Alex Vergara Gil | 13 Jan 15:26 2015
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gjs condor bug

Hello

I found a bug in the file GateMacfileParser.cc of the jobsplitter:
it expect a space between "/gate/actor/addActor DoseActor" and the
name of the macro; in
the remaining macros the TAB character is ok but not here, so there is
something wrong with the GateMacfileParser.cc of the jobsplitter

A possible solution can be

void GateMacfileParser::SearchForActors(G4int splitNumber,ofstream&
output, ofstream& splitfile)
if (macline.contains("/gate/actor/addActor"))
  {
    G4int pos = macline.find_first_of(" ");
++ if (pos<=0) pos = macline.find_first_of("\t");
    G4String tmp = macline.substr(pos+1);
    pos = tmp.find_first_of(" ");
++ if (pos<=0) pos = tmp.find_first_of("\t");
    G4String actorType = tmp.substr(0,pos);
    G4String actorName = tmp.substr(pos+1);
    listOfActorType.push_back(actorType);
    listOfActorName.push_back(actorName);
  }

but in this way it expect two spaces or two tabs, actually it may
happen there can be combined spaces and tabs so a better solution is
needed but in this way at least it handles tabs

Regards
(Continue reading)

zhangran | 12 Jan 17:53 2015
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total number of primaries in CT simulation

Dear Gate users,
   I ran into a problem with CT simulation using vgate 7.0. When I use
setTotalNumberOfPrimaries 1000
everything is fine, however, when I use
setTotalNumberOfPrimaries 100000
there is a segmentation fault. Anyone knows why?

Thanks
<div><div dir="ltr">
<div>
<div>
<div>
<div>Dear Gate users,<br>
</div>&nbsp;&nbsp; I ran into a problem with CT simulation using vgate 7.0. When I use <br>setTotalNumberOfPrimaries 1000<br>
</div>everything is fine, however, when I use<br>setTotalNumberOfPrimaries 100000<br>
</div>there is a segmentation fault. Anyone knows why? <br><br>
</div>Thanks<br>
</div></div>
Richard Lacroix | 12 Jan 17:31 2015
Picon

Re: Error compiling Gate v7.0

Thanks to John Apostolakis.
My problem was that I was using Geant4 10.01 but Gate v7.0 needs Geant4 9.6

Richard Lacroix
Analyste en informatique
_____________________
Université de Sherbrooke
Faculté de Génie
Génie Électrique et Génie Informatique
2500 Boul. Université
Sherbrooke, Qc
J1K 2R1 Canada
Tél. (819) 821-8000 ext. 62877 Fax (819) 821-7937
 Richard.Lacroix-1QfbC9zU/iChfOjOx0WucA@public.gmane.org
  www.usherbrooke.ca/gelecinfo

Le 2015-01-09 10:29, John Apostolakis a écrit :
Just a quick word, in case it is useful.

It seems that you are using an incompatible version of Geant4.

Have you checked which version(s) GATE 7.0 supports ?

John
===================================================


On 09 Jan 2015, at 14:33, Richard Lacroix <Richard.Lacroix-1QfbC9zU/iChfOjOx0WucA@public.gmane.org> wrote:

Hi all,

I'm trying to compile Gate v7.0 on Red Hat 6.6  and I get the following error


Building CXX object CMakeFiles/Gate.dir/source/physics/src/GateSourceVoxellized.cc.o
Building CXX object CMakeFiles/Gate.dir/source/physics/src/GateSourcePencilBeamMessenger.cc.o
Building CXX object CMakeFiles/Gate.dir/source/physics/src/GateNeutronInelasticPB.cc.o
/home2/lacr1801/tmp/gate_v7.0/source/physics/src/GateSingleParticleSourceMessenger.cc: In member function ‘void GateSingleParticleSourceMessenger::IonCommand(G4String)’:
/home2/lacr1801/tmp/gate_v7.0/source/physics/src/GateSingleParticleSourceMessenger.cc:1528: error: ‘class G4ParticleTable’ has no member named ‘GetIon’
make[2]: *** [CMakeFiles/Gate.dir/source/physics/src/GateSingleParticleSourceMessenger.cc.o] Error 1
make[2]: *** Attente des tâches non terminées....
make[1]: *** [CMakeFiles/Gate.dir/all] Error 2
make: *** [all] Error 2


Help please
--

Richard Lacroix
Analyste en informatique
_____________________
Université de Sherbrooke
Faculté de Génie
Génie Électrique et Génie Informatique
2500 Boul. Université
Sherbrooke, Qc
J1K 2R1 Canada
Tél. (819) 821-8000 ext. 62877 Fax (819) 821-7937
 Richard.Lacroix-1QfbC9zU/iChfOjOx0WucA@public.gmane.org
  www.usherbrooke.ca/gelecinfo

_______________________________________________
Gate-users mailing list
Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users


<div>
    <div class="moz-cite-prefix">Thanks to John Apostolakis.<br>
      My problem was that I was using Geant4 10.01 but Gate v7.0 needs
      Geant4 9.6<br><br><div class="moz-signature">
        <p>Richard
                    Lacroix<br>
                    Analyste en informatique<br>
                  _____________________<br>Universit&eacute;
                    de Sherbrooke<br>
                    Facult&eacute; de G&eacute;nie<br>
                    G&eacute;nie
                    &Eacute;lectrique et G&eacute;nie Informatique<br>2500
                    Boul. Universit&eacute;<br>
                    Sherbrooke, Qc<br>
                    J1K 2R1 Canada<br>
                    T&eacute;l.
                    (819) 821-8000 ext. 62877 Fax (819) 821-7937<br>
                    &nbsp;<a href="mailto:Richard.Lacroix <at> .USherbrooke.ca">Richard.Lacroix@...</a><br>
                  &nbsp; <a href="http://www.usherbrooke.ca/gelecinfo">www.usherbrooke.ca/gelecinfo</a><br></p>
      </div>
      Le 2015-01-09 10:29, John Apostolakis a &eacute;crit&nbsp;:<br>
</div>
    <blockquote cite="mid:FCB7F05E-E2F2-4DCA-A936-02AF5733F96B@..." type="cite">
      <div class="moz-text-html" lang="x-unicode">
        <div class="">Just a quick word, in case it is useful.</div>
        <div class=""><br class=""></div>
        It seems that you are using an incompatible version of Geant4.
        <div class=""><br class=""></div>
        <div class="">Have you checked which version(s) GATE 7.0
          supports ?</div>
        <div class="">
<br class=""><div apple-content-edited="true" class=""><span class="Apple-style-span"><span class="Apple-style-span">
                <div class="">
                  <span class="Apple-style-span">
                    <div class="">
                      <span class="Apple-style-span">
                        <div class="">
                          <span class="Apple-style-span">
                            <div class="">
                              <span class="Apple-style-span">
                                <div class="">
                                  <div class="">John</div>
                                  <div class="">
                                    <div apple-content-edited="true" class=""><span class="Apple-style-span"><span class="Apple-style-span">
                                          <div class="">
                                            <div class="">===================================================</div>
                                            <div class=""><br class=""></div>
                                          </div>
                                        </span></span></div>
                                  </div>
                                </div>
                              </span>
</div>
                          </span>
</div>
                      </span>
</div>
                  </span>
</div>
              </span></span></div>
          <br class=""><div>
            <blockquote type="cite" class="">
              <div class="">On 09 Jan 2015, at 14:33, Richard Lacroix
                &lt;<a moz-do-not-send="true" href="mailto:Richard.Lacroix@..." class="">Richard.Lacroix@...</a>&gt;
                wrote:</div>
              <br class="Apple-interchange-newline"><div class="">
                <div bgcolor="#FFFFFF" text="#000000" class="">Hi all,<br class=""><br class="">
                  I'm trying to compile Gate v7.0 on Red Hat 6.6&nbsp; and I
                  get the following error<br class=""><br class=""><br class="">
                  Building CXX object
                  CMakeFiles/Gate.dir/source/physics/src/GateSourceVoxellized.cc.o<br class="">
                  Building CXX object
CMakeFiles/Gate.dir/source/physics/src/GateSourcePencilBeamMessenger.cc.o<br class="">
                  Building CXX object
                  CMakeFiles/Gate.dir/source/physics/src/GateNeutronInelasticPB.cc.o<br class="">
                  /home2/lacr1801/tmp/gate_v7.0/source/physics/src/≤a moz-do-not-send="true" href="http://GateSingleParticleSourceMessenger.cc" class="">GateSingleParticleSourceMessenger.cc</a>:
                  In member function &lsquo;void
                  GateSingleParticleSourceMessenger::IonCommand(G4String)&rsquo;:<br class="">
                  /home2/lacr1801/tmp/gate_v7.0/source/physics/src/≤a moz-do-not-send="true" href="http://GateSingleParticleSourceMessenger.cc" class="">GateSingleParticleSourceMessenger.cc</a>:1528:
                  error: &lsquo;class
                      G4ParticleTable&rsquo; has no member named &lsquo;GetIon&rsquo;<br class="">
                  make[2]: ***
                  [CMakeFiles/Gate.dir/source/physics/src/GateSingleParticleSourceMessenger.cc.o]
                  Error 1<br class="">
                  make[2]: *** Attente des t&acirc;ches non termin&eacute;es....<br class="">
                  make[1]: *** [CMakeFiles/Gate.dir/all] Error 2<br class="">
                  make: *** [all] Error 2<br class=""><br class=""><br class="">
                  Help please
                  <div class="moz-signature">-- <br class=""><p class="">Richard Lacroix<br class="">
                                Analyste en informatique<br class="">
                              _____________________<br class="">Universit&eacute;
                                de Sherbrooke<br class="">
                                Facult&eacute; de G&eacute;nie<br class="">
                                G&eacute;nie &Eacute;lectrique et G&eacute;nie Informatique<br class="">2500 Boul. Universit&eacute;<br class="">
                                Sherbrooke, Qc<br class="">
                                J1K 2R1 Canada<br class="">
                                T&eacute;l. (819) 821-8000 ext. 62877 Fax (819)
                                821-7937<br class="">
                                &nbsp;<a moz-do-not-send="true" href="mailto:Richard.Lacroix <at> .USherbrooke.ca" class="">Richard.Lacroix@...</a><br class="">
                              &nbsp; <a moz-do-not-send="true" href="http://www.usherbrooke.ca/gelecinfo" class="">www.usherbrooke.ca/gelecinfo</a><br class=""></p>
                  </div>
                </div>
                _______________________________________________<br class="">
                Gate-users mailing list<br class=""><a moz-do-not-send="true" href="mailto:Gate-users@...rg" class="">Gate-users@...</a><br class=""><a class="moz-txt-link-freetext" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a>
</div>
            </blockquote>
          </div>
          <br class="">
</div>
      </div>
    </blockquote>
    <br>
</div>
Matthew Belley | 12 Jan 16:09 2015

Citation for spleen material definition used in examples?

Dear All,

I would be grateful if someone could point me to the citation or source that was used to derive this material definition: 

/example_Radiotherapy/example3/data/GateMaterials.db lists Spleen as:

Spleen: d=1.06 g/cm3 ; n=11
        +el: name=Hydrogen  ; f=0.103
        +el: name=Carbon    ; f=0.113
        +el: name=Nitrogen  ; f=0.032
        +el: name=Oxygen    ; f=0.741
        +el: name=Sodium    ; f=0.001
        +el: name=Phosphor  ; f=0.003
        +el: name=Sulfur    ; f=0.002
        +el: name=Chlorine  ; f=0.002
        +el: name=Potassium ; f=0.003
        +el: name=Calcium   ; f=0.0
        +el: name=Scandium  ; f=0.0

I notice it is very close to the ICRU-44 soft tissue and blood definitions, but it is not identical:

Thank you,

--
Matthew Belley 

Doctoral Candidate
Medical Physics Graduate Program, Duke University 
Duke Radiation Dosimetry Laboratory, Duke University Medical Center 
Durham, North Carolina 27705
<div><div dir="ltr">
<div>Dear All,</div>
<div><br></div>
<div>I would be grateful if someone could point me to the citation or source that was used to derive this material definition:&nbsp;</div>
<div><br></div>
<blockquote><div>/example_Radiotherapy/example3/data/GateMaterials.db lists Spleen as:</div></blockquote>
<div>
<blockquote>
<div>
<div><br></div>
<div>Spleen: d=1.06 g/cm3 ; n=11</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Hydrogen &nbsp;; f=0.103</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Carbon &nbsp; &nbsp;; f=0.113</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Nitrogen &nbsp;; f=0.032</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Oxygen &nbsp; &nbsp;; f=0.741</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Sodium &nbsp; &nbsp;; f=0.001</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Phosphor &nbsp;; f=0.003</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Sulfur &nbsp; &nbsp;; f=0.002</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Chlorine &nbsp;; f=0.002</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Potassium ; f=0.003</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Calcium &nbsp; ; f=0.0</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; +el: name=Scandium &nbsp;; f=0.0</div>
</div>
<div><br></div>
</blockquote>I notice it is very close to the ICRU-44 soft tissue and blood definitions, but it is not identical:</div>
<div><ul><li>
<a href="http://physics.nist.gov/PhysRefData/XrayMassCoef/tab2.html">http://physics.nist.gov/PhysRefData/XrayMassCoef/tab2.html</a><br>
</li></ul></div>
<div><br></div>
<div>Thank you,<br><blockquote><div><br></div></blockquote>
</div>-- <br><div class="gmail_signature"><div dir="ltr"><div>Matthew Belley&nbsp;<div><br></div>
<div>Doctoral <span>Candidate</span>
</div>
<div>Medical Physics Graduate Program, Duke University&nbsp;</div>
<div>Duke Radiation Dosimetry Laboratory, Duke University Medical Center&nbsp;</div>
<div>Durham, North Carolina 27705</div>
</div></div></div>
</div></div>
David Larsson | 12 Jan 10:32 2015
Picon
Picon

New output file for new time slice

Dear GATE-users,

 

does anyone know if it is possible to prompt GATE to create a new (ASCII)-output file for each new time slice of the simulation? I.e. files on the form (e.g.) “test_Singles_xxx.dat” with xxx given by the present time slice.

 

I know that the “imageCT” output has this setup, but it would be very handy if I could get this also for the regular data output. Anyone knows how to do this (or if it’s even possible)?

 

Best regards,

 

David Larsson

<div>
<div class="WordSection1">
<p class="MsoNormal">Dear GATE-users,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal"><span lang="EN-US">does anyone know if it is possible to prompt GATE to create a new (ASCII)-output file for each new time slice of the simulation? I.e. files on the form (e.g.) &ldquo;test_Singles_xxx.dat&rdquo; with xxx given by the present time
 slice. <p></p></span></p>
<p class="MsoNormal"><span lang="EN-US"><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span lang="EN-US">I know that the &ldquo;imageCT&rdquo; output has this setup, but it would be very handy if I could get this also for the regular data output. Anyone knows how to do this (or if it&rsquo;s even possible)?<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US"><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span lang="EN-US">Best regards,<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US"><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span lang="EN-US">David Larsson<span><p></p></span></span></p>
</div>
</div>
Leda Lorenzon | 9 Jan 21:32 2015
Picon

Radioactive source with decay scheme

Dear Gate,
how can I simulate a radioactive source considering its decay scheme?
For instance, I would like to simulate a Tc-99m source with this decay scheme:

========================================

# == Energy (kev) Abundance ============

# ========================================

20.669                     0.0112000

21.0235                  0.00177000

89.6                        1.04000e-05

140.511                   0.885000

142.683                   0.000230000

232.7                       8.40000e-08

322.4                       9.60000e-07


Kind regards and best wishes,

Leda Lorenzon


<div><div dir="ltr">
<div>Dear Gate,</div>
<div>how can I simulate a radioactive source considering its decay scheme?</div>
<div>For instance, I would like to simulate a Tc-99m source with this decay scheme:</div>
<div><span lang="IT"><p>========================================</p>
<p># == Energy (kev)  Abundance  ============</p>
<p># ========================================</p>
<p>       20.669&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      0.0112000</p>
<p>      21.0235&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;    0.00177000</p>
<p>         89.6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;    1.04000e-05</p>
<p>      140.511&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;       0.885000</p>
<p>      142.683&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;   0.000230000</p>
<p>        232.7&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;    8.40000e-08</p>
<p>        322.4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;    9.60000e-07</p>
<p><br></p>
<p>Kind regards and best wishes,</p>
<p>Leda Lorenzon</p>
<p><br></p></span></div>
</div></div>
Karl Spuhler | 9 Jan 02:46 2015

Trying to write a curved CT scanner

Hello all,

I am trying to adapt the scanner system used in the exampleCT/fast template to a curved system. I am currently creating an arc shape using a portion of a cylinder and then attempting to attach a module on top of this as such shown below in my code. Unfortunately this is not working. Does anyone have a working template for a curved scanner? Ideally one where I could change the resolution using a command for the number of pixels in the x,y directions or know how I could achieve such a thing?

#############
##CTscanner##
#############

/gate/world/daughters/name CTscanner
/gate/world/daughters/insert cylinder
/gate/CTscanner/setMaterial Air
/gate/CTscanner/vis/setColor cyan
/gate/CTscanner/geometry/setRmax 100 cm
/gate/CTscanner/geometry/setRmin 99 cm
/gate/CTscanner/geometry/setHeight 6. cm
/gate/CTscanner/geometry/setPhiStart 65 deg
/gate/CTscanner/geometry/setDeltaPhi 50 deg
/gate/CTscanner/placement/setTranslation 0. 0. 50. cm
/gate/CTscanner/placement/alignToY 
/gate/CTscanner/vis/forceSolid
/gate/CTscanner/vis/setVisible 1


############
###MODULE###
############

/gate/CTscanner/daughters/name module
/gate/CTscanner/daughters/insert cylinder 
/gate/module/geometry/setRmax 100 cm
/gate/module/geometry/setRmin 99 cm
/gate/module/geometry/setHeight 6. cm
/gate/module/geometry/setPhiStart 65 deg
/gate/module/geometry/setDeltaPhi 50 deg
/gate/module/setMaterial Silicon
/gate/module/vis/forceWireframe
/gate/module/vis/setColor white

#ATTACH SYSTEM
/gate/systems/CTscanner/module/attach module

#ATTACH LAYER
/gate/module/attachCrystalSD




--
Karl Spuhler

SUNY Stony Brook
PhD Student
(845)249-6836


<div><div dir="ltr">Hello all,<div><br></div>
<div>I am trying to adapt the scanner system used in the exampleCT/fast template to a curved system. I am currently creating an arc shape using a portion of a cylinder and then attempting to attach a module on top of this as such shown below in my code. Unfortunately this is not working. Does anyone have a working template for a curved scanner? Ideally one where I could change the resolution using a command for the number of pixels in the x,y directions or know how I could achieve such a thing?</div>
<div><br></div>
<div>
<div>#############</div>
<div>##CTscanner##</div>
<div>#############</div>
<div><br></div>
<div>/gate/world/daughters/name CTscanner</div>
<div>/gate/world/daughters/insert cylinder</div>
<div>/gate/CTscanner/setMaterial Air</div>
<div>/gate/CTscanner/vis/setColor cyan</div>
<div>/gate/CTscanner/geometry/setRmax 100 cm</div>
<div>/gate/CTscanner/geometry/setRmin 99 cm</div>
<div>/gate/CTscanner/geometry/setHeight 6. cm</div>
<div>/gate/CTscanner/geometry/setPhiStart 65 deg</div>
<div>/gate/CTscanner/geometry/setDeltaPhi 50 deg</div>
<div>/gate/CTscanner/placement/setTranslation 0. 0. 50. cm</div>
<div>/gate/CTscanner/placement/alignToY&nbsp;</div>
<div>/gate/CTscanner/vis/forceSolid</div>
<div>/gate/CTscanner/vis/setVisible 1</div>
<div><br></div>
<div><br></div>
<div>############</div>
<div>###MODULE###</div>
<div>############</div>
<div><br></div>
<div>/gate/CTscanner/daughters/name module</div>
<div>/gate/CTscanner/daughters/insert cylinder&nbsp;</div>
<div>/gate/module/geometry/setRmax 100 cm</div>
<div>/gate/module/geometry/setRmin 99 cm</div>
<div>/gate/module/geometry/setHeight 6. cm</div>
<div>/gate/module/geometry/setPhiStart 65 deg</div>
<div>/gate/module/geometry/setDeltaPhi 50 deg</div>
<div>/gate/module/setMaterial Silicon</div>
<div>/gate/module/vis/forceWireframe</div>
<div>/gate/module/vis/setColor white</div>
<div><br></div>
<div>#ATTACH SYSTEM</div>
<div>/gate/systems/CTscanner/module/attach module</div>
<div><br></div>
<div>#ATTACH LAYER</div>
<div>/gate/module/attachCrystalSD</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">Karl Spuhler<div><br></div>
<div>SUNY Stony Brook</div>
<div>PhD Student</div>
<div>(845)249-6836</div>
<div><h1><br></h1></div>
</div></div>
</div>
</div></div>
Wonmo Sung | 9 Jan 02:42 2015
Picon

Rotation of phase space source

Dear GATE users


I would like to rotate the phase space source.


command line for phase space were following


/gate/source/addSource IAEA phaseSpace

/gate/source/IAEA/addPhaseSpaceFile input/6MeV_SF4_IAEA_SUM.1.IAEAphsp

/gate/source/IAEA/setRotationAxis 1 0 0

/gate/source/IAEA/setRotationAngle 90 deg


output were

***** COMMAND NOT FOUND </gate/source/IAEA/setRotationAxis 1 0 0> *****
***** Batch is interrupted!! *****

It seems like there is no command to rotate phase space source.
Am I right?
Please give me comments if you know how to rotate the phase space source.
Thanks for your answers in advance!


Regards,

Wonmo Sung

<div>
<p></p>
<p>Dear GATE users</p>
<p><br></p>
<p>I would like to rotate the phase space source.</p>
<p><br></p>
<p>command line for phase space were following</p>
<p><br></p>
<p>/gate/source/addSource IAEA phaseSpace</p>
<p>/gate/source/IAEA/addPhaseSpaceFile input/6MeV_SF4_IAEA_SUM.1.IAEAphsp</p>
<p>/gate/source/IAEA/setRotationAxis 1 0 0</p>
<p>/gate/source/IAEA/setRotationAngle 90 deg</p>
<div><br></div>
<div>output were</div>
<div><br></div>
<div>
<div>
<span>***** COMMAND NOT FOUND &lt;/gate/source/IAEA/setRotationAxis 1 0 0&gt; *****≤/span><br clear="none"><span>***** Batch is interrupted!! *****≤/span>
</div>
<div><br></div>
<div>It seems like there is no command to rotate phase space source.</div>
<div>Am I right?</div>
<div>Please give me comments if you know how to rotate the phase space source.</div>
<div>Thanks for your answers in advance!</div>
</div>
<p><br></p>
<p>Regards,</p>
<p>Wonmo Sung</p>

</div>
André Miguel Monteiro | 8 Jan 17:33 2015
Picon

Forcedwireframe visualization of volumes


Dear Gate users,


I want to create a half sphere phantom that has a tumor inside it. To see the tumor I am using the command  /gate/phantom/vis/forceWireframe so I can see the daughter volume. But what I get, which is represented in the phantom.png picture, is weird!! If I apply /gate/daughter_volume/vis/forceWireframe it doesn't show anyting...

 

So I followed the user guide and did the first part of defining the scanner geometry with the same command /gate/name_of_the_volume/vis/forceWireframe that gave me the result showed by the figure forcedwire.png


Shouldn't the result be a dashed line?


I am using /gate/geometry/rebuild​ to get the geometry of the volumes.


Thank you in advance.


Cheers,


André Miguel Monteiro



--------------------------------
MSc Student in Biomedical and Biophysics Engineering at Faculty of Sciences of the University of Lisbon

Institute of Biophysics and Biomedical Engineering
Faculty of Sciences, University of Lisbon
Campo Grande
1749-016 Lisbon

Room Office: 1.02
Extension: 20509
Email: ammonteiro-IY2GDWxKiro@public.gmane.org
<div>
<p><br></p>
<p>Dear Gate users,<br></p>
<p><br></p>
<p>I want to create a half sphere&nbsp;phantom that has a tumor inside it. To see the tumor&nbsp;I am using the command&nbsp;&nbsp;<span>/gate/p</span><span>hantom/vis/forceWireframe
 so I can see the daughter volume. But what I get,&nbsp;which&nbsp;is represented in the phantom.png picture,&nbsp;is weird!! If I apply
<span>
/gate/daughter_volume</span><span>/vis/forceWireframe</span> it doesn't show anyting...</span><br></p>
<p><span>&nbsp;</span></p>
<p><span>So I followed the user guide and did the first part of defining the scanner geometry with the same command&nbsp;<span>/gate/name_of_the_volume</span><span>/vis/forceWireframe</span>
 that gave me the result showed by the figure forcedwire.png</span></p>
<p><span><br></span></p>
<p><span>Shouldn't the result be a dashed line?</span></p>
<p><span><br></span></p>
<p>I am using&nbsp;/gate/geometry/rebuild&#8203; to get the geometry of the volumes.<br></p>
<p><br></p>
<p>Thank you in advance.<br></p>
<p><br></p>
<p>Cheers,<br></p>
<p><br></p>
<p>Andr&eacute; Miguel Monteiro<br></p>
<div>
<div name="divtagdefaultwrapper">
<div class="BodyFragment">
<div class="PlainText">
<br><br>--------------------------------<br>MSc Student in Biomedical and Biophysics Engineering at Faculty of Sciences of the University of Lisbon<br><br><span dir="ltr"><span lang="en">Institute</span><span lang="en">
</span><span lang="en">of Biophysics and</span><span lang="en"> </span><span lang="en">Biomedical Engineering</span><span lang="en"><br></span><span lang="en">Faculty</span><span lang="en"> </span><span lang="en">of Sciences, University</span><span lang="en">
</span><span lang="en">of Lisbon</span><br>
Campo Grande<br>
1749-016 Lisbon<br><br></span>Room Office: 1.02<br><span dir="ltr">Extension: 20509
<br>
Email: ammonteiro@...</span>
</div>
<div class="PlainText">
<span dir="ltr">LinkedIn Profile:&nbsp;</span><a tabindex="0" href="http://linkedin.com/in/andremmonteiro">http://linkedin.com/in/andremmonteiro</a><span dir="ltr"><br>
Website: <a tabindex="0" href="http://www.ibeb.fc.ul.pt/" target="_blank">http://www.ibeb.fc.ul.pt/</a></span><br>
</div>
</div>
</div>
</div>
</div>
André Miguel Monteiro | 8 Jan 11:50 2015
Picon

Create an ellipsoid volume

Dear Gate users,


Is there a possibility to create half of an ellipsoid volume with axis a and b equal to 14 and height equal to 13?


Thank you,


André Miguel Monteiro





--------------------------------
MSc Student in Biomedical and Biophysics Engineering at Faculty of Sciences of the University of Lisbon

Institute of Biophysics and Biomedical Engineering
Faculty of Sciences, University of Lisbon
Campo Grande
1749-016 Lisbon

Room Office: 1.02
Extension: 20509
Email: ammonteiro-IY2GDWxKiro@public.gmane.org
<div>
<p>Dear Gate users,<br></p>
<p><br></p>
<p>Is there a possibility to create half of an ellipsoid volume&nbsp;with axis a and b equal to 14 and height equal to 13?<br></p>
<p><br></p>
<p>Thank you,<br></p>
<p><br></p>
<p>Andr&eacute; Miguel Monteiro<br></p>
<p><br></p>
<p><br></p>
<div>
<div name="divtagdefaultwrapper">
<div class="BodyFragment">
<div class="PlainText">
<br><br>--------------------------------<br>MSc Student in Biomedical and Biophysics Engineering at Faculty of Sciences of the University of Lisbon<br><br><span dir="ltr"><span lang="en">Institute</span><span lang="en">
</span><span lang="en">of Biophysics and</span><span lang="en"> </span><span lang="en">Biomedical Engineering</span><span lang="en"><br></span><span lang="en">Faculty</span><span lang="en"> </span><span lang="en">of Sciences, University</span><span lang="en">
</span><span lang="en">of Lisbon</span><br>
Campo Grande<br>
1749-016 Lisbon<br><br></span>Room Office: 1.02<br><span dir="ltr">Extension: 20509
<br>
Email: ammonteiro@...</span>
</div>
<div class="PlainText">
<span dir="ltr">LinkedIn Profile:&nbsp;</span><a tabindex="0" href="http://linkedin.com/in/andremmonteiro">http://linkedin.com/in/andremmonteiro</a><span dir="ltr"><br>
Website: <a tabindex="0" href="http://www.ibeb.fc.ul.pt/" target="_blank">http://www.ibeb.fc.ul.pt/</a></span><br>
</div>
</div>
</div>
</div>
</div>
Martin Vallières | 8 Jan 09:19 2015
Picon

Re: GATE installation problem - gcc compiler options

Hi Hermann,

Thank you very much for your reply. Using root version 5.34 solved the problem!

For the record, the following installation was successful on Ubuntu 14.04 with gcc v4.8.2:
- root v5.34.24
- geant4 v4.9.6.p03
- gate v7.0

Cheers,
Martin

On 15-01-08 12:44 AM, Hermann Fuchs wrote:
Hi Martin,

this is due to an incompatibility with the newest root version.
Try using an older root version such as version 5.34.

Cheers,
Hermann

Am 8. Januar 2015 00:32:34 MEZ, schrieb "Martin Vallières" <martin.carrier-vallieres-Qbh6zKbeHLYtq+zhY6Lx4A@public.gmane.org>:
Dear GATE users, I am trying to installl GATE v7.0 on my computer with Ubuntu 14.04 and gcc version 4.8.2. I have successfully installed root v6.02.02 and geant4 v10.01. During the compilation of GATE, I get the following error: "[ 6%] Building CXX object CMakeFiles/Gate.dir/Gate.cc.o In file included from /usr/include/c++/4.8/atomic:38:0, from /home/martin/Programs/PET_SIM/root-6.02.02/include/Rtypes.h:37, from /home/martin/Programs/PET_SIM/root-6.02.02/include/TObject.h:31, from /home/martin/Programs/PET_SIM/root-6.02.02/include/TNamed.h:26, from /home/martin/Programs/PET_SIM/root-6.02.02/include/TDirectory.h:25, from /home/martin/Programs/PET_SIM/root-6.02.02/include/TROOT.h:29, from /home/martin/Programs/PET_SIM/gate_v7.0/source/physics/include/GateSourcePhaseSpace.hh:14, from /home/martin/Programs/PET_SIM/gate_v7.0/source/physics/include/GateSourceMgr.hh:18, from /home/martin/Programs/PET_SIM/gate_v7.0/Gate.cc:30: /usr/include/c++/4.8/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options." Does anyone know how to solve this problem? Where can I enable those compiler flags (-std=c++11 or -std=gnu++11)? Thank you so much for you help, Martin Gate-users mailing list Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

<div>
    Hi Hermann,<br><br>
    Thank you very much for your reply. Using root version 5.34 solved
    the problem!<br><br>
    For the record, the following installation was successful on Ubuntu
    14.04 with gcc v4.8.2:<br>
    - root v5.34.24<br>
    - geant4 v4.9.6.p03<br>
    - gate v7.0<br><br>
    Cheers,<br>
    Martin<br><br><div class="moz-cite-prefix">On 15-01-08 12:44 AM, Hermann Fuchs
      wrote:<br>
</div>
    <blockquote cite="mid:9489_1420695878_54AE1945_9489_227_1_C65003B7-43A3-4A5B-816A-E7986667B44A@..." type="cite">

      Hi Martin,<br><br>
      this is due to an incompatibility with the newest root version.<br>
      Try using an older root version such as version 5.34.<br><br>
      Cheers,<br>
      Hermann<br><br><div class="gmail_quote">Am 8. Januar 2015 00:32:34 MEZ, schrieb
        "Martin Valli&egrave;res"
        <a class="moz-txt-link-rfc2396E" href="mailto:martin.carrier-vallieres@...">&lt;martin.carrier-vallieres@...&gt;</a>:
        <blockquote class="gmail_quote">
          Dear GATE users,

I am trying to installl GATE v7.0 on my computer with Ubuntu 14.04 and 
gcc version 4.8.2. I have successfully installed root v6.02.02 and 
geant4 v10.01.

During the compilation of GATE, I get the following error:

"[  6%] Building CXX object CMakeFiles/Gate.dir/≤a moz-do-not-send="true" href="http://Gate.cc">Gate.cc</a>.o
In file included from /usr/include/c++/4.8/atomic:38:0,
                  from 
/home/martin/Programs/PET_SIM/root-6.02.02/include/Rtypes.h:37,
                  from 
/home/martin/Programs/PET_SIM/root-6.02.02/include/TObject.h:31,
                  from 
/home/martin/Programs/PET_SIM/root-6.02.02/include/TNamed.h:26,
                  from 
/home/martin/Programs/PET_SIM/root-6.02.02/include/TDirectory.h:25,
                  from 
/home/martin/Programs/PET_SIM/root-6.02.02/include/TROOT.h:29,
                  from 
/home/martin/Programs/PET_SIM/gate_v7.0/source/physics/include/GateSourcePhaseSpace.hh:14,
                  from 
/home/martin/Programs/PET_SIM/gate_v7.0/source/physics/include/GateSourceMgr.hh:18,
                  from /home/martin/Programs/PET_SIM/gate_v7.0/<a moz-do-not-send="true" href="Gate.cc:30">Gate.cc:30</a>:
/usr/include/c++/4.8/bits/c++0x_warning.h:32:2: error: #error This file 
requires compiler and library support for the ISO C++ 2011 standard. 
This support is currently experimental, and must be enabled with the 
-std=c++11 or -std=gnu++11 compiler options."

Does anyone know how to solve this problem? Where can I enable those 
compiler flags (-std=c++11 or -std=gnu++11)?

Thank you so much for you help,
Martin

Gate-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Gate-users@...ngatecollaboration.org">Gate-users@...</a>
<a moz-do-not-send="true" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a>

        </blockquote>
      </div>
    </blockquote>
    <br>
</div>

Gmane