Alex Vergara Gil | 4 Jun 18:17 2015
Picon

guide: using Eclipse IDE for Gate development

Dear Gaters

 I had several issues using Eclipse IDE for developing Gate, mainly
because it is a java based IDE with gtk2 UI.
  The main issue is that it fails and closes repeatedly in Kubuntu.
Solution: install gtk2-engines and in system preferences -> Look &
Feel -> gtk change gtk theme to whatever but oxygen. Problem solved!
  Another issue is that Eclipse doesn't recognize Geant4 nor Root.
Solution: go to Eclipse -> Project -> Properties and in C/C++ General
-> Paths and Symbols -> includes -> GNU C++ add the following
directories: /usr/local/include/Geant4 and /usr/include/root (choose
your Geant4 and root installation folders if these are not your case).
Problem solved! Now you can travel with F3.

I hope this helps all those enthusiast who wants to contribute to gate.
Regards
Alex

PS: I am open to assist all those who wants to use Eclipse as main IDE
for developing Gate, first rule install cdt and egit plugins.
Parisa Tahery | 4 Jun 16:18 2015
Picon

GATE 7.1 installation (Parisa)

Dear users,

Following launching the make command for GATE 7.1 installation, I encountered these errors.
Can someone help me?
 
Best regards
Parisa

/home/GATE7.1/gate_v7.1/source/digits_hits/src/GateMaterialMuHandler.cc: In member function ‘void GateMaterialMuHandler::SimulateMaterialTable()’:
/home/GATE7.1/gate_v7.1/source/digits_hits/src/GateMaterialMuHandler.cc:389:132: error: no matching function for call to ‘G4VEmProcess::SelectModelForMaterial(double&, long unsigned int&)’
/home/G4.2/G4.10.1/geant4.10.01-install/include/Geant4/G4VEmProcess.hh:468:13: note: candidate is: G4VEmModel* G4VEmProcess::SelectModelForMaterial(G4double, size_t&) const
/home/GATE7.1/gate_v7.1/source/digits_hits/src/GateMaterialMuHandler.cc:393:84: error: no matching function for call to ‘G4VEmProcess::SelectModelForMaterial(double&, long unsigned int&)’
/home/G4.2/G4.10.1/geant4.10.01-install/include/Geant4/G4VEmProcess.hh:468:13: note: candidate is: G4VEmModel* G4VEmProcess::SelectModelForMaterial(G4double, size_t&) const
/home/GATE7.1/gate_v7.1/source/digits_hits/src/GateMaterialMuHandler.cc:402:132: error: no matching function for call to ‘G4VEmProcess::SelectModelForMaterial(double&, long unsigned int&)’
/home/G4.2/G4.10.1/geant4.10.01-install/include/Geant4/G4VEmProcess.hh:468:13: note: candidate is: G4VEmModel* G4VEmProcess::SelectModelForMaterial(G4double, size_t&) const
make[2]: *** [CMakeFiles/Gate.dir/source/digits_hits/src/GateMaterialMuHandler.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Gate.dir/all] Error 2
make: *** [all] Error 2

 


<div><div>
<div>Dear users,</div>
<div><br></div>
<div>Following launching the make command for GATE 7.1 installation, I encountered these errors.</div>
<div>Can someone help me?</div>
<div dir="ltr">&nbsp; <br>
</div>
<div dir="ltr">Best regards</div>
<div dir="ltr">Parisa <br>
</div>
<div dir="ltr"><br></div>
<div dir="ltr">/home/GATE7.1/gate_v7.1/source/digits_hits/src/GateMaterialMuHandler.cc: In member function &lsquo;void GateMaterialMuHandler::SimulateMaterialTable()&rsquo;:<br class="">/home/GATE7.1/gate_v7.1/source/digits_hits/src/GateMaterialMuHandler.cc:389:132: error: no matching function for call to &lsquo;G4VEmProcess::SelectModelForMaterial(double&amp;, long unsigned int&amp;)&rsquo;<br class="">/home/G4.2/G4.10.1/geant4.10.01-install/include/Geant4/G4VEmProcess.hh:468:13: note: candidate is: G4VEmModel* G4VEmProcess::SelectModelForMaterial(G4double, size_t&amp;) const<br class="">/home/GATE7.1/gate_v7.1/source/digits_hits/src/GateMaterialMuHandler.cc:393:84: error: no matching function for call to &lsquo;G4VEmProcess::SelectModelForMaterial(double&amp;, long unsigned int&amp;)&rsquo;<br class="">/home/G4.2/G4.10.1/geant4.10.01-install/include/Geant4/G4VEmProcess.hh:468:13: note: candidate is: G4VEmModel* G4VEmProcess::SelectModelForMaterial(G4double, size_t&amp;) const<br class="">/home/GATE7.1/gate_v7.1/source/digits_hits/src/GateMaterialMuHandler.cc:402:132: error: no matching function for call to &lsquo;G4VEmProcess::SelectModelForMaterial(double&amp;, long unsigned int&amp;)&rsquo;<br class="">/home/G4.2/G4.10.1/geant4.10.01-install/include/Geant4/G4VEmProcess.hh:468:13: note: candidate is: G4VEmModel* G4VEmProcess::SelectModelForMaterial(G4double, size_t&amp;) const<br class="">make[2]: *** [CMakeFiles/Gate.dir/source/digits_hits/src/GateMaterialMuHandler.cc.o] Error 1<br class="">make[2]: *** Waiting for unfinished jobs....<br class="">make[1]: *** [CMakeFiles/Gate.dir/all] Error 2<br class="">make: *** [all] Error 2<br class=""><br class="">&nbsp;</div>
<div dir="ltr"><br></div>
<div dir="ltr"><br></div>
</div></div>
David Sarrut | 4 Jun 11:14 2015
Picon
Picon

Re: Using IAEA phase spaces


your are almost there ! Just create your own copy (fork) of Gate repository inside your github account, you will be able to push your branch onto this copy. 

Once completed, you will be able to create a pull-request from your Gate repo to the official Gate repo. 

sorry for this not so simple procedure, but is allows us to really follow what happens. 

ideally, a very simple simulation test (with a very small phase space!) could be needed to ensure everything is and remains ok. 

thanks, 
David
PS: I put gate-users in copy to inform on how to do a pull-request.

On Thu, Jun 4, 2015 at 10:58 AM, <germano.russo-EuptgrTo+aS8M3too/+dENBPR1lH4CV8@public.gmane.org> wrote:
Dear David,

I tried to do what you suggested, but I am not allowed to push my
locally-created branch in the repository, so to proceed with a
pull-request.

Here is the procedure I followed:

   git clone https://github.com/OpenGATE/Gate/

   git checkout -b fixIAEAphspSource

   vim Gate/source/general/include/GateIAEAConfig.h
   vim Gate/source/physics/src/GateSourcePhaseSpace.cc

   git commit Gate/source/general/include/GateIAEAConfig.h -m "..."
   git commit Gate/source/physics/src/GateSourcePhaseSpace.cc -m "..."

   git push origin fixIAEAphspSource

The reply to the last command was:

   Username for 'https://github.com': germanorusso
   Password for 'https://germanorusso-9UaJU3cA/F/QT0dZR+AlfA@public.gmane.org':
   remote: Permission to OpenGATE/Gate.git denied to germanorusso.
   fatal: unable to access 'https://github.com/OpenGATE/Gate/': The
requested URL returned error: 403

Since it is the first time for me to use GIT, I am probably missing
something stupid.

Thanks,
Germano




On Thu, 4 Jun 2015 07:14:28 +0200, David Sarrut
<David.Sarrut <at> creatis.insa-lyon.fr> wrote:
> Hello Germano,
>
> thank you very much for those inputs. There have been some
considerations
> about IAEA in Gate in the mailing list recently, you may want to have a
> look.
>
> Regarding your suggestions, could you please propose a pull-request via
the
> Gate repository : https://github.com/OpenGATE/Gate so that we include
the
> corrections in the next release ?
>
> Basically :
> - create a github account
> - clone from the Gate develop branch
> - commit your code modification in your branch
> - submit pull-request
>
> thanks a lot !
> David
>
>
> On Wed, Jun 3, 2015 at 6:04 PM, <germano.russo-EuptgrTo+aS8M3too/+dENBPR1lH4CV8@public.gmane.org>
wrote:
>
>> Dear all,
>>
>> I recently tried to use as source an IAEA phase space, specifically the
>> one named "VarianClinaciX_6MV_20x20_aboveMLC_w1.IAEAphsp" (downloadable
>> from https://www-nds.iaea.org/phsp/photon1/), via the
>> "/gate/source/[Source
>> name]/addPhaseSpaceFile" macro command.
>>
>> The simulation (Gate 7.0) run smoothly, however I got meaningless
>> results.
>> Digging into the related Gate source code, I believe I found a few bugs
>> which I report to you asking for confirmation.
>>
>>    1) In the function 'GateSourcePhaseSpace::OpenIAEAFile()' the call
>> 'pIAEARecordType->initialize()' is placed after
>> 'pIAEAReader->getRecordContents(pIAEARecordType)'. These two lines
shall
>> be
>> swapped, otherwise the record contents information extracted form the
>> IAEA
>> header and stored in the the object pointed by pIAEARecordType is
cleared
>> by the initialisation operation.
>>
>>    2) The "GateIAEA*" source files appear to be based on an old C++
>> implementation for handling phase spaces distributed by the IAEA. Some
>> things seem to be outdated, for instance in the "GateIAEAConfig.h" the
>> definition 'typedef long IAEA_I32' must be replaced with 'typedef int
>> IAEA_I32' in order to conform to the current "*.IAEAphsp" file format.
>>
>>    3) In the function 'GateSourcePhaseSpace::GenerateIAEAVertex()' the
>> 'pIAEARecordType->w' variable seems to be misused in the expression 'dz
>> *=
>> pIAEARecordType->w'. The 'pIAEARecordType->w' variable contains the Z
>> direction cosine of the particle, not just its sign. So it should
rather
>> be
>> 'dz = pIAEARecordType->w'. Since the 'pIAEARecordType->w' variable is
>> slightly smaller than 1, this mistake causes small errors in the
>> normalisation of the momentum (and hence of the kinetic energy).
>>
>> After having applied these correction, I was able to obtain a
reasonable
>> output dose distribution.
>> Could you please check the above and give me a feedback? Thanks!
>>
>> Kind regards,
>>
>> Germano Russo
>> R&D I-See (Internet - Simulation Evaluation Envision) company
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>




--
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
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"
_________________________________
<div>
<div dir="ltr">
<br><div>your are almost there ! Just create your own copy (fork) of Gate repository inside your github account, you will be able to push your branch onto this copy.&nbsp;</div>
<div><br></div>
<div>Once completed, you will be able to create a pull-request from your Gate repo to the official Gate repo.&nbsp;</div>
<div><br></div>
<div>sorry for this not so simple procedure, but is allows us to really follow what happens.&nbsp;</div>
<div><br></div>
<div>ideally, a very simple simulation test (with a very small phase space!) could be needed to ensure everything is and remains ok.&nbsp;</div>
<div><br></div>
<div>thanks,&nbsp;</div>
<div>David</div>
<div>PS: I put gate-users in copy to inform on how to do a pull-request.</div>
</div>
<div class="gmail_extra">
<br><div class="gmail_quote">On Thu, Jun 4, 2015 at 10:58 AM,  <span dir="ltr">&lt;<a href="mailto:germano.russo <at> i-seecomputing.com" target="_blank">germano.russo@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">Dear David,<br><br>
I tried to do what you suggested, but I am not allowed to push my<br>
locally-created branch in the repository, so to proceed with a<br>
pull-request.<br><br>
Here is the procedure I followed:<br><br>
&nbsp; &nbsp;git clone <a href="https://github.com/OpenGATE/Gate/" target="_blank">https://github.com/OpenGATE/Gate/</a><br><br>
&nbsp; &nbsp;git checkout -b fixIAEAphspSource<br><br>
&nbsp; &nbsp;vim Gate/source/general/include/GateIAEAConfig.h<br>
&nbsp; &nbsp;vim Gate/source/physics/src/GateSourcePhaseSpace.cc<br><br>
&nbsp; &nbsp;git commit Gate/source/general/include/GateIAEAConfig.h -m "..."<br>
&nbsp; &nbsp;git commit Gate/source/physics/src/GateSourcePhaseSpace.cc -m "..."<br><br>
&nbsp; &nbsp;git push origin fixIAEAphspSource<br><br>
The reply to the last command was:<br><br>
&nbsp; &nbsp;Username for '<a href="https://github.com" target="_blank">https://github.com</a>': germanorusso<br>
&nbsp; &nbsp;Password for '<a href="https://germanorusso-9UaJU3cA/F/QT0dZR+AlfA <at> public.gmane.org" target="_blank">https://germanorusso-9UaJU3cA/F/QT0dZR+AlfA <at> public.gmane.org</a>':<br>
&nbsp; &nbsp;remote: Permission to OpenGATE/Gate.git denied to germanorusso.<br>
&nbsp; &nbsp;fatal: unable to access '<a href="https://github.com/OpenGATE/Gate/" target="_blank">https://github.com/OpenGATE/Gate/</a>': The<br>
requested URL returned error: 403<br><br>
Since it is the first time for me to use GIT, I am probably missing<br>
something stupid.<br><br>
Thanks,<br>
Germano<br><div class="HOEnZb"><div class="h5">
<br><br><br><br>
On Thu, 4 Jun 2015 07:14:28 +0200, David Sarrut<br>
&lt;<a href="mailto:David.Sarrut@...">David.Sarrut <at> creatis.insa-lyon.fr</a>&gt; wrote:<br>
&gt; Hello Germano,<br>
&gt;<br>
&gt; thank you very much for those inputs. There have been some<br>
considerations<br>
&gt; about IAEA in Gate in the mailing list recently, you may want to have a<br>
&gt; look.<br>
&gt;<br>
&gt; Regarding your suggestions, could you please propose a pull-request via<br>
the<br>
&gt; Gate repository : <a href="https://github.com/OpenGATE/Gate" target="_blank">https://github.com/OpenGATE/Gate</a> so that we include<br>
the<br>
&gt; corrections in the next release ?<br>
&gt;<br>
&gt; Basically :<br>
&gt; - create a github account<br>
&gt; - clone from the Gate develop branch<br>
&gt; - commit your code modification in your branch<br>
&gt; - submit pull-request<br>
&gt;<br>
&gt; thanks a lot !<br>
&gt; David<br>
&gt;<br>
&gt;<br>
&gt; On Wed, Jun 3, 2015 at 6:04 PM, &lt;<a href="mailto:germano.russo <at> i-seecomputing.com">germano.russo@...</a>&gt;<br>
wrote:<br>
&gt;<br>
&gt;&gt; Dear all,<br>
&gt;&gt;<br>
&gt;&gt; I recently tried to use as source an IAEA phase space, specifically the<br>
&gt;&gt; one named "VarianClinaciX_6MV_20x20_aboveMLC_w1.IAEAphsp" (downloadable<br>
&gt;&gt; from <a href="https://www-nds.iaea.org/phsp/photon1/" target="_blank">https://www-nds.iaea.org/phsp/photon1/</a>), via the<br>
&gt;&gt; "/gate/source/[Source<br>
&gt;&gt; name]/addPhaseSpaceFile" macro command.<br>
&gt;&gt;<br>
&gt;&gt; The simulation (Gate 7.0) run smoothly, however I got meaningless<br>
&gt;&gt; results.<br>
&gt;&gt; Digging into the related Gate source code, I believe I found a few bugs<br>
&gt;&gt; which I report to you asking for confirmation.<br>
&gt;&gt;<br>
&gt;&gt;&nbsp; &nbsp; 1) In the function 'GateSourcePhaseSpace::OpenIAEAFile()' the call<br>
&gt;&gt; 'pIAEARecordType-&gt;initialize()' is placed after<br>
&gt;&gt; 'pIAEAReader-&gt;getRecordContents(pIAEARecordType)'. These two lines<br>
shall<br>
&gt;&gt; be<br>
&gt;&gt; swapped, otherwise the record contents information extracted form the<br>
&gt;&gt; IAEA<br>
&gt;&gt; header and stored in the the object pointed by pIAEARecordType is<br>
cleared<br>
&gt;&gt; by the initialisation operation.<br>
&gt;&gt;<br>
&gt;&gt;&nbsp; &nbsp; 2) The "GateIAEA*" source files appear to be based on an old C++<br>
&gt;&gt; implementation for handling phase spaces distributed by the IAEA. Some<br>
&gt;&gt; things seem to be outdated, for instance in the "GateIAEAConfig.h" the<br>
&gt;&gt; definition 'typedef long IAEA_I32' must be replaced with 'typedef int<br>
&gt;&gt; IAEA_I32' in order to conform to the current "*.IAEAphsp" file format.<br>
&gt;&gt;<br>
&gt;&gt;&nbsp; &nbsp; 3) In the function 'GateSourcePhaseSpace::GenerateIAEAVertex()' the<br>
&gt;&gt; 'pIAEARecordType-&gt;w' variable seems to be misused in the expression 'dz<br>
&gt;&gt; *=<br>
&gt;&gt; pIAEARecordType-&gt;w'. The 'pIAEARecordType-&gt;w' variable contains the Z<br>
&gt;&gt; direction cosine of the particle, not just its sign. So it should<br>
rather<br>
&gt;&gt; be<br>
&gt;&gt; 'dz = pIAEARecordType-&gt;w'. Since the 'pIAEARecordType-&gt;w' variable is<br>
&gt;&gt; slightly smaller than 1, this mistake causes small errors in the<br>
&gt;&gt; normalisation of the momentum (and hence of the kinetic energy).<br>
&gt;&gt;<br>
&gt;&gt; After having applied these correction, I was able to obtain a<br>
reasonable<br>
&gt;&gt; output dose distribution.<br>
&gt;&gt; Could you please check the above and give me a feedback? Thanks!<br>
&gt;&gt;<br>
&gt;&gt; Kind regards,<br>
&gt;&gt;<br>
&gt;&gt; Germano Russo<br>
&gt;&gt; R&amp;D I-See (Internet - Simulation Evaluation Envision) company<br>
&gt;&gt; _______________________________________________<br>
&gt;&gt; Gate-users mailing list<br>
&gt;&gt; <a href="mailto:Gate-users@...">Gate-users@...</a><br>
&gt;&gt; <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
&gt;&gt;<br><br>
</div></div>
</blockquote>
</div>
<br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U 1044<div>Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>28 rue La&euml;nnec, 69373 Lyon cedex 08<br>Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>_________________________________</div>
<div>&nbsp;"2 + 2 = 5,&nbsp; for extremely large values of 2"<br>_________________________________</div>
</div></div>
</div>
</div>
germano.russo | 3 Jun 18:04 2015

Using IAEA phase spaces

Dear all,

I recently tried to use as source an IAEA phase space, specifically the
one named "VarianClinaciX_6MV_20x20_aboveMLC_w1.IAEAphsp" (downloadable
from https://www-nds.iaea.org/phsp/photon1/), via the "/gate/source/[Source
name]/addPhaseSpaceFile" macro command.

The simulation (Gate 7.0) run smoothly, however I got meaningless results.
Digging into the related Gate source code, I believe I found a few bugs
which I report to you asking for confirmation.

   1) In the function 'GateSourcePhaseSpace::OpenIAEAFile()' the call
'pIAEARecordType->initialize()' is placed after
'pIAEAReader->getRecordContents(pIAEARecordType)'. These two lines shall be
swapped, otherwise the record contents information extracted form the IAEA
header and stored in the the object pointed by pIAEARecordType is cleared
by the initialisation operation.

   2) The "GateIAEA*" source files appear to be based on an old C++
implementation for handling phase spaces distributed by the IAEA. Some
things seem to be outdated, for instance in the "GateIAEAConfig.h" the
definition 'typedef long IAEA_I32' must be replaced with 'typedef int
IAEA_I32' in order to conform to the current "*.IAEAphsp" file format.

   3) In the function 'GateSourcePhaseSpace::GenerateIAEAVertex()' the
'pIAEARecordType->w' variable seems to be misused in the expression 'dz *=
pIAEARecordType->w'. The 'pIAEARecordType->w' variable contains the Z
direction cosine of the particle, not just its sign. So it should rather be
'dz = pIAEARecordType->w'. Since the 'pIAEARecordType->w' variable is
slightly smaller than 1, this mistake causes small errors in the
normalisation of the momentum (and hence of the kinetic energy).

After having applied these correction, I was able to obtain a reasonable
output dose distribution.
Could you please check the above and give me a feedback? Thanks!

Kind regards,

Germano Russo
R&D I-See (Internet - Simulation Evaluation Envision) company
Marc Chamberland | 3 Jun 17:46 2015
Picon
Picon

Re: system choice for energy centroid

I had a quick look at the source code and can’t see anything obvious. However, it was recently re-written,
so there might still be bugs in it. From my limited experience and knowledge, I’d stick with the
cylindrical PET system for now. Also, can you post what you get when you do:

/gate/systems/cylindricalPET/describe

after you’ve defined your entire system? No idea if it’ll be of any help, but when I run into bugs like
this, I throw everything at the wall and see what sticks, so to speak. 

Marc



> On Jun 3, 2015, at 11:14, Devin VanElburg <vanelbud <at> tbh.net> wrote:
> 
> Thanks for your input Marc!
> 
> I'm not particularly comfortable with C++, so I don't want to be poking around at the code. There must be
something I'm missing. I'll keep plugging away, and hopefully I find out what's causing my issue.
> 
> Devin Van Elburg
> 
> ------------------------
> Physics w/ c/ Biomedical Physics
> Lakehead University
> 
> 
> >>> Marc Chamberland 06/03/15 10:16 AM >>>
> Thanks, Devin. That’s much more clear.
> 
> I’ve never used anything but the default policy. However at first sight, it looks like you’re doing
everything right. Maybe someone with more experience can chime in, but it’s also possible this is a bug.
If you’re comfortable with C++, I’d suggest you take a quick look at the area of the code where the error
message is produced and see if anything jumps at you.
> 
> Marc
> 
> 
>> On Jun 3, 2015, at 10:04, Devin VanElburg <vanelbud <at> tbh.net> wrote:
>> 
>> Hello Marc, 
>> 
>> I'll try and explain a little better what I'm trying to do. I have defined my system as a PETscanner and
attached the daughter volumes as follows:
>> 
>> /gate/systems/PETscanner/level1/attach headblock
>> /gate/systems/PETscanner/level2/attach crystalboard
>> /gate/systems/PETscanner/level3/attach crystal
>> /gate/systems/PETscanner/layer0/attach lyso
>> /gate/lyso/attachCrystalSD
>> 
>> where 'crystal' is repeated as a cubicArray (24x24) and 'headblock' is repeated twice with a ring
repeater. I now have two opposing lyso crystals with the attached CrystalSD. When using the default
readout policy:
>> 
>> /gate/digitizer/Singles/readout/setPolicy TakeEnergyWinner
>> 
>> My simulation runs fine, and the root output I receive is expected (511keV peak as I am using a Na-22 source
for positron annihilation) for both Singles and Coincidences. However, when I try:
>> 
>> /gate/digitizer/Singles/readout/setPolicy TakeEnergyCentroid
>> 
>> I get a break with the following message:
>> 
>> [systems/PETscanner::FindComponent]:
>>     Could not find the request system component 'crystal'!
>> 
>> -------- EEEE ------- G4Exception-START -------- EEEE -------
>> *** G4Exception : ProcessPulseList
>>       issued by : GateReadout::ProcessPulseList
>> Failed to get the array component corresponding to the crystal. Abort.
>> 
>> *** Fatal Exception *** core dump ***
>> -------- EEEE -------- G4Exception-END --------- EEEE -------
>> 
>> 
>> *** G4Exception: Aborting execution ***
>> Aborted (core dumped)
>> 
>> 
>> What I take from this is that I need to use a system that I can attach a volume to a so-called 'crystal' level.
I've been playing with cylindricalPET and redefined my system as follows:
>> 
>> /gate/systems/cylindricalPET/rsector/attach headblock
>> /gate/systems/cylindricalPET/module/attach crystalboard
>> /gate/systems/cylindricalPET/crystal/attach crystal
>> /gate/systems/cylindricalPET/layer0/attach lyso
>> /gate/lyso/attachCrystalSD
>> 
>> that way, I have attached my 'crystal' volume to a 'crystal' level in the system hierarchy as I assume the
error message suggested. Even still, I get the break segmentation violation. I also get the same error
when switching to TakeEnergyCentroid for the cylindricalPET example that GATE supplies. The wiki says
to ensure the Depth is taken just above the crystal, which I did. In fact I tried running it with the depth at
all levels and they all failed. I'm at a loss, I can't seem to get the TakeEnergyCentroid policy to work
despite my best efforts!
>> 
>> By the way, ignore my comment with my previous email concerning the number of plates with a ring repeater.
That was a readout depth issue and it's working now.
>> 
>> I'd appreciate any help I can get here!
>> 
>> Regards,
>> Devin Van Elburg
>> 
>> ------------------------
>> Physics w/ c/ Biomedical Physics
>> Lakehead University
>> 
>> 
>> 
>> 
>> >>> Marc Chamberland 06/02/15 5:00 PM >>>
>> Hi Devin,
>> 
>> I’m not sure I understand what you’re trying to do and what failed to work. Can you provide more details?
>> 
>> Also, did you attach a crystalSD to your plates, as outlined here: http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.1:Attaching_the_sensitive_detectors#The_crystalSD

>> 
>> Cheers,
>> Marc
>> 
>> 
>> 
>> __________________________
>> 
>> Marc Chamberland, PhD
>> Department of Physics
>> Carleton University
>> Ottawa (ON)
>> 
>>> On Jun 2, 2015, at 16:49, Devin VanElburg <vanelbud <at> tbh.net> wrote:
>>> 
>>> Hello gate users,
>>> 
>>> I am simulating a PET system with two plates. I would like to use the takeEnergyCentroid option for the
digitizer's readout. However, I need to attach a volume to a 'crystal' of a system (according to the error
message I keep getting). Thus a PETscanner system cannot work since it uses level1-4 and layers for system
attachment. The I tried a cylindricalPET system with a ring repeater of 2, and that also didn't work.
Interestingly, cylindricalPET works for a 4+ plate ring system, but no singles or coincidences in the
output for 2-3 plates (with only the ring repeat number changed). Can anyone offer any insight as to what I
should do?
>>> 
>>> Regards,
>>> Devin Van Elburg
>>> 
>>> ------------------------
>>> Physics w/ c/ Biomedical Physics
>>> Lakehead University
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users <at> lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

>> 
> 

_______________________________________________
Gate-users mailing list
Gate-users <at> lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
David Larsson | 3 Jun 11:31 2015
Picon
Picon

Bin_GATE matching mac-files

Dear Gaters,

I'm trying to convert generated (PET)-root files to STIR compatible projection data, so I've looked into the provided 'Bin_GATE_v1.0.c'-script.

In order to understand the basics of it I'm though wondering if there is a matching .mac-file (or set of .mac-files) from which the input root-file has been generated. The reason I'm asking is that I'm simply trying to connect some of the input parameters (resectors, no. of sinogram bins, etc.) to a specified actual geometrical setup (in order to in a next step adapt the parameters to my specific setup). 

I've been looking around some of the example/benchmark scripts but can't seem to match any specifically to the Bin_GATE-script. Does anyone know if such exist or not?

Thanks in advance for the help.

David Larsson
PhD Student – Medical Engineering and Imaging
<div>
<div>
<div><span lang="sv">
<div><span>Dear Gaters,<br><br>
I'm trying to convert generated (PET)-root files to STIR compatible projection data, so I've looked into the provided 'Bin_GATE_v1.0.c'-script.<br><br>
In order to understand the basics of it I'm though wondering if there is a matching .mac-file (or set of .mac-files) from which the input root-file has been generated. The reason I'm asking is that I'm simply trying to connect some of the input parameters (resectors,
 no. of sinogram bins, etc.) to a specified actual geometrical setup (in order to in a next step adapt the parameters to my specific setup).&nbsp;<br><br>
I've been looking around some of the example/benchmark scripts but can't seem to match any specifically to the Bin_GATE-script. Does anyone know if such exist or not?<br><br>
Thanks in advance for the help.<br><br>
David Larsson</span></div>
<div><span><span>PhD Student &ndash; Me</span><span lang="en-US">dical Engineering and Imaging</span></span></div>
</span></div>
</div>
</div>
Devin VanElburg | 2 Jun 22:49 2015
Picon

system choice for energy centroid

Hello gate users,

I am simulating a PET system with two plates. I would like to use the takeEnergyCentroid option for the digitizer's readout. However, I need to attach a volume to a 'crystal' of a system (according to the error message I keep getting). Thus a PETscanner system cannot work since it uses level1-4 and layers for system attachment. The I tried a cylindricalPET system with a ring repeater of 2, and that also didn't work. Interestingly, cylindricalPET works for a 4+ plate ring system, but no singles or coincidences in the output for 2-3 plates (with only the ring repeat number changed). Can anyone offer any insight as to what I should do?

Regards,
Devin Van Elburg

------------------------
Physics w/ c/ Biomedical Physics
Lakehead University
<div>Hello gate users,<br><br>I am simulating a PET system with two plates. I would like to use the takeEnergyCentroid option for the digitizer's readout. However, I need to attach a volume to a 'crystal' of a system (according to the error message I keep getting). Thus a PETscanner system cannot work since it uses level1-4 and layers for system attachment. The I tried a cylindricalPET system with a ring repeater of 2, and that also didn't work. Interestingly, cylindricalPET works for a 4+ plate ring system, but no singles or coincidences in the output for 2-3 plates (with only the ring repeat number changed). Can anyone offer any insight as to what I should do?<br><br>Regards,<br>Devin Van Elburg<br><br>------------------------<br>Physics w/ c/ Biomedical Physics<br>Lakehead University<br>
</div>
David Mills | 2 Jun 16:46 2015
Picon

Spectrum calculations in vGate?

Hello,

I’m trying to get started with Gate using the latest vGate virtual machine.

My aim is to simulate the detected spectrum of a polychromatic X-Ray beam after passing it though various
materials. All of the examples seem rather more complex than this, is there a simple linear 
Source -> Sample -> Detector
example anywhere that I can build upon to get started?

I’m happy to start with either a spectrum generated from Speckcal or simulating an impact X-Ray source.

Regards,
David
--
Dr. David Mills
Queen Mary, University of London
Dental Biophysics Section 
Oral Growth and Development
Institute of Dentistry
Francis Bancroft Building 
London E1 4NS
UK

020 7882 5978
07904 121783
skype : webshed

Débora Salvado | 1 Jun 15:59 2015
Picon

Activity distribution in volume sources

Dear all,

In a volume source, for example, a cylinder phantom, if you set the activity to 5MBq, does it mean the total activity inside the phantom is 5MBq (ie. 5/phantomVolume MBq per mm) or is it the activity at any point in the phantom? I assume it's the first case, but can anyone confirm this to me please?

Regards,
Débora


Debora Salvado, MSc
PhD Student
University College London
INM, UCLH,
(T-5) 235 Euston Road
London NW1 2BU
UK
<div><div dir="ltr">
<div>
<div>
<div>Dear all,<br><br>
</div>In a volume source, for example, a cylinder phantom, if you set the activity to 5MBq, does it mean the total activity inside the phantom is 5MBq (ie. 5/phantomVolume MBq per mm) or is it the activity at any point in the phantom? I assume it's the first case, but can anyone confirm this to me please?<br><br>
</div>Regards,<br>
</div>D&eacute;bora<br><br><br clear="all"><div><div><div><div>
<div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>
<span></span><span><span></span><span>Debora Salvado, MSc</span></span><br><div><span><span>PhD Student<br></span></span></div>
<span><span>University College London<br>INM, UCLH, </span></span><span><span><span><span><span> (T-5) </span></span></span>235 Euston Road<br></span></span><span><span>London NW1 2BU<br></span></span><span><span>UK</span></span><span><span></span></span><br>
</div></div></div></div></div></div>
</div></div></div></div>
</div></div>
Pedro Correia | 1 Jun 11:57 2015
Picon

Simulate energy spectrum of 22Na source measured with LYSO

Dear Gaters

I’m trying to simulate the energy spectrum of a 22Na radiation source measured by a LYSO scintillator. 


The typical approach should be the use of the digitizer, with all the parameters of the LYSO defined in the
Materials.xml, wright?
However, for my application I want to evaluate the optical losses of my system, that uses a dual ended
readout system for each LYSO scintillator, i.e. a PMT reads each polished end of the LYSO, while the other
four lateral surfaces are teflon wrapped. 

I’ve tried to use the optical photons produced by each interaction inside the LYSO, with an yield of
~28000 photons/MeV:
	- At the two ends, I defined two perfect_apd surfaces, in which all the incident photons are detected
	- Until now, I’ve considered 100% efficiency in the photon detection
	
After the simulation, I used the opticaladder module of the digitizer in each of the two PMTs. I finally get
two energy spectrums histograms in my Root file (each for each PMT detector). I sum the two spectruns, in
coincidence, so I was expecting to observe the 22Na source after that, but nothing similar to that appears
in the spectrum.

Can someone tell me if this approach is possible (obtain the source spectrum simulating the optical
photons detections)? In affirmative case, the problem should be in my code. Otherwise I need to try a
different thing. 


Best regards, 

Pedro Correia, PhD student, 
University of Aveiro, Portugal
_______________________________________________
Gate-users mailing list
Gate-users <at> lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
David Sarrut | 1 Jun 11:07 2015
Picon
Picon

Re: Issues on voxelized dose calculations for a phantom (using Hounsfield converter)

Hello Alex, 

pull-request #23 is now merged, thanks again. I will ask for a configuration in the dashboard to be compiled daily with cxx11 enabled. 

David

On Thu, May 28, 2015 at 3:14 PM, Alex Vergara Gil <alexvergaragil-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear David

On pull request https://github.com/OpenGATE/Gate/pull/23 I added both
the changes to make Gate c++11 compatible and the fix of the mentioned
bug.

Regards
Alex

2015-05-28 8:13 GMT-04:00, Alex Vergara Gil <alexvergaragil-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>:
> Dear David
>
> There is another things, code 'elegancy' lead to some specific
> enhances that must be taken in consideration:
>
> 1. Indentation: helps to read better the code so bugs and unnecessary
> sentences raise from all their hidden places, specially when you make
> automatic indentation.
> 2. changing from i++ to ++i as I explain leads to optimization of code
> since it avoid a whole extra step at each call.
> 3. Using std::vector functionalities lead to code enhancement since it
> use a really optimized method for travel among lists.
> 4. Using structured vectors is a security enhancement since you can no
> longer create vector from different sizes, avoiding to not initialize
> some of them and the corresponding segmentation fault when calling.
>
> I know there are a bunch of changes, but I can run all my macros with
> them, decreasing a little the memory consumption, increasing a little
> the histories per second and finally when I look now at the code it
> seems made in modern times ;)
>
> Regards
> Alex
>
> 2015-05-28 7:24 GMT-04:00, Alex Vergara Gil <alexvergaragil-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>:
>> Hello David
>>
>> As I said on github, you can create a testing branch so I can still
>> contribute with great amount of changes and user can test them and
>> report bugs, this will not affect Gate at all and we all be happy ;)
>>
>> Regards
>> Alex
>>
>> 2015-05-28 2:11 GMT-04:00, David Sarrut
>> <David.Sarrut-0ZXfWqjJkvJNgumx+FIHDcc1ZZbpBbUC@public.gmane.org>:
>>> Hello Alex,
>>>
>>> as said on github (see https://github.com/OpenGATE/Gate/issues/22),
>>> could
>>> you please provide a separate pull-request for this issue, *without*
>>> replacement of std::vector -> please keep it simple. Even if the code is
>>> not so good, I acknowledge that ;) refrain to changing it to be more
>>> 'elegant' as it could lead to unexpected issues.
>>>
>>> dont get me wrong, I really appreciate your contribution, but we need to
>>> ensure to not break something ...
>>>
>>> thanks,
>>> David
>>>
>>> On Tue, May 26, 2015 at 2:02 PM, Alex Vergara Gil
>>> <alexvergaragil <at> gmail.com>
>>> wrote:
>>>
>>>> Dear David
>>>>
>>>> Indeed, doing that replace solved the bug, not only for range
>>>> translator but also for hounsfield translator, in my pull request are
>>>> the necessary changes with a bunch of code enhacements (basically a
>>>> lot of replacements to use std::vector functionalities).
>>>>
>>>> Look now at one of my results on a phantom compared with FLUKA.
>>>>
>>>> Regards
>>>> Alex
>>>>
>>>> 2015-05-26 3:32 GMT-04:00, David Sarrut
>>>> <David.Sarrut-0ZXfWqjJkvJNgumx+FIHDcc1ZZbpBbUC@public.gmane.org
>>>> >:
>>>> > Hello Alex,
>>>> >
>>>> > I looked at your coments on the range translator and indeed, there is
>>>> > a
>>>> > bug. Could you please test if replacing the line
>>>> > if(r2> pImage->GetOutsideValue()+1){
>>>> > with
>>>> > if(r2>= pImage->GetOutsideValue()+1){
>>>> >
>>>> > solve the issue ?
>>>> >
>>>> > Thanks you indeed to propose me to be coauthor of the paper, but I
>>>> > really
>>>> > did nothing to this work, so I cannot accept, this is not fair ;)
>>>> >
>>>> > I am however interested to read the draft if possible.
>>>> >
>>>> > As journal, I can suggest maybe : http://jnm.snmjournals.org or
>>>> > http://www.springer.com/medicine/nuclear+medicine/journal/259
>>>> >
>>>> > David
>>>> >
>>>> >
>>>> >
>>>> > On Thu, May 21, 2015 at 1:34 PM, Alex Vergara Gil
>>>> > <alexvergaragil-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
>>>> > wrote:
>>>> >
>>>> >> Dear David
>>>> >>
>>>> >> I think I have solved the bug, I ran several tests and I think
>>>> >> results
>>>> >> are fine now for both range and hounsfield translators.
>>>> >>
>>>> >> Next days I will be writing my results. If you want I will send you
>>>> >> the draft I will prepare so you can coauthor the paper, is there a
>>>> >> magazine you may recommended?
>>>> >>
>>>> >> Suggested title: "Using Gate for Molecular Radiotherapy Dosimetry on
>>>> >> clinical environments"
>>>> >>
>>>> >> Regards
>>>> >> Alex
>>>> >>
>>>> >> 2015-05-20 1:12 GMT-04:00, David Sarrut
>>>> >> <David.Sarrut-0ZXfWqjJkvJNgumx+FIHDcc1ZZbpBbUC@public.gmane.org
>>>> >> >:
>>>> >> > Hello Alex,
>>>> >> >
>>>> >> > I will study this issue probably next week,
>>>> >> >
>>>> >> > thanks again for reporting,
>>>> >> > David
>>>> >> >
>>>> >> > On Tue, May 19, 2015 at 10:49 PM, Alex Vergara Gil
>>>> >> > <alexvergaragil-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
>>>> >> >> wrote:
>>>> >> >
>>>> >> >> Dear David
>>>> >> >>
>>>> >> >> I have modified my macros and now I have a good patient dose
>>>> >> >> image,
>>>> so
>>>> >> >> I think Hounsfield Translator is free of bugs, I will try to put
>>>> >> >> Air
>>>> >> >> as first segmentation material to see whats happens, but in the
>>>> >> >> way
>>>> >> >> I
>>>> >> >> am seeing this Hounsfield is far better approach for the problem.
>>>> >> >>
>>>> >> >> I will update my templates to achieve this macro and when is
>>>> >> >> ready
>>>> >> >> I
>>>> >> >> will publish my results.
>>>> >> >> On issue #18 I put all my progress, This image was obtained with
>>>> >> >> geant4 10.1.1 + gate with all modifications of pull request #21
>>>> >> >> applied.
>>>> >> >>
>>>> >> >> Regards
>>>> >> >> Alex
>>>> >> >>
>>>> >> >> 2015-05-19 14:29 GMT-04:00, Alex Vergara Gil <
>>>> alexvergaragil <at> gmail.com
>>>> >> >:
>>>> >> >> > Dear David
>>>> >> >> >
>>>> >> >> > I am trying to move my workflow to Hounsfield converter, since
>>>> >> >> > I
>>>> can
>>>> >> >> > get the range translator to work properly (In Patient Phantom 2
>>>> >> >> > you
>>>> >> >> > may see that a material - Muscle - is taken as air). Up to now
>>>> >> >> > I
>>>> >> >> > have
>>>> >> >> > successfully ran a voxelized physical phantom as you may see in
>>>> >> >> > the
>>>> >> >> > image (cylinder phantom 1), but when using a patient phantom
>>>> >> >> > thing
>>>> >> >> > goes really odd! Somehow geometry are no longer rendered
>>>> >> >> > correctly
>>>> >> >> > (patient phantom 1). I am trying to check what is wrong with
>>>> >> >> > the
>>>> >> >> > images but I see no errors, even the density map I export from
>>>> >> >> > gate
>>>> >> >> > is
>>>> >> >> > fine (patient density phantom 1). I also see no relative
>>>> differences
>>>> >> >> > between the cylinder and patient macros, except for the image
>>>> >> >> > properties.
>>>> >> >> >
>>>> >> >> > Regards
>>>> >> >> > Alex
>>>> >> >> >
>>>> >> >>
>>>> >> >
>>>> >> >
>>>> >> >
>>>> >> > --
>>>> >> > David Sarrut, Phd
>>>> >> > Directeur de recherche CNRS
>>>> >> > CREATIS, UMR CNRS 5220, Inserm U 1044
>>>> >> > 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"
>>>> >> > _________________________________
>>>> >> >
>>>> >>
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > David Sarrut, Phd
>>>> > Directeur de recherche CNRS
>>>> > CREATIS, UMR CNRS 5220, Inserm U 1044
>>>> > 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"
>>>> > _________________________________
>>>> >
>>>>
>>>
>>>
>>>
>>> --
>>> David Sarrut, Phd
>>> Directeur de recherche CNRS
>>> CREATIS, UMR CNRS 5220, Inserm U 1044
>>> 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"
>>> _________________________________
>>>
>>
>



--
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
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"
_________________________________
<div><div dir="ltr">Hello Alex,&nbsp;<div><br></div>
<div>pull-request #23 is now merged, thanks again. I will ask for a configuration in the <a href="http://my.cdash.org/index.php?project=GATE">dashboard</a> to be compiled daily with cxx11 enabled.&nbsp;</div>
<div><br></div>
<div>David</div>
<div class="gmail_extra">
<br><div class="gmail_quote">On Thu, May 28, 2015 at 3:14 PM, Alex Vergara Gil <span dir="ltr">&lt;<a href="mailto:alexvergaragil@..." target="_blank">alexvergaragil@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">Dear David<br><br>
On pull request <a href="https://github.com/OpenGATE/Gate/pull/23" target="_blank">https://github.com/OpenGATE/Gate/pull/23</a> I added both<br>
the changes to make Gate c++11 compatible and the fix of the mentioned<br>
bug.<br><br>
Regards<br><span class="HOEnZb">Alex<br></span><div class="HOEnZb"><div class="h5">
<br>
2015-05-28 8:13 GMT-04:00, Alex Vergara Gil &lt;<a href="mailto:alexvergaragil@...">alexvergaragil@...</a>&gt;:<br>
&gt; Dear David<br>
&gt;<br>
&gt; There is another things, code 'elegancy' lead to some specific<br>
&gt; enhances that must be taken in consideration:<br>
&gt;<br>
&gt; 1. Indentation: helps to read better the code so bugs and unnecessary<br>
&gt; sentences raise from all their hidden places, specially when you make<br>
&gt; automatic indentation.<br>
&gt; 2. changing from i++ to ++i as I explain leads to optimization of code<br>
&gt; since it avoid a whole extra step at each call.<br>
&gt; 3. Using std::vector functionalities lead to code enhancement since it<br>
&gt; use a really optimized method for travel among lists.<br>
&gt; 4. Using structured vectors is a security enhancement since you can no<br>
&gt; longer create vector from different sizes, avoiding to not initialize<br>
&gt; some of them and the corresponding segmentation fault when calling.<br>
&gt;<br>
&gt; I know there are a bunch of changes, but I can run all my macros with<br>
&gt; them, decreasing a little the memory consumption, increasing a little<br>
&gt; the histories per second and finally when I look now at the code it<br>
&gt; seems made in modern times ;)<br>
&gt;<br>
&gt; Regards<br>
&gt; Alex<br>
&gt;<br>
&gt; 2015-05-28 7:24 GMT-04:00, Alex Vergara Gil &lt;<a href="mailto:alexvergaragil@...">alexvergaragil@...</a>&gt;:<br>
&gt;&gt; Hello David<br>
&gt;&gt;<br>
&gt;&gt; As I said on github, you can create a testing branch so I can still<br>
&gt;&gt; contribute with great amount of changes and user can test them and<br>
&gt;&gt; report bugs, this will not affect Gate at all and we all be happy ;)<br>
&gt;&gt;<br>
&gt;&gt; Regards<br>
&gt;&gt; Alex<br>
&gt;&gt;<br>
&gt;&gt; 2015-05-28 2:11 GMT-04:00, David Sarrut<br>
&gt;&gt; &lt;<a href="mailto:David.Sarrut@...">David.Sarrut@...</a>&gt;:<br>
&gt;&gt;&gt; Hello Alex,<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; as said on github (see <a href="https://github.com/OpenGATE/Gate/issues/22" target="_blank">https://github.com/OpenGATE/Gate/issues/22</a>),<br>
&gt;&gt;&gt; could<br>
&gt;&gt;&gt; you please provide a separate pull-request for this issue, *without*≤br>
&gt;&gt;&gt; replacement of std::vector -&gt; please keep it simple. Even if the code is<br>
&gt;&gt;&gt; not so good, I acknowledge that ;) refrain to changing it to be more<br>
&gt;&gt;&gt; 'elegant' as it could lead to unexpected issues.<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; dont get me wrong, I really appreciate your contribution, but we need to<br>
&gt;&gt;&gt; ensure to not break something ...<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; thanks,<br>
&gt;&gt;&gt; David<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; On Tue, May 26, 2015 at 2:02 PM, Alex Vergara Gil<br>
&gt;&gt;&gt; &lt;<a href="mailto:alexvergaragil@...">alexvergaragil <at> gmail.com</a>&gt;<br>
&gt;&gt;&gt; wrote:<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt;&gt; Dear David<br>
&gt;&gt;&gt;&gt;<br>
&gt;&gt;&gt;&gt; Indeed, doing that replace solved the bug, not only for range<br>
&gt;&gt;&gt;&gt; translator but also for hounsfield translator, in my pull request are<br>
&gt;&gt;&gt;&gt; the necessary changes with a bunch of code enhacements (basically a<br>
&gt;&gt;&gt;&gt; lot of replacements to use std::vector functionalities).<br>
&gt;&gt;&gt;&gt;<br>
&gt;&gt;&gt;&gt; Look now at one of my results on a phantom compared with FLUKA.<br>
&gt;&gt;&gt;&gt;<br>
&gt;&gt;&gt;&gt; Regards<br>
&gt;&gt;&gt;&gt; Alex<br>
&gt;&gt;&gt;&gt;<br>
&gt;&gt;&gt;&gt; 2015-05-26 3:32 GMT-04:00, David Sarrut<br>
&gt;&gt;&gt;&gt; &lt;<a href="mailto:David.Sarrut@...">David.Sarrut@...</a><br>
&gt;&gt;&gt;&gt; &gt;:<br>
&gt;&gt;&gt;&gt; &gt; Hello Alex,<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt; I looked at your coments on the range translator and indeed, there is<br>
&gt;&gt;&gt;&gt; &gt; a<br>
&gt;&gt;&gt;&gt; &gt; bug. Could you please test if replacing the line<br>
&gt;&gt;&gt;&gt; &gt; if(r2&gt; pImage-&gt;GetOutsideValue()+1){<br>
&gt;&gt;&gt;&gt; &gt; with<br>
&gt;&gt;&gt;&gt; &gt; if(r2&gt;= pImage-&gt;GetOutsideValue()+1){<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt; solve the issue ?<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt; Thanks you indeed to propose me to be coauthor of the paper, but I<br>
&gt;&gt;&gt;&gt; &gt; really<br>
&gt;&gt;&gt;&gt; &gt; did nothing to this work, so I cannot accept, this is not fair ;)<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt; I am however interested to read the draft if possible.<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt; As journal, I can suggest maybe : <a href="http://jnm.snmjournals.org" target="_blank">http://jnm.snmjournals.org</a> or<br>
&gt;&gt;&gt;&gt; &gt; <a href="http://www.springer.com/medicine/nuclear+medicine/journal/259" target="_blank">http://www.springer.com/medicine/nuclear+medicine/journal/259</a><br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt; David<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt; On Thu, May 21, 2015 at 1:34 PM, Alex Vergara Gil<br>
&gt;&gt;&gt;&gt; &gt; &lt;<a href="mailto:alexvergaragil@...">alexvergaragil@...</a>&gt;<br>
&gt;&gt;&gt;&gt; &gt; wrote:<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; Dear David<br>
&gt;&gt;&gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; I think I have solved the bug, I ran several tests and I think<br>
&gt;&gt;&gt;&gt; &gt;&gt; results<br>
&gt;&gt;&gt;&gt; &gt;&gt; are fine now for both range and hounsfield translators.<br>
&gt;&gt;&gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; Next days I will be writing my results. If you want I will send you<br>
&gt;&gt;&gt;&gt; &gt;&gt; the draft I will prepare so you can coauthor the paper, is there a<br>
&gt;&gt;&gt;&gt; &gt;&gt; magazine you may recommended?<br>
&gt;&gt;&gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; Suggested title: "Using Gate for Molecular Radiotherapy Dosimetry on<br>
&gt;&gt;&gt;&gt; &gt;&gt; clinical environments"<br>
&gt;&gt;&gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; Regards<br>
&gt;&gt;&gt;&gt; &gt;&gt; Alex<br>
&gt;&gt;&gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; 2015-05-20 1:12 GMT-04:00, David Sarrut<br>
&gt;&gt;&gt;&gt; &gt;&gt; &lt;<a href="mailto:David.Sarrut@...yon.fr">David.Sarrut@...</a><br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;:<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; Hello Alex,<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; I will study this issue probably next week,<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; thanks again for reporting,<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; David<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; On Tue, May 19, 2015 at 10:49 PM, Alex Vergara Gil<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; &lt;<a href="mailto:alexvergaragil <at> gmail.com">alexvergaragil@...</a><br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; wrote:<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; Dear David<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; I have modified my macros and now I have a good patient dose<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; image,<br>
&gt;&gt;&gt;&gt; so<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; I think Hounsfield Translator is free of bugs, I will try to put<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; Air<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; as first segmentation material to see whats happens, but in the<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; way<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; I<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; am seeing this Hounsfield is far better approach for the problem.<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; I will update my templates to achieve this macro and when is<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; ready<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; I<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; will publish my results.<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; On issue #18 I put all my progress, This image was obtained with<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; geant4 10.1.1 + gate with all modifications of pull request #21<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; applied.<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; Regards<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; Alex<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; 2015-05-19 14:29 GMT-04:00, Alex Vergara Gil &lt;<br>
&gt;&gt;&gt;&gt; <a href="mailto:alexvergaragil@...">alexvergaragil <at> gmail.com</a><br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;:<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; Dear David<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; I am trying to move my workflow to Hounsfield converter, since<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; I<br>
&gt;&gt;&gt;&gt; can<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; get the range translator to work properly (In Patient Phantom 2<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; you<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; may see that a material - Muscle - is taken as air). Up to now<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; I<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; have<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; successfully ran a voxelized physical phantom as you may see in<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; the<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; image (cylinder phantom 1), but when using a patient phantom<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; thing<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; goes really odd! Somehow geometry are no longer rendered<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; correctly<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; (patient phantom 1). I am trying to check what is wrong with<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; the<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; images but I see no errors, even the density map I export from<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; gate<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; is<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; fine (patient density phantom 1). I also see no relative<br>
&gt;&gt;&gt;&gt; differences<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; between the cylinder and patient macros, except for the image<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; properties.<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; Regards<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt; Alex<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; --<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; David Sarrut, Phd<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; Directeur de recherche CNRS<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; CREATIS, UMR CNRS 5220, Inserm U 1044<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; 28 rue La&euml;nnec, 69373 Lyon cedex 08<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; Tel : <a href="tel:04%2078%2078%2051%2051" value="+33478785151">04 78 78 51 51</a> / <a href="tel:06%2074%2072%2005%2042" value="+33674720542">06 74 72 05 42</a><br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; <a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; _________________________________<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;&nbsp; "2 + 2 = 5,&nbsp; for extremely large values of 2"<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt; _________________________________<br>
&gt;&gt;&gt;&gt; &gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;&gt;<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt; &gt; --<br>
&gt;&gt;&gt;&gt; &gt; David Sarrut, Phd<br>
&gt;&gt;&gt;&gt; &gt; Directeur de recherche CNRS<br>
&gt;&gt;&gt;&gt; &gt; CREATIS, UMR CNRS 5220, Inserm U 1044<br>
&gt;&gt;&gt;&gt; &gt; Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>
&gt;&gt;&gt;&gt; &gt; 28 rue La&euml;nnec, 69373 Lyon cedex 08<br>
&gt;&gt;&gt;&gt; &gt; Tel : 04 78 78 51 51 / 06 74 72 05 42<br>
&gt;&gt;&gt;&gt; &gt; <a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>
&gt;&gt;&gt;&gt; &gt; _________________________________<br>
&gt;&gt;&gt;&gt; &gt;&nbsp; "2 + 2 = 5,&nbsp; for extremely large values of 2"<br>
&gt;&gt;&gt;&gt; &gt; _________________________________<br>
&gt;&gt;&gt;&gt; &gt;<br>
&gt;&gt;&gt;&gt;<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; --<br>
&gt;&gt;&gt; David Sarrut, Phd<br>
&gt;&gt;&gt; Directeur de recherche CNRS<br>
&gt;&gt;&gt; CREATIS, UMR CNRS 5220, Inserm U 1044<br>
&gt;&gt;&gt; Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>
&gt;&gt;&gt; 28 rue La&euml;nnec, 69373 Lyon cedex 08<br>
&gt;&gt;&gt; Tel : 04 78 78 51 51 / 06 74 72 05 42<br>
&gt;&gt;&gt; <a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>
&gt;&gt;&gt; _________________________________<br>
&gt;&gt;&gt;&nbsp; "2 + 2 = 5,&nbsp; for extremely large values of 2"<br>
&gt;&gt;&gt; _________________________________<br>
&gt;&gt;&gt;<br>
&gt;&gt;<br>
&gt;<br>
</div></div>
</blockquote>
</div>
<br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U 1044<div>Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>28 rue La&euml;nnec, 69373 Lyon cedex 08<br>Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>_________________________________</div>
<div>&nbsp;"2 + 2 = 5,&nbsp; for extremely large values of 2"<br>_________________________________</div>
</div></div>
</div>
</div></div>

Gmane