[Gate-users] Gate-users Digest, Vol 173, Issue 2

Sat Oct 3 13:01:48 CEST 2020

Thx David for replying,
The error I'm getting looks a common error and has nothing to do with file output format. I'm not using a different output format. I'm only using doseActor with mhd file format.  Another thing is that if I  switch the materials around the mac works fine.!!!
For instance the mac works in only the following two cases
Case 1:Assign a material B (Air) to the worldAssign a material A ( newly defined material) to the daughter X of worldAssign a material C (newly defined material) to the daughter Y of X (mother)Assign a material A ( newly defined material) to the daughter Z of Y
case 2:Assign a material A (newly defined material) to the worldAssign a material B (Air) to the daughter X of worldAssign a material C (newly defined material) to the daughter Y of X (mother)Assign a material A to the daughter Z of Y
The mac does NOT work if Assign a material B (Air) to the worldAssign a material B ( Air ) to the daughter X of worldAssign a material C (newly defined material) to the daughter Y of X (mother)Assign a material A ( newly defined material) to the daughter Z of Y
Any help or hints is greatly appreciated
Message: 2
Date: Fri, 2 Oct 2020 14:59:14 +0000
From: David Boersma <david.boersma at acmit.at>
To: "gate-users at lists.opengatecollaboration.org"
    <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Errors in assigning materials to daughters
Message-ID: <fdc0de391b6a43ab846318b018f6e4e2 at acmit.at>
Content-Type: text/plain; charset="utf-8"

Hi Abdalmajeid,

Welcome to GATE!

The error message looks like something that has nothing to do with materials, but rather with the image format that you would like to read from or write to.

Could you send us the actual macro file that is giving you this error?

/David

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Abdalmajeid M. Alyassin, Ph.D.
Professor of Medical Physics
Physics Department
Faculty of Science
Yarmouk University
21163 Irbid, Jordan
URL:http://faculty.yu.edu.jo/alyassin
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    On Saturday, October 3, 2020, 01:22:06 PM GMT+3, gate-users-request at lists.opengatecollaboration.org <gate-users-request at lists.opengatecollaboration.org> wrote:  

 Send Gate-users mailing list submissions to
    gate-users at lists.opengatecollaboration.org

To subscribe or unsubscribe via the World Wide Web, visit
    http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
or, via email, send a message with subject or body 'help' to
    gate-users-request at lists.opengatecollaboration.org

You can reach the person managing the list at
    gate-users-owner at lists.opengatecollaboration.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Gate-users digest..."

Today's Topics:

  1. Errors in assigning materials to daughters (Abdalmajeid Alyassin)
  2. Re: Errors in assigning materials to daughters (David Boersma)
  3. Extracting energy spectra from ROOT file (Melissa Cruz)

----------------------------------------------------------------------

Message: 1
Date: Fri, 2 Oct 2020 12:53:57 +0000 (UTC)
From: Abdalmajeid Alyassin <am_alyassin at yahoo.com>
To: "gate-users at lists.opengatecollaboration.org"
    <gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] Errors in assigning materials to daughters
Message-ID: <168734706.1064466.1601643237455 at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi;
I'm a new user to vGate, ... & I have a question regarding assigning materials to daughters of new volumes:
For instance;I created a volume called box X which is a daughter of world, and assigned it a defined material from the GateMaterials.db file. I also created a daughter Y of X and assigned it a newly defined material from  the GateMaterials.db file. Then, I created a daughter Z of Y and assigned it another newly defined material in the GataMaterials.db. When I initialize the /gate/run/initialize, I get an error 
GateImageT.icc (l.75): Unknown image file extension. Supported extensions are : .vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm
the mac works fine, if Material X = Material Z but give the above error otherwise. Are there any conditions about assigning materials to volumes & daughter of volumes?
Any help is greatly appreciated?
Regards
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20201002/ccff4ee3/attachment-0001.html>

------------------------------

Message: 2
Date: Fri, 2 Oct 2020 14:59:14 +0000
From: David Boersma <david.boersma at acmit.at>
To: "gate-users at lists.opengatecollaboration.org"
    <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Errors in assigning materials to daughters
Message-ID: <fdc0de391b6a43ab846318b018f6e4e2 at acmit.at>
Content-Type: text/plain; charset="utf-8"

Hi Abdalmajeid,

Welcome to GATE!

The error message looks like something that has nothing to do with materials, but rather with the image format that you would like to read from or write to.

Could you send us the actual macro file that is giving you this error?

/David

________________________________
Von: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> im Auftrag von Abdalmajeid Alyassin <am_alyassin at yahoo.com>
Gesendet: Freitag, 2. Oktober 2020 14:53:57
An: gate-users at lists.opengatecollaboration.org
Betreff: [Gate-users] Errors in assigning materials to daughters

Hi;

I'm a new user to vGate, ... & I have a question regarding assigning materials to daughters of new volumes:

For instance;
I created a volume called box X which is a daughter of world, and assigned it a defined material from the GateMaterials.db file. I also created a daughter Y of X and assigned it a newly defined material from  the GateMaterials.db file. Then, I created a daughter Z of Y and assigned it another newly defined material in the GataMaterials.db. When I initialize the /gate/run/initialize, I get an error

GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :
.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm

the mac works fine, if Material X = Material Z but give the above error otherwise. Are there any conditions about assigning materials to volumes & daughter of volumes?

Any help is greatly appreciated?

Regards
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20201002/d352b3cd/attachment-0001.html>

------------------------------

Message: 3
Date: Sat, 3 Oct 2020 11:12:22 +0100
From: Melissa Cruz <ms.cruz at campus.fct.unl.pt>
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] Extracting energy spectra from ROOT file
Message-ID:
    <CANAstRnV8=LCgo8avLyC5WVk3LSjgdSuZJVwq0_X7yt6gtNy6w at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Gate users,

I'm running a simulation on Gatelab (my pc wouldn't run it on my lifetime),
and need to plot the number of counts vs energy that reach my detector, but
when I try to use the energySpectrum actor I always get an segmentation
violation error,

 *** Break *** segmentation violation
Error in <TUnixSystem::StackTrace> script /cvmfs/
biomed.egi.eu/vip/gate/gate_release_8.1/root/etc/gdb-backtrace.sh

Due to this, I had to disable the actor and use the usual ROOT output, but
although I've been searching through Gate and ROOT users guides and also
messages on mailing lists, I can't find information on how to perform this
analysis.

I'm not an experienced ROOT user, but my Gate macros are all written as
indicated in Gate users guide, and I can't seem to find how to extract this
data from the output file, or how to plot two different leaves against each
other (which I believe would be the total nb primaries vs energy in
singles)? It seems to me that all the information I found teaches how to
plot the spectrum obtained from the actor or how to plot 1D histogram just
from one leave.

I've spent days also looking to .C files in the Gate Contributions Folder
in vGate, and it could be that the answer to my question is really straight
foreword, but I'm getting really frustrated and my deadline is aproaching.
Could someone teach me how to do this (noone in my department can help me
neither), please?

Many thanks in advance,
Kind regards,
Sofia Cruz
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20201003/c07121ec/attachment-0001.html>

------------------------------

Subject: Digest Footer

_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

------------------------------

End of Gate-users Digest, Vol 173, Issue 2
******************************************

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20201003/402f0c49/attachment-0001.html>