[Gate-users] Towards Gate 9.0 (Report of GATEv8.2 bugs)

[Zhengzhi Liu]

Dear David,

Can I share some problems I have with Gate 8, which may be caused by bugs?
I believe I am not the only GATE user who came across these issues.

Problem 1: * Coincident sorter*
On top of the imcompatibility with genericRepeater as reported by Han Gyu,
the built in coincident sorter is problematic in realistic situations. It
works fine under ideal conditions as described in the Gate user manual
v8.0. Taking the *cylindricalPET* as example, a cylindricalPET system can
have 5 hierarchies at most, i.e., sector, module, submode, crystal, layer.
This is to build an simplistic PET system. However, in real life, the
crystal may have a wrapper, and detectors may be placed in some supporting
structure and shielding. When I insert any other geometry into the system
(for example, I added an aluminum wrapper for crystals, whether I attach it
the system or not ), the coincidence sorter would fail immediately, but
singles generation works fine.

Problem 2: *work with voxelized source and Phantom*
First, I can't get the built in example code (benchImageNavigators/pet)
work. Second, it looks like no body has ever succeeded in visualing their
voxelized source. The earliest email
<http://lists.opengatecollaboration.org/pipermail/gate-users/2010-April/004126.html>
about
voxelized source visualization can date back to *10 years* agao, could you
make an official reply to that or update it in the upcoming version?

Thank you very much for your time reading and considering the problems.
Sincerely

Zhengzhi






On Wed, Feb 19, 2020 at 7:21 AM David Sarrut <
David.Sarrut at creatis.insa-lyon.fr> wrote:

>
> excellent, thanks to both of you!
>
> On Wed, Feb 19, 2020 at 12:23 PM 강한규 <lovehangulp at naver.com> wrote:
>
>> Dear David, and Christian,
>>
>>
>>
>> Thanks for your kind response.
>>
>>
>>
>> For the bug#1: I uploaded an issue about the GATE bug with
>> cubicArray.(issue#296)
>>
>>
>>
>> For the bug#2: Christian (included in this email) will handle the
>> coincidence sorter issue wit his own pull requests (PR) on the git hub.
>>
>>
>>
>> Best regards,
>>
>>
>>
>> Han Gyu
>>
>>
>>
>> --------
>>
>> Han Gyu Kang, Ph.D, Researcher
>>
>> National Institute of Radiological Sciences (NIRS)
>> National Institutes for Quantum and Radiological Science and Technology
>> (QST)
>>  4-9-1 Anagawa, Inage-ku, Chiba 263-8555, JAPAN
>>
>>
>>
>> -----Original Message-----
>> *From:* "David Sarrut"<David.Sarrut at creatis.insa-lyon.fr>
>> *To:* "강한규"<lovehangulp at naver.com>;
>> *Cc:* "gate-users"<gate-users at lists.opengatecollaboration.org>;
>> *Sent:* 2020-02-19 (수) 17:25:22 (GMT+09:00)
>> *Subject:* Re: [Gate-users] Towards Gate 9.0 (Report of GATEv8.2 bugs)
>>
>> Hello 강한규,
>>
>> thanks very much for the very clear report!
>>
>> For bug#1: I am not expert in cubicArray repeater (I wrote the
>> genericRepeater long time ago). We should investigate, but not sure it will
>> be done for 9.0. Can you please put your email as an issue on github so
>> that we keep memory of it?
>>
>> For bug#2: sorry, I cannot remember of the patch you mention (I probably
>> forget this, my bad). Could you please provide the patch as a PR ? It will
>> be included rapidly!
>>
>> Thanks a lot, do not hesitate to ask if need help for the PR
>>
>> Thank again,
>> David
>>
>>
>>
>> On Wed, Feb 19, 2020 at 9:08 AM 강한규 <lovehangulp at naver.com> wrote:
>>
>> Dear David Sarrut,
>>
>>
>>
>> Let me share the bugs of GATEv8.2.
>>
>> I tried to simulate a *PEM (Positron emission mammography)* scanner with
>> GATEv8.2.(slide#3-8)
>>
>> For the system type, "*PETscanne*r" was used because of the non-fixed
>> geometry.
>>
>>
>>
>> *Bug#1: Check pattern with the cubicArray repeater.*
>>
>> When the back-to-back source (red) is at the center of the scanner, there
>> was no problem.
>>
>> However, as the source was placed close to the one detector side, the
>> check pattern was appeared on the detector response.(slide#10)
>>
>> This problem can be solved by using genericRepeater.(slide#11-12)
>>
>> Unfortunately, however, the coincidence sorter does not work with the
>> genericRepeater.
>>
>>
>>
>>
>>
>> *Bug#2: Coincidence sorter does not work with the genericRepeater
>> (slide#13-16)*
>>
>>          The coincidence sorter issue could be solved by using git patch
>> which was proposed by Christian Pommaranz (
>> pommranz at astro.uni-tuebingen.de).
>>
>>          After several steps of GATE macro and source code modification,
>> the PEM scanner simulation worked successfully.(slide#16)
>>
>>          However, for the beginners of GATE, it is going to hard to do it
>> by themselves.
>>
>>
>>
>>
>> Hopefully, the abovementioned bugs would be resolved in the GATEv9.0.
>>
>>
>>
>> Best regards,
>>
>>
>>
>> Han Gyu Kang, Ph.D.
>>
>>
>>
>> Imaging Physics Group, NIRS-QST, Japan.
>>
>>
>>
>> -----Original Message-----
>> *From:* "David Sarrut"<David.Sarrut at creatis.insa-lyon.fr>
>> *To:* "gate-users"<gate-users at lists.opengatecollaboration.org>;
>> *Cc:*
>> *Sent:* 2020-02-19 (수) 16:28:07 (GMT+09:00)
>> *Subject:* [Gate-users] Towards Gate 9.0
>>
>> Dear all,
>>
>> We are currently preparing the next Gate release, version 9.0, based on
>> the current Geant4 release 10.6. This version includes a bunch of novelties
>> compared to the previous 8.2 version (hence the jump in version number).
>>
>> Please, if you want to include new feature or bug correction in this
>> version, *submit your PullRequest (PR) asap*. We usually ask to have one
>> PR with source code only in the main Gate repository, another PR with one
>> example in the GateContrib repository, and some documentation changes via
>> readthedocs <https://opengate.readthedocs.io/en/latest/>. In any case,
>> do not hesitate to contact us for any help, we are happy to help !
>>
>> *For all*: please we need help to perform tests. Gate is a large beast
>> and we still do not have a proper unit test system (working on it). This is
>> simple: download and compile the branch "develop" and test it with your own
>> simulation to see if anything is fine. Please, report us is anything seems
>> strange. On our side, we have some benchmarks but they do not cover all the
>> parts of Gate. Continuous integration
>> <https://en.wikipedia.org/wiki/Continuous_integration> on github via
>> Azure is currently being implemented (thanks to Thomas!) and will be ready
>> soon.
>>
>> In advance, many many thanks to all recent contributors: Fatima, Anders,
>> Mathieu, Thomas, David, Marta, Loic, Sam, Christian, Mateuz etc ... I am
>> sure I forget people, sorry ... I will properly update the list of
>> contributors in the following weeks :)
>>
>> The ETA for the next release is early March.
>>
>> David
>>
>> --
>> 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"
>> _________________________________
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>>
>>
>> --
>> 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"
>> _________________________________
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
>
> --
> 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"
> _________________________________
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
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