[Gate-users] Report of GATEv8.2 bugs

Sat Mar 7 05:28:32 CET 2020

Hi Maxime,

Thank you very much. It works well. But how come it was coded in this way?
Level1, level2, ..., level4, and layer0, not consistent, right?
Anyhow, that is the resolution for now. Thank you very much.

Wish you a wonderful weekend.
Best regards,

Zhengzhi

On Fri, Mar 6, 2020 at 7:46 PM Maxime Toussaint <
Maxime.Toussaint at usherbrooke.ca> wrote:

> Greetings,
>
> Sorry, I explained myself poorly. level1 to level4 are okay. What I meant
> was to change level5 to either layer0 or layer1.
>
> Bests,
> Maxime Toussaint
> ------------------------------
> *De :* Zhengzhi Liu <zliu36 at stanford.edu>
> *Envoyé :* 6 mars 2020 22:39
> *À :* Maxime Toussaint <Maxime.Toussaint at USherbrooke.ca>
> *Objet :* Re: [Gate-users] Report of GATEv8.2 bugs
>
> Hi Maxime,
>
> Thank you very much as well. I tried your suggestion of replacing level1
> to level5 with layer0 to layer4 in PETScaner. It failed at layer2 and does
> not allow me to add layer2 and later layers. It worked fine with 2layers.
> Could you please verify this with your code by adding some simple dummy
> layers to your code?
> Here is the errormsg:
> [image: Screenshot from 2020-03-06 19-37-02.png]
>
> Thank you very much sincerely.
>
> Zhengzhi
>
> On Fri, Mar 6, 2020 at 7:04 PM Maxime Toussaint <
> Maxime.Toussaint at usherbrooke.ca> wrote:
>
> Greetings,
>
> I quickly looked at the code and I think I found the problem. In short,
> the documentation is correct for the current version of the Gate code on
> github but not for Gate 8.2.
>
> If we look at [1], we see that a change was made from having
> PETscanner/scanner system with components called layer0/layer1 to one
> called level5. That change was committed the 9th of May 2019 while Gate 8.2
> seems to be a Februray 2019 version of the code.
>
> I tried using layer0 (and later layer1) and Gate did not produce any
> warning nor bug. Note that this does not prove that the resulting system
> work.
>
> Also, "PETscanner" is a valid system definition. I will propose a
> modification of the table 1.2 to make it more explicit.
>
> This situation does highlight a little problem. From my understanding, the
> current version of the user guide follow the code on github but it is also
> used for the current stable version of Gate (8.2 at the moment). If I am
> correct, I would propose that a version of the user guide, extracted at the
> same time as the official version, be saved separately from the "latest"
> and a note added saying something like "correction to the user guide are
> only applied on the latest version". After all, we can't expect anyone to
> adapt all versions of the user guide each time the user guide is enhanced.
>
> Hope that I could help and have a nice day,
> Maxime Toussaint
>
>
> [1]
> https://github.com/OpenGATE/Gate/blame/cbe7ffb1c3222b5c1801eb7bc8b703253540e6b1/source/geometry/src/GateScannerSystem.cc
> <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGate%2Fblame%2Fcbe7ffb1c3222b5c1801eb7bc8b703253540e6b1%2Fsource%2Fgeometry%2Fsrc%2FGateScannerSystem.cc&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7Ca971d6afd43c4d17ddde08d7c24949ce%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637191492338352392&sdata=0tnuCu9tvsChRVm3SDxUCDOJ9SpRttb70TPFsZ5VJaM%3D&reserved=0>
> ------------------------------
> *De :* Gate-users <gate-users-bounces at lists.opengatecollaboration.org> de
> la part de Matthew Strugari <matthew.strugari at dal.ca>
> *Envoyé :* 6 mars 2020 20:57
> *À :* Zhengzhi Liu <zliu36 at stanford.edu>; gate-users <
> gate-users at lists.opengatecollaboration.org>
> *Objet :* Re: [Gate-users] Report of GATEv8.2 bugs
>
>
> Hi Zhengzhi,
>
>
>
> According to the user manual (Section 1.5.1
> https://opengate.readthedocs.io/en/latest/defining_a_system_scanner_ct_pet_spect_optical.html#defining-the-systems
> <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fdefining_a_system_scanner_ct_pet_spect_optical.html%23defining-the-systems&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7Ca971d6afd43c4d17ddde08d7c24949ce%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637191492338352392&sdata=%2BOyRHqqtKsH6tb6OA12YUa9MelxQnO%2B2Od%2FVliHcntM%3D&reserved=0>),
> the system name must be one of those available in Table 1.1. In the image
> you provided, this would be Table 4.1. I’m not sure which version of the
> user manual you are referring to, but the most up to date information can
> be found on readthedocs. Nonetheless, your error of COMMAND NOT FOUND shows
> that you defined the system name to be PETscanner which is not a valid
> system name. Replace “PETscanner” with “scanner” and you should be able to
> assign level5 with the defined functionality.
>
>
>
> Regards,
>
> Matthew
>
>
>
> *From: *Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
> on behalf of Zhengzhi Liu <zliu36 at stanford.edu>
> *Date: *Friday, March 6, 2020 at 7:30 PM
> *To: *gate-users <gate-users at lists.opengatecollaboration.org>
> *Subject: *Re: [Gate-users] Report of GATEv8.2 bugs
>
>
>
> According to the user manual, 5 levels can be attached. However, I am not
> able to attach any 5th level. Please share your thoughts if you have some
> experience.  Thanks a lot.
>
>
>
>
>
>
>
> On Fri, Mar 6, 2020 at 3:17 PM Zhengzhi Liu <zliu36 at stanford.edu> wrote:
>
> Report of a potential bug:
>
>
>
> It looks PETScanner only allows 4 layers to be attached, whenever I tried
> to attach the 5th layer (no matter what the geometry is), it throws the
> errormsg.  Has anyone been able to attach a 5 level to PETScanner?  My
> understanding is Gate doesn't recognize the keyword *level5*.
>
>
>
> Thanks for reading.
>
>
>
> Sincere greetings,
>
> Zhengzhi
>
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