<div dir="ltr">I wasn't setting up a root file as an output...Thanks for letting me know now I guess that solves everything.<div><br></div><div style>Carlos</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Wed, Mar 13, 2013 at 1:54 PM, Jonathan Moody <span dir="ltr"><<a href="mailto:jbm139@gmail.com" target="_blank">jbm139@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Carlos,<br>
<br>
From the Gate source code it looks like setting
"recordSeptalPenetration" to true should create new branches
called "septalNb" in the Hit and Singles tree of the output root
file. It does not look like this septal data is available with
any other type of output. You don't see the "septalNb" branches
in the root file?<br>
--<br>
Jon<div><div class="h5"><br>
<br>
<br>
On 3/13/2013 1:39 PM, Carlos Uribe wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Jon,
<div><br>
</div>
<div>Yes the collimator is attached to the phantomSD. </div>
<div><br>
</div>
<div>When I run my code with the </div>
<div><br>
</div>
<div>
<div style="font-family:arial,sans-serif;font-size:13px">
<span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/recordSeptalPenetration
true</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/setSeptalVolumeName
collimator</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:14.296875px">I don't get errors or
anything like that...the code works fine. I just don't
get any output related to septal penetration information.</span></div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Mar 13, 2013 at 7:44 AM, Jon
Moody <span dir="ltr"><<a href="mailto:jbmoody@umich.edu" target="_blank">jbmoody@umich.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>I have not used this feature. When you said you
tried it and it didn't work what happened?<br>
Was the collimator attached to the phantomSD by the
command<br>
<br>
/gate/collimator/attachPhantomSD<br>
<br>
--<br>
Jon
<div>
<div><br>
<br>
On 3/12/2013 5:52 PM, Carlos Uribe wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Thanks for the reply Jonathan..
<div><br>
</div>
<div>
<div style="font-family:arial,sans-serif;font-size:13px">Do
you know then how can I use </div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/recordSeptalPenetration
true</span></div>
<div style="font-family:arial,sans-serif;font-size:13px">
<span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/setSeptalVolumeName
collimator</span></div>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">with this
way of specifying the collimator?</span></div>
<div style="font-family:arial,sans-serif;font-size:13px">
<span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">Carlos</span></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Mar 12, 2013 at
11:18 AM, Jonathan Moody <span dir="ltr"><<a href="mailto:jbm139@gmail.com" target="_blank">jbm139@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Carlos,<br>
<br>
I think "parallelbeam" collimator
construction has not been working right
since Gate v.5.0.0, so the other option is
to use cubicArray and linear repeaters as
Giuseppe mentioned. In this case, the
septal thickness is defined implicitly in
the two repeatVectors. For hexagonal
shaped holes the second and third
components of the cubicArray repeatVector
are:<br>
<br>
Ry = hole_diameter + septal_thickness<br>
Rz = Ry * sqrt(3)<br>
<br>
where hole_diameter is defined across the
flat sides. The corresponding two
components of the linear repeatVector are:<br>
<br>
Ly = Ry / 2 <br>
Lz = Rz / 2 <br>
<br>
(the x-components of both repeatVectors
are 0). Then the cubicArray
repeatNumberY/Z determine the number of
holes in each direction divided by 2.<br>
--<br>
Jon
<div>
<div><br>
<br>
<br>
On 3/12/2013 1:16 PM, Carlos Uribe
wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Hi Giuseppe,
<div><br>
</div>
<div>Thanks for your reply...I tried
it but it still doesn't solve the
problem.</div>
<div><br>
</div>
<div>I know that I can use your
specified macro to create a
collimator step by step. However,
I do want to use the option given
in the guide using the </div>
<div><br>
</div>
<div>/gate/SPECThead/daughters/insert
parallelbeam<br>
</div>
<div><br>
</div>
<div>This has a parameter that
specifies the septal thickness</div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/colli/geometry/setSeptalThickness
0.2 cm </span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)">I
guess I will be able to track
the septal penetration using</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/recordSeptalPenetration
true</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/setSeptalVolumeName
collimator</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div><font color="#000000"><span style="line-height:14.296875px">I've
tried this using the macro
that you suggested and it
doesn't work. I assume that
you need to set the septal
thickness shown in the guide's
example. If there's another
way that someone knows to make
it work please let me know.</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px"><br>
</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px">Thanks,</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px"><br>
</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px">Carlos</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px"><br>
</span></font></div>
</div>
<div class="gmail_extra"> <br>
<br>
<div class="gmail_quote">On Tue, Mar
12, 2013 at 5:26 AM, Giuseppe
Magro <span dir="ltr"><<a href="mailto:beppe.magro@gmail.com" target="_blank">beppe.magro@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div><br>
</div>
/gate/colli/setMaterial Lead<br>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">(instead
of setMaterialName)</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">
Example (shielding as mother
volume):</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">
<div class="gmail_extra">#=====================================</div>
<div class="gmail_extra">#
Collimator</div>
<div class="gmail_extra">#=====================================</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">/gate/shielding/daughters/name
collimator</div>
<div class="gmail_extra">/gate/shielding/daughters/insert
box</div>
<div class="gmail_extra">/gate/collimator/geometry/setXLength
3. cm</div>
<div class="gmail_extra">/gate/collimator/geometry/setYLength
19. cm</div>
<div class="gmail_extra">/gate/collimator/geometry/setZLength
28. cm</div>
<div class="gmail_extra">/gate/collimator/placement/setTranslation
-2. 0. 0. cm</div>
<div class="gmail_extra">/gate/collimator/setMaterial
Lead</div>
<div class="gmail_extra">/gate/collimator/vis/setColor
red</div>
<div class="gmail_extra">
/gate/collimator/vis/forceWireframe</div>
<div class="gmail_extra">/gate/collimator/describe</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">/gate/collimator/daughters/name
hole</div>
<div class="gmail_extra">
/gate/collimator/daughters/insert
hexagone</div>
<div class="gmail_extra">/gate/hole/geometry/setHeight
3. cm</div>
<div class="gmail_extra">/gate/hole/geometry/setRadius
.15 cm</div>
<div class="gmail_extra">/gate/hole/placement/setRotationAxis
0 1 0</div>
<div class="gmail_extra">/gate/hole/placement/setRotationAngle
90 deg</div>
<div class="gmail_extra">/gate/hole/placement/setTranslation
0. -0.25 -0.25 cm #</div>
<div class="gmail_extra">/gate/hole/setMaterial
Air</div>
<div class="gmail_extra">
/gate/hole/describe</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">/gate/hole/repeaters/insert
cubicArray</div>
<div class="gmail_extra">/gate/hole/cubicArray/setRepeatNumberX
1</div>
<div class="gmail_extra">
/gate/hole/cubicArray/setRepeatNumberY
18 #9</div>
<div class="gmail_extra">/gate/hole/cubicArray/setRepeatNumberZ
27 #9</div>
<div class="gmail_extra">/gate/hole/cubicArray/setRepeatVector
0. 1. 1. cm</div>
<div class="gmail_extra">
/gate/hole/cubicArray/autoCenter
true #false </div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">/gate/hole/repeaters/insert
linear</div>
<div class="gmail_extra">/gate/hole/linear/setRepeatNumber
2</div>
<div class="gmail_extra">
/gate/hole/linear/setRepeatVector
0. 0.5 0.5 cm</div>
<div class="gmail_extra">/gate/hole/linear/autoCenter
false </div>
<div><br>
</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>Giuseppe M.</div>
<div>PhD Student - CNAO <br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
12 March 2013 12:00, <span dir="ltr"><<a href="mailto:gate-users-request@lists.opengatecollaboration.org" target="_blank">gate-users-request@lists.opengatecollaboration.org</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Send
Gate-users mailing list
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or, via email, send a
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<br>
When replying, please
edit your Subject line
so it is more specific<br>
than "Re: Contents of
Gate-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Parallel hole
Collimator (Carlos
Uribe)<br>
2. Re: ASCII output
(Carlos Uribe)<br>
3. Re: Process for
Photon Evaporation
(Hermann Fuchs)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 11 Mar 2013
11:31:41 -0700<br>
From: Carlos Uribe <<a href="mailto:carluri@phas.ubc.ca" target="_blank">carluri@phas.ubc.ca</a>><br>
To: "<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>"<br>
<<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: [Gate-users]
Parallel hole Collimator<br>
Message-ID:<br>
<CAPJy_1TcFTKwiEpu_Zicc=+<a href="mailto:UKYN3hfHMjvhumfzWL6AxyZ%2B1Sg@mail.gmail.com" target="_blank">UKYN3hfHMjvhumfzWL6AxyZ+1Sg@mail.gmail.com</a>><br>
Content-Type:
text/plain;
charset="iso-8859-1"<br>
<br>
Hello everyone,<br>
<br>
I'm following the user's
guide<br>
<a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Defining_a_system" target="_blank">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Defining_a_system</a><br>
trying to model a
parallel hole
collimator.<br>
<br>
The guide shows the
following example:<br>
<br>
/gate/SPECThead/daughters/name
colli<br>
<br>
#specify that the
parallel beam collimator
setup must be used<br>
/gate/SPECThead/daughters/insert
parallelbeam<br>
<br>
#set the collimator
material<br>
/gate/colli/setMaterialName
Lead<br>
<br>
#set the collimator
dimensions<br>
/gate/colli/geometry/setDimensionX
70 cm<br>
/gate/colli/geometry/setDimensionY
80 cm<br>
<br>
#set the thickness of
the collimator<br>
/gate/colli/geometry/setHeight
3 cm<br>
<br>
#specify the hole radius<br>
/gate/colli/geometry/setInnerRadius
0.5 cm<br>
<br>
#set the septal
thickness to the
required distance
between the holes<br>
/gate/colli/geometry/setSeptalThickness
0.2 cm<br>
/gate/colli/placement/alignToX<br>
/gate/colli/placement/setRotationAxis
0 0 1<br>
/gate/colli/placement/setRotationAngle
-90 deg<br>
<br>
<br>
I'm getting a problem as
follows:<br>
<br>
/opt/simulation/gate_v6.2/source/geometry/src/GateVVolume.cc
(l.179): The<br>
material of the volume
side hole 1 is not
defined.<br>
<br>
Anyone knows how to fix
this?<br>
<br>
Thanks,<br>
<br>
--<br>
Carlos F Uribe<br>
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<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 11 Mar 2013
12:40:11 -0700<br>
From: Carlos Uribe <<a href="mailto:carluri@phas.ubc.ca" target="_blank">carluri@phas.ubc.ca</a>><br>
To: samira nezhad <<a href="mailto:sn90113@gmail.com" target="_blank">sn90113@gmail.com</a>><br>
Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>"<br>
<<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: Re:
[Gate-users] ASCII
output<br>
Message-ID:<br>
<CAPJy_1QZT9uYF1VmobA3Mk2xMfS_2MRTmQfv41x=<a href="mailto:2nVvdJ2ssg@mail.gmail.com" target="_blank">2nVvdJ2ssg@mail.gmail.com</a>><br>
Content-Type:
text/plain;
charset="iso-8859-1"<br>
<br>
I had the same problem
and here is how I fixed
it<br>
<br>
In the <a href="http://GateConfiguration.h.in" target="_blank">GateConfiguration.h.in</a>
<<a href="http://gateconfiguration.h.in/" target="_blank">http://gateconfiguration.h.in/</a>>
file found<br>
within the home folder
of Gate, change this
line:<br>
<br>
<br>
#cmakedefine
GATE_USE_FILE
@GATE_USE_FILE@<br>
<br>
<br>
to this:<br>
<br>
#cmakedefine
GATE_ANALYSIS_USE_FILE
@GATE_ANALYSIS_USE_FILE@<br>
<br>
<br>
Recompile Gate and it
should now work!<br>
<br>
Cheers,<br>
<br>
Carlos<br>
<br>
<br>
On Sun, Mar 10, 2013 at
3:10 AM, samira nezhad
<<a href="mailto:sn90113@gmail.com" target="_blank">sn90113@gmail.com</a>>
wrote:<br>
<br>
> Dear all,<br>
><br>
> I need to ASCII
output but by gate6.2 i
couldn't get it .<br>
> when use this
command<br>
>
/gate/output/ascii/enable<br>
><br>
> It gives this error
message:<br>
><br>
> COMMAND NOT FOUND<br>
><br>
> I appreciate if you
guide me, thanks in
advance<br>
><br>
> Best regards,<br>
><br>
><br>
><br>
>
_______________________________________________<br>
> Gate-users mailing
list<br>
> <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
><br>
> --<br>
> Carlos F Uribe<br>
><br>
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<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 12 Mar 2013
10:11:10 +0100<br>
From: Hermann Fuchs <<a href="mailto:hermann.fuchs@meduniwien.ac.at" target="_blank">hermann.fuchs@meduniwien.ac.at</a>><br>
To: Carlos Uribe <<a href="mailto:carluri@phas.ubc.ca" target="_blank">carluri@phas.ubc.ca</a>><br>
Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>"<br>
<<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: Re:
[Gate-users] Process for
Photon Evaporation<br>
Message-ID:<br>
<<a href="mailto:1363079470.5371.3.camel@strahlen41.strahlen.meduniwien.ac.at" target="_blank">1363079470.5371.3.camel@strahlen41.strahlen.meduniwien.ac.at</a>><br>
Content-Type:
text/plain;
charset="utf-8"<br>
<br>
That is an interesting
question.<br>
<br>
Could you keep me
informed on your
findings?<br>
If it isn't already in
Gate it should be easy
to add.<br>
Just contact me and I
can help you with this
or implement it for you.<br>
<br>
Best reards,<br>
Hermann<br>
<br>
On Fri, 2013-03-08 at
12:22 -0800, Carlos
Uribe wrote:<br>
> Hello everybody,<br>
><br>
><br>
><br>
> Can anyone please
tell me which process to
add to my Physics list
in<br>
> order to see the
de-exitation of the
metastable daughter?<br>
><br>
><br>
> The parent follows
a beta-minus decay which
works great except I
don't<br>
> see the gammas
generated by the
metastable daughter.<br>
><br>
><br>
> I am using<br>
>
/gate/physics/addProcess
RadioactiveDecay<br>
><br>
><br>
> but apparently,
Geant4 handles the
meta-stable states
through the<br>
> existing
photo-evaporation code;<br>
><br>
><br>
><br>
> How do I set the
photon evaporation
process?<br>
><br>
><br>
> Thanks in advance,<br>
> --<br>
><br>
><br>
> Carlos F Uribe<br>
><br>
>
_______________________________________________<br>
> Gate-users mailing
list<br>
> <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
<br>
<br>
--<br>
-------------<br>
DI Hermann Fuchs<br>
Christian Doppler
Laboratory for Medical
Radiation Research for
Radiation Oncology<br>
Department of Radiation
Oncology<br>
Medical University
Vienna<br>
W?hringer G?rtel 18-20<br>
A-1090 Wien<br>
<br>
Tel. <a href="tel:%2B%2043%20%2F%201%20%2F%2040%20400%207271" value="+431404007271" target="_blank">+ 43 /
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Carlos F Uribe<br clear="all"><div><br></div>-- <br>Carlos F Uribe
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