sdata=PUrUjK11X8vc9OyWqSthSAZtjknf7uLiQO6v5rcFTDc%3D&reserved=0> 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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