<div dir="ltr">Hello,<div><br></div><div>I have proposed a fix for the <span style="font-size:12.8px">ImageRegionalizedVolume </span>bug (<a href="https://github.com/OpenGATE/Gate/pull/101" target="_blank">https://github.com/OpenGATE/<wbr>Gate/pull/101</a>).</div><div><br></div><div>This problem will no longer appear in the upcoming version of Gate.<br></div><div><br></div><div>Sincerely,</div><div><br></div><div>Thomas</div><div class="gmail_extra"><br clear="all"><div><div class="gmail-m_2232955037563543921gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><b><font color="#444444">Thomas DESCHLER</font></b><br><font color="#666666" style="font-size:12.8px">Doctorant en P</font><font color="#666666" style="font-size:12.8px">hysique des Rayonnements</font><font color="#666666"><br><a href="http://www.iphc.cnrs.fr/" target="_blank"><font color="#666666">Institut Pluridisciplinaire Hubert Curien</font></a><br><a href="http://www.iphc.cnrs.fr/spip.php?page=rubrique&id_rubrique=143" target="_blank"><font color="#666666">Département Recherches Subatomiques</font></a> - <a href="http://www.iphc.cnrs.fr/-Ramses-.html" target="_blank"><font color="#666666">Groupe Ramses</font></a><br>Bâtiment 35, Bureau 208<br></font></div><div dir="ltr"><font color="#666666"><br></font></div><div dir="ltr"><a href="https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=Thomas.Deschler@iphc.cnrs.fr" title="[GMCP] Compose a new mail to Thomas.Deschler@iphc.cnrs.fr" rel="noreferrer" target="_blank"><font color="#666666">Thomas.Deschler@iphc.cnrs.fr</font></a></div><div><font color="#666666"><a href="tel:+33388106395" target="_blank"><font color="#666666">(+33) 03 88 10 63 95</font></a><br><a href="tel:+33620960749" target="_blank"><font color="#666666">(+33) 06 20 96 07 49</font></a></font><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">2017-02-13 17:07 GMT+01:00 Maxime Chauvin <span dir="ltr"><<a href="mailto:maxime.chauvin@inserm.fr" target="_blank">maxime.chauvin@inserm.fr</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Hello Nicolas,<div><br></div><div>Yes I remember this. It is a bug I think.</div><div>I just set min, max: -1,4 in my<i> <span>data/waterbottle_HU2mat.txt</span></i></div><div><i>And then it doesn’t complain.</i></div><div><i><br></i></div><div><i>This is just a fix and hopefully this bug will be corrected soon.</i></div><div><i><br></i></div><div><i>Cheers,</i></div><div><i> Maxime</i></div><div><br><div><blockquote type="cite"><div><div class="gmail-m_2232955037563543921h5"><div>On 13 Feb 2017, at 16:38, Triltsch, Nicolas <<a href="mailto:nicolas.triltsch@tum.de" target="_blank">nicolas.triltsch@tum.de</a>> wrote:</div><br class="gmail-m_2232955037563543921m_1504270692636721028Apple-interchange-newline"></div></div><div><div><div class="gmail-m_2232955037563543921h5">
<div bgcolor="#FFFFFF"><p>Hey David & Maxime,</p><p>Thanks for your advice. I tried to use the option
ImageRegionalizedVolume (plus the distance map) instead of
ImageNestedParametrisedVolume, but it gives the following error:</p><p>"<i>[Physic-0] The following Geant4's physic-list is enabled
:emlivermore</i><i><br>
</i><i><a href="http://gatevimagevolume.cc" target="_blank">GateVImageVolume.cc</a> (l.363): The image contains HU indices
out of range of the HU range found in
data/waterbottle_HU2mat.txt</i><i><br>
</i><i>min, max:0, 4.</i><i><br>
</i><i>min, max in image: -1, 3</i><i><br>
</i><i>Abort.</i><br>
"</p><p>I am confused by this error as I am using the the same HU2mat.txt
and .mhd+.raw files as before. Does the new Parameterization
method require different material descriptors or what could be the
reason? My image contains of 4 materials only: Air (index 0),
water (index 1), plastic (index 2) and lead (index 3).<br>
</p><p> Cheers,</p><p>Nico<br>
</p>
<div class="gmail-m_2232955037563543921m_1504270692636721028moz-cite-prefix">On 02/10/2017 04:57 PM, David Sarrut
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hello, </div>
<div><br>
</div>
<div><span style="font-size:12.8px">To my knowledge,
RegularParameterization with flag skipEqualMaterials is
still buggy (it should be disabled: if someone know this
code, please propose a pull request to correct or disable
this option). </span><br>
</div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Use either: </span></div>
<div><span style="font-size:12.8px">-
ImageNestedParametrisedVolume : simple conventional
navigator, similar to regular, (slightly faster)</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">- ImageRegionalizedVolume as
proposed by Maxime. It could be 3-4 times faster in some
cases but it depends on what you are storing during the
simulation. If it is a dose map, take care to the
statistical uncertainties. If you are only interested in
particle outgoing the volume (for imaging for example), it
is safe to use. Of course, the speed up depends on the
voxelized volume (faster if lot of similar material). </span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Doc is here: <a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V8.0:Voxelized_Source_and_Phantom#Nested_parameterization_method" target="_blank">http://wiki.opengatecoll<wbr>aboration.org/index.php/Users_<wbr>Guide_V8.0:Voxelized_Source_<wbr>and_Phantom#Nested_<wbr>parameterization_method</a></span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">David</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Feb 10, 2017 at 4:45 PM, Maxime
Chauvin <span dir="ltr"><<a href="mailto:maxime.chauvin@inserm.fr" target="_blank">maxime.chauvin@inserm.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word">Hello Nicolas,
<div><br>
</div>
<div>I had the same problem as you and couldn’t fix it. On
the other hand there is a even more efficient way using</div>
<div>ImageRegionalizedVolume. It will further speed up the
simulation especially if your geometry has a lot of
common voxel</div>
<div>and you will get rid of this warning.</div>
<div><br>
</div>
<div>Cheers,</div>
<div> Maxime </div>
<div><br>
<div>
<blockquote type="cite">
<div>
<div class="gmail-m_2232955037563543921m_1504270692636721028h5">
<div>On 10 Feb 2017, at 14:41, Triltsch, Nicolas
<<a href="mailto:nicolas.triltsch@tum.de" target="_blank">nicolas.triltsch@tum.de</a>>
wrote:</div>
<br class="gmail-m_2232955037563543921m_1504270692636721028m_-7303347453256307962Apple-interchange-newline">
</div>
</div>
<div>
<div>
<div class="gmail-m_2232955037563543921m_1504270692636721028h5">
<div bgcolor="#FFFFFF"><p>Hello,</p><p>I tried to speed up my simulation by
choosing Regular Parameterization (with
flag skipEqualMaterials to 1) instead of
Nested Parameterization, because my Volume
got a lot of voxels with the same
material. It did indeed speed up the
simulation by a factor of 15, but some
projections of my CT simulation failed
(error: segmentation fault; crash).</p><p>Now I saw that during the initialization
phase of gate it states the following: <br>
</p><p><i>### WARNING ### setSkipEqualMaterials
at false !! The Geant4 method is not
safe since the release 9.5 - Need to be
fixed</i><br>
<br>
</p>
I am pretty sure that this warning is
somehow connected to the warning. Does
anyone know if there had been a bug fix for
Geant4 v10.2.2?<br>
<br>
In the appendix there is a screenshot of the
error.<br>
<br>
Cheers,<br>
Nico<br>
<pre class="gmail-m_2232955037563543921m_1504270692636721028m_-7303347453256307962moz-signature" cols="72">--
B.Sc. Nicolas Triltsch
Masterand
Technische Universität München
Physik-Department
Lehrstuhl für Biomedizinische Physik E17
James-Franck-Straße 1
85748 Garching b. München
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<div dir="ltr">David Sarrut, Phd<br>
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CREATIS, UMR CNRS 5220, Inserm U1206
<div>Centre de lutte contre le cancer Léon Bérard<br>
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______________________________<wbr>___</div>
<div> "2 + 2 = 5, for extremely large values of 2"<br>
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<pre class="gmail-m_2232955037563543921m_1504270692636721028moz-signature" cols="72">--
B.Sc. Nicolas Triltsch
Masterand
Technische Universität München
Physik-Department
Lehrstuhl für Biomedizinische Physik E17
James-Franck-Straße 1
85748 Garching b. München
Tel: <a href="tel:+49%2089%2028912591" value="+498928912591" target="_blank">+49 89 289 12591</a>
<a class="gmail-m_2232955037563543921m_1504270692636721028moz-txt-link-abbreviated" href="mailto:nicolas.triltsch@tum.de" target="_blank">nicolas.triltsch@tum.de</a>
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