tag:blogger.com,1999:blog-18058569804507567662024-03-19T12:30:44.564+01:00Will work for science.Medical Physics, Particle Therapy and Computing.Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.comBlogger27125tag:blogger.com,1999:blog-1805856980450756766.post-19785422079438042092014-03-06T18:11:00.000+01:002014-03-06T18:11:43.532+01:00A Stopping Power App for Android<br />
<br />
We (<a href="http://www.phys.au.dk/aptg">as in APTG</a>) have just released the <a href="https://play.google.com/store/apps/details?id=dk.au.aptg.dEdx">dE/dx Android app on Google Play</a>!<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrz77SesE_EAkglkA-gstffpqoSgBIbEyo9Hf_kX3TCBrzs_Bemc59Y0eXQPENvaYfruIbyCUOJaXmAFUNRkqqnk1kfZITUnqmwXTPsCnKC5C9Hp7wFo5kes1WqRd2RV84BMhAQpbYYEE/s1600/Screenshot_2014-03-06-13-06-28.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrz77SesE_EAkglkA-gstffpqoSgBIbEyo9Hf_kX3TCBrzs_Bemc59Y0eXQPENvaYfruIbyCUOJaXmAFUNRkqqnk1kfZITUnqmwXTPsCnKC5C9Hp7wFo5kes1WqRd2RV84BMhAQpbYYEE/s1600/Screenshot_2014-03-06-13-06-28.png" height="320" width="192" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Screnshot of the dE/dx app, ver. 1.0 from my LG Nexus 4 phone.</td></tr>
</tbody></table>
<br />
The app is written by student Casper Cristensen in collaboration with the <a href="http://phys.au.dk/">Dept. of Physics and Astronomy</a> and the <a href="http://www.iha.dk/">School of Engineering</a> at <a href="http://www.au.dk/">Aarhus University</a>. The app is based on the stopping power library <a href="http://sourceforge.net/projects/libdedx/">libdEdx</a>-1.2.1 which was presented in an <a href="http://willworkforscience.blogspot.dk/2012/06/libdedx-120-released-stopping-powers.html">earlier blog entry</a> here.<br />
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The cool thing about the app is that all tables are stored locally on phone (this is why it needs access to USB memory), so no network access is necessary - useful if you want to look up stopping power while working in a shielded area with no network.<br />
<br />
In summary the features are:<br />
<ul>
<li>ICRU 49 and ICRU 73 (revised version) electronic stopping power tables</li>
<li>MSTAR tables provided by <a href="https://www-nds.iaea.org/stopping/">Helmut Paul</a></li>
<li>BETHE_EXT00, a generic algorithm as used in SHIELD-HIT12A. Applicable for <b>any</b> ion to <b>all </b>278 ICRU compounds (beware, use with care, <a href="http://www.sciencedirect.com/science/article/pii/S0168583X13007520">can be off at lower energies)</a>, .</li>
<li>no network access needed after installation</li>
<li>calculation of CSDA range of particle in target material</li>
<li>inverse CSDA lookups possible (if you need to figure out what specific energy is needed to produce a certain range in a material.</li>
</ul>
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<b>Disclaimer</b>: of course we do not claim correct reproduction of any of the data, use at own responsibility!<br />
<br />
Thanks to:<br />
<br />
<ul>
<li>Casper Christensen (programming this app)</li>
<li>Jesper Rosholm Tørresø (being Casper's supervisor and our contact person to the engineering school)</li>
<li>Jakob Toftegaard (writing most of the libdEdx backend and <a href="http://dedx.au.dk/">dedx.au.dk</a> webpage)</li>
</ul>
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<br />
Enjoy! :-)<br />
<br />
<img border="0" src="http://neptun.phys.au.dk/%7Ebassler/stat/w_ww4s.gif" />Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com2tag:blogger.com,1999:blog-1805856980450756766.post-53213636297744431602013-10-20T21:25:00.001+02:002013-10-21T14:29:57.129+02:00I Just Bought a DosimeterI recently bought a cheap personal dosimeter by the Ukrainian company <a href="http://www.soeks.eu/">SOEKS</a>. The best time to buy these is, when there has *not* recently been a nuclear disaster - prices are more reasonable then. I went for their "Defender" model, since it is capable of measuring accumulated dose, and I do not need fast counting provided by those devices with two GM-tubes.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6cxnE6eZwfZ4Yb5vkVGr7Et_qCgj6jMvkc-xXciYOWW5RQ4lxhXZk6tgZtOjEzvm-DIKXrwJcmwVea61WUI281cb1YcOolbIrtgZvySntFv_K638AgMQSnLrdAOFsz3tc65BwiNkIQLM/s1600/ffedddde03b448f729c75be78fb3b2e8.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6cxnE6eZwfZ4Yb5vkVGr7Et_qCgj6jMvkc-xXciYOWW5RQ4lxhXZk6tgZtOjEzvm-DIKXrwJcmwVea61WUI281cb1YcOolbIrtgZvySntFv_K638AgMQSnLrdAOFsz3tc65BwiNkIQLM/s1600/ffedddde03b448f729c75be78fb3b2e8.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The SOEKS Defender dosimeter. <a href="http://soeks.ru/en/catalog/dozimetr_defender/">www.soeks.ru</a></td></tr>
</tbody></table>
Ok, I said "dose", but in fact I am not sure what it measures, it should be the operational quantity "personal dose equivalent", but it could also be something completely different (see <a href="http://www.icrp.org/publication.asp?id=ICRP%20Publication%20103">ICRP 103</a>). In fact I would not be surprised if they do some sort of "dose equivalent" calibration following ICRP 26 protocol from 1971. Many still confuse this.). Just for now, I'll just call it "dose", well knowingly that this is wrong.<br />
<br />
It is the first time I order stuff from Ukraine, but shipment was really professional. They even email you a picture of your parcel with your address on, before they ship it. Contrary to some of the reports, I had no trouble with customs either. It was directly delivered to my institute address with no fuzz. Good thing!<br />
<br />
Unboxing it, I found a nifty small gadget, which fits in a pocket, It comes with rechargeable AAA batteries (SOEKS brand, these people are really dedicated!), which can be recharged via the USB connector. I might have preferred AA batteries, as these simply perform much better than AAAs. But still, nice that you can always switch to normal batteries if you are in the field, run out of power and have no time to recharge.<br />
<br />
One thing I really miss though, is a loop for attaching a lanyard. :-/<br />
<br />
Switching it on, I immediately measured the normal background radiation levels here in Aarhus, around 0.12 µSv/hour.<br />
<br />
One of the first things I tried out, was to take it along a trip to Turkey (yeah, the <a href="http://fias.uni-frankfurt.de/historical/nufra2013/">NUFRA2013 conference</a>), to see what dose I'd receive during the flight.<br />
<br />
I left it turned on while my cabin luggage was X-rayed. I did this three times, and each of these measurements gave 0.8 µSv.<br />
<br />
On board the airplane I could measure a background level of roughly 2 µSv/hour, triggering the "Dangerous radiation" warning of the dosimeter. The threshold for the warning can be adjusted by the user. The 2 µSv/hour is probably a very conservative measurement anyway, as the device does not count the contribution from neutrons.<br />
<br />
Video documentation of that flight (at roughly 10 km altitude):<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.youtube.com/embed/5p4kRMrlC-Q?feature=player_embedded' frameborder='0'></iframe></div>
<br />
Dose rate increased rapidly when we came above 8 km altitude. Under 8 km, it was pretty much just the background radiation. For the 4-5 hour trip from Antalya to Amsterdam I measured a total dose of 8.19 µSv. (This is 10 times the amount my luggage received when it was X-rayed. Very interesting.)<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFfvaKY-0XgMXe3Spc_0VfTUc890brwZh-3eS1K0ntzTHjhRwsKkyHbZ2LU9sizIhmRCbqzIbLu01NsM76Gvhp6118-3-zHM2DnL2eFVhaqxuSv6mYrvw-ezPNRl9GqVCMtu1Hh-vZInY/s1600/IMG_20131007_094249.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFfvaKY-0XgMXe3Spc_0VfTUc890brwZh-3eS1K0ntzTHjhRwsKkyHbZ2LU9sizIhmRCbqzIbLu01NsM76Gvhp6118-3-zHM2DnL2eFVhaqxuSv6mYrvw-ezPNRl9GqVCMtu1Hh-vZInY/s400/IMG_20131007_094249.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Arrived at Shiphol, Amsterdam from Antalya. Flight time 4 hours 47 minutes. Accumulated dose 8.19 µSv.</td></tr>
</tbody></table>
At our institute I can test the dosimeter at several sources. None of them are calibrated in any way, it is merely to see some signal. The strongest sources we have at the institute are couple of Americium-Beryllium sources for neutron generation. Whenever you have neutron fields you also have plenty of gammas, and if the sources is packed in a hydrogen rich moderator material there are also energetic protons (recoiling hydrogen nuclei).<br />
<br />
The AmBe source sown below is locked up in a safe, but even when the safe is closed, you can see an elevated photon background in a meters distance:<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivuHKG4tA-YfhIvS-gJjB6XIIwRrwQpNANj-YujVN3WvxGsKZWJ2pqNgJi7PzdMP3lo0nAgra-utZyojX8QDotMzwUh0EgWVNUzKtgKM6qI4AtQLeHz5YAdWvpBCKcUHF8TIkEJ-yWh00/s1600/IMG_20131018_152135.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivuHKG4tA-YfhIvS-gJjB6XIIwRrwQpNANj-YujVN3WvxGsKZWJ2pqNgJi7PzdMP3lo0nAgra-utZyojX8QDotMzwUh0EgWVNUzKtgKM6qI4AtQLeHz5YAdWvpBCKcUHF8TIkEJ-yWh00/s400/IMG_20131018_152135.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Elevated background radiation near the neutron cabinet.</td></tr>
</tbody></table>
<br />
Inside the safe, the AmBe source is located in a paraffin moderator. The source is used for various activation experiments, where you can lower the materials to be activated into the two plastic tubes.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjS2GX7DYoGSgJ5SuknPsKkzUxTCnA84ZBDs6y7PpT5iWE7DmuQeBLkpbCKMyjJ87IREq7H3MK6L0YU5wTZGWEuHrn8F7mX5DxSu4URaKItAnD2KduPhD-wt1fCq7L0yZq5zkOOA8q8K_g/s1600/IMG_20131017_145926.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjS2GX7DYoGSgJ5SuknPsKkzUxTCnA84ZBDs6y7PpT5iWE7DmuQeBLkpbCKMyjJ87IREq7H3MK6L0YU5wTZGWEuHrn8F7mX5DxSu4URaKItAnD2KduPhD-wt1fCq7L0yZq5zkOOA8q8K_g/s400/IMG_20131017_145926.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The AmBe neutron source is hidden in the paraffin block. Through the tubes you can immerse various materials for neutron activation analysis.</td></tr>
</tbody></table>
<br />
Here, I recorded the highest dose rate recorded so far, 320 µSv/hour. Again, this is probably not a very correct measure, since that area is flooded with neutrons as well. How neutron interact depends strongly on the target material.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEifKYKhgvNw3u3n1xyYp2vXMsz9-z_sNQJTVQ5GR710cfo5EP4EbrzGgU2G_6jwAVSU3fRky33G-OWy7MavYY9_n-gQOgAIhUdJWMPneKt75JckDfygeTwWbIK2WVwfmmTCaNJ2mtcuxt4/s1600/IMG_20131018_152420.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEifKYKhgvNw3u3n1xyYp2vXMsz9-z_sNQJTVQ5GR710cfo5EP4EbrzGgU2G_6jwAVSU3fRky33G-OWy7MavYY9_n-gQOgAIhUdJWMPneKt75JckDfygeTwWbIK2WVwfmmTCaNJ2mtcuxt4/s400/IMG_20131018_152420.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">320 µSv/h. Occupational limit is 20 mSv/year, public limit is 1 mSv/year, so let's quickly close the door again.</td></tr>
</tbody></table>
<br />
We have several dosimeters at the institute, so I tried to compare the elevated background with a calibrated device, the quite common and more pricey "<a href="http://www.gammascout.com/">Gamma scout</a>" dosimeter:<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1O6uMXm0Teh-6EbWlK7sqIOKMap7CGVVbIR4OcYTmAUZNV9jfoKhsDuI8fs0tgp-B4moO5IAeiD5C0WlqO6AcwiP_FysF92IwkIUH6qDsAqGl4qFCp4IYWoFrDpNfPgRkbr_PX3HAS1I/s1600/IMG_20131018_152914.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1O6uMXm0Teh-6EbWlK7sqIOKMap7CGVVbIR4OcYTmAUZNV9jfoKhsDuI8fs0tgp-B4moO5IAeiD5C0WlqO6AcwiP_FysF92IwkIUH6qDsAqGl4qFCp4IYWoFrDpNfPgRkbr_PX3HAS1I/s400/IMG_20131018_152914.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Comparison of the SOEKS Defender against a Gamma Scout. In fact this was the best agreement I ever saw between the two devices.</td></tr>
</tbody></table>
They both measure the same background to approximately 0.7 µSv/hour, but the agreement varied a lot depending where in the room I was. Mostly, I noticed a considerable underestimation of the dose reported by the SOEKS device, sometimes up to a factor of 2. Probably this is just the precision you can get, it's good enough for my (non-work related) purposes. If you want high-precision monitoring, you need professional equipment which is well calibrated, and that is certainly a different price tag.<br />
<br />
I also have a little Japanese silver medallion. I activated it by leaving it in on top of the AmBe paraffin block. Neutrons generate Ag-110 and Ag-108 isotopes with T_1/2 of 26 sec and 2.4 min, respectively. I could follow the cooling down of the medal with the dosimeter:<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjoTYx7t_N2_MBZakAnrAZoV57zyCd1GCEEBSQb3gIOKvsZEKlQmq4ebMbUaF4sEXhVtwqvs9yxbglc44WY8Z2htJR_dqgeagU3jgVGRl5nhZvGUIKqABxfQw-kC7urAZiLxuQDxfDGsg/s1600/IMG_20131018_152522.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjoTYx7t_N2_MBZakAnrAZoV57zyCd1GCEEBSQb3gIOKvsZEKlQmq4ebMbUaF4sEXhVtwqvs9yxbglc44WY8Z2htJR_dqgeagU3jgVGRl5nhZvGUIKqABxfQw-kC7urAZiLxuQDxfDGsg/s400/IMG_20131018_152522.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Japanese silver medallion activated by neutrons. After 15-30 minutes it cools down to normal background levels.</td></tr>
</tbody></table>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhw1dU3daXdiStCtRhXMyjojKaICP95scifqblYKjnLyaZn9IJjhlJ_ubLDOkKJKz6VJEEPa5B6hsbq94BS0vXQ7sQPny-lsx8ruz4oK4MSupVVCFqADx35Jttfbj6HxuvENpvQRcU9Eww/s1600/IMG_20131018_152731.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhw1dU3daXdiStCtRhXMyjojKaICP95scifqblYKjnLyaZn9IJjhlJ_ubLDOkKJKz6VJEEPa5B6hsbq94BS0vXQ7sQPny-lsx8ruz4oK4MSupVVCFqADx35Jttfbj6HxuvENpvQRcU9Eww/s400/IMG_20131018_152731.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Various sources for student exercises.</td></tr>
</tbody></table>
<br />
Anyway, I still hope to find time to realize my <a href="http://en.wikipedia.org/wiki/Chernobyl_Nuclear_Power_Plant">Chernobyl</a> visit, will certainly bring this handy device with me. :)<br />
<br />
<br />
-------------------<br />
<br />
P.s.: Not really related, I recently came across a very old video of how I in my young ages <a href="http://www.youtube.com/watch?v=jJhmONzPP5A">zapped a CCD detector using a medical linear accelerator</a>. The chip suffering in the video is an engineering grade CCD47-20 by EEV (E2V / Marconi), which was intended to fly on a satellite mission. <a href="http://link.springer.com/article/10.1007/s00411-010-0275-3#page-1">I later also irradiated one with protons</a>. (Sorry, video is a polyglot mix of German and Danish.)<br />
<br />
<img border="0" src="http://neptun.phys.au.dk/%7Ebassler/stat/w_ww4s.gif" />Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com4tag:blogger.com,1999:blog-1805856980450756766.post-86079170812881848392012-11-21T21:17:00.002+01:002012-11-22T02:11:23.252+01:00SHIELD-HIT12A demo version releasedHere is a little sneak-preview of the upcoming release of <a href="https://svn.nfit.au.dk/trac/shieldhit">SHIELD-HIT12A</a>.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghaLsTu8UxySiuMgjG2fS2SCPLgnzi57huZkvzTDELv4xcDRGVn95J2eH2zqeul-kHjUoCY6b0vWZFDhWD_S_WxVw0z46qE8Ua21ed3vv2w1DmrMQbqckIPruYYESBhbdXmHEZixqTvTo/s320/66.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghaLsTu8UxySiuMgjG2fS2SCPLgnzi57huZkvzTDELv4xcDRGVn95J2eH2zqeul-kHjUoCY6b0vWZFDhWD_S_WxVw0z46qE8Ua21ed3vv2w1DmrMQbqckIPruYYESBhbdXmHEZixqTvTo/s320/66.jpg" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://willworkforscience.blogspot.de/2010/10/monte-carlo-programs-in-particle.html">Pimp my Niva...</a> (artist's impression of SHIELD-HIT12A).</td></tr>
</tbody></table>
<br />
SHIELD-HIT12A is a <a href="http://willworkforscience.blogspot.de/2010/10/monte-carlo-programs-in-particle.html">Monte Carlo particle transport code</a> capable of transporting heavy ions through arbitrary media. The -A fork was made in 2010 from <a href="http://www.inr.troitsk.ru/shield/index.html">SHIELD-HIT08</a>, and since then we have added plenty of new features, solved many bugs, increased calculation speed and optimized the nuclear models to new data on carbon-12 fragmentation.<br />
<br />
A free demo version where the random seed and statistics are fixed to 10.000 particles can be downloaded from the <a href="https://svn.nfit.au.dk/trac/shieldhit/wiki">project development page</a>. There are builds for <a href="http://www.debian.org/devel/debian-installer/">Linux</a> and <a href="http://en.wikipedia.org/wiki/Windows_1.0">Windows</a> systems (32- and 64 bit). It is a beta-release, but we would like to bring this demo version to a broader community, and thereby hopefully also fix some more bugs before we release the full version.<br />
<br />
The new features in SHIELD-HIT12A are:<br />
<ul>
<li>New simplified material and beam parameter parser in free format and extensible without breaking downward compability.</li>
<li>Including <a href="http://physics.nist.gov/cgi-bin/Star/compos.pl">279 ICRU default materials</a> and elements, it has never been so easy to specify a material.</li>
<li>New beam model: divergence and focus distance can now be specified (thanks to Uli Weber from Marburg).</li>
<li>Arbitrary starting beam directions now possible.</li>
<li>New routine for Vavilov straggling, 5-6 times faster than the original one by <a href="http://www.sciencedirect.com/science/article/pii/0168583X9090749K">Rotondi and Montagna</a> which was used in Geant3.21. In total, this alone means a speed improvement of roughly 30-40%.</li>
<li>Ripple filter has two modes of operation, Monte Carlo type or Modulus type.</li>
<li>Logarithmic energy binning in SPC files for <a href="http://bio.gsi.de/DOCS/TRiP98/DOCS/trip98.html">TRiP</a></li>
<li>Full howto for generating DDD files for TRiP</li>
<li>Now only three input files are needed to setup a run.</li>
<li>Improved <a href="http://neptun.phys.au.dk/~bassler/SHIELD_HIT/SHIELDHIT12A_UsersGuide.pdf">documentation</a>.</li>
<li>Scoring by zones using detect.dat (complementary to Cartesian mesh and cylindrical scoring)</li>
<li>Alanine response model included, so SHIELD-HIT12A can directly calculate the dose equivalent response in alanine.</li>
<li>Flat circular and square beams can be defined</li>
<li>Neutron data for natural Argon was added (needed for detailed simulations of air)</li>
<li>Another ton of bug fixes.</li>
</ul>
<div>
Of course SHIELD-HIT12A includes the features from SHIELD-HIT10A (which was never released):</div>
<div>
<ul>
<li>Totally new (parallelizable) scoring system:</li>
<ul>
<li>Arbitrary Mesh and Cylindrical scoring</li>
<li>Lots of detectors such as energy, fluence, dose-averaged LET, track-averaged LET, average velocity (beta), dose to medium (where medium can be changed if you want to calculate stopping power ratios) etc....</li>
</ul>
<li>finally SHIELD-HIT10A is parallelizable</li>
<ul>
</ul>
<li>New random number generator, which gives a massive performance boost</li>
<li>New adjusted inelastic cross sections for carbon ions based on recent data</li>
<li>Fine tuning of the fermi-breakup parameters</li>
<li>SHIELD-HIT10A can be configured without accessing the source code anymore, so no programming knowledge required to use SHIELD-HIT10A.</li>
<li>SHIELD-HIT10A is installable</li>
<li>Runs on linux again, even when compiling with code optimizations, ok with GNU gfortran, Intel and Portland compilers.</li>
<li>Many bug fixes</li>
</ul>
<div>
Enjoy! And please drop me a line when you find bugs in the software and errors in the manual, they are there, but we hid them well. :o)</div>
</div>
<div>
<br /></div>
<div>
<br /></div>
<div>
----</div>
<div>
<br /></div>
<img border="0" src="http://neptun.phys.au.dk/%7Ebassler/stat/w_ww4s.gif" />Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com2tag:blogger.com,1999:blog-1805856980450756766.post-62528950645757521902012-11-16T11:34:00.000+01:002012-11-17T03:01:04.733+01:00Medical physics papers on the arXiv: Some statsLast year I made a post about the state of <a href="http://willworkforscience.blogspot.com/2011/01/open-access-medical-physics-and.html">open access in medical physics</a> and the use of <a href="http://arxiv.org/">arXiv.org</a> to make medical physics papers freely available to everyone. Today I've decided to follow that up by taking a look at what is going on over at arXiv.org and sorting through some of their data.<br /><br />The arXiv is "an openly accessible, moderated repository for scholarly articles in specific scientific disciplines". Beyond simply allowing all comers to read and download the articles they host, the arXiv also makes information about its vast collection easily available via a set of <a href="http://arxiv.org/help/api/index">APIs</a>. I decided to make use of the API to download meta-data (i.e. author, title, abstract, etc) for all articles in the medical physics category. Let's take a look!<br /><br />First some raw numbers. As of mid-November 2012, the <a href="http://arxiv.org/list/physics.med-ph/recent">physics.med-ph</a> category had (about) 980 articles. Those 980 articles where co-listed in 76 of the possible 126 other arXiv categories along with the medical physics category. In Figure 1 I've plotted the number of submissions by year (with a partial count for 2012). It's clear that the submission rate to physics.med-ph has greatly increased. On the plot I've fit a logistic growth curve (<a href="http://en.wikipedia.org/wiki/Gompertz_function">Gompertz</a>), as I'm assuming that the submission number will saturate at some point. You can see faint exponential and linear fits as well. The logistic model predicts 174 submissions for 2012, but 140-145 seems more likely this year.<br />
<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisomz4JSVStnpYb1_aFXFrd2TiWUe3yN7JjbdxzUJlJR71Nf0Mobcw4LAqFyFAPrJ8dmxs84hBRIZj3qsPxAj-0gpwThPphfZsb_x_DRcHvsAvJWvFlzMQfmz4M6aNqHGDvCDe4ePrHat5/s1600/arXiv-submissions-per-year2.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="301" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisomz4JSVStnpYb1_aFXFrd2TiWUe3yN7JjbdxzUJlJR71Nf0Mobcw4LAqFyFAPrJ8dmxs84hBRIZj3qsPxAj-0gpwThPphfZsb_x_DRcHvsAvJWvFlzMQfmz4M6aNqHGDvCDe4ePrHat5/s400/arXiv-submissions-per-year2.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 1. Submissions per year to the physics.med-ph category on arXiv.org.</td></tr>
</tbody></table>
<div class="separator" style="clear: both; text-align: center;">
</div>
<br />Another item of interest is how the medical physics category fits into arXiv. If you've browsed physics.med-ph before, you know that it contains a broader range of topics than the popular "medical physics" journals, such as Physics in Medicine and Biology or Medical Physics. As mentioned above, many of the 980 articles were listed in multiple categories (663 to be exact). Figure 2 shows the most popular co-categories for articles in physics.med-ph. As might be expected, biophysics (physics.bio-ph) was the most popular co-category, along with topics that seem well aligned, such as instrumentation and detectors (physics.ins-det), organs and tissues (q-bio.TO), and computational physics (physics.comp-ph). But less obvious categories were also co-submitted as well, such as chaotic dynamics (nlin.CD).<br /><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiK58Kq5oF_RScVWLzZXSj5-5SMPtzXXqTEDmKWAyvwGnyVkDEJDS-sU340hIXIclo3F0ANY6Vm5U7pRb8_64MSdXxMhPBQlx19Uq5vllsYqZMk4P1hcoECUR_qriVa7qQWpjuWGqDPsCTG/s1600/co-categories1.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="301" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiK58Kq5oF_RScVWLzZXSj5-5SMPtzXXqTEDmKWAyvwGnyVkDEJDS-sU340hIXIclo3F0ANY6Vm5U7pRb8_64MSdXxMhPBQlx19Uq5vllsYqZMk4P1hcoECUR_qriVa7qQWpjuWGqDPsCTG/s400/co-categories1.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 2. "Co-categories" of papers submitted to physics.med-ph.</td></tr>
</tbody></table>
To try to get a better idea of how these categories interplay with one another, I made some simple network graph visualizations. Figures 3 and 4 show the connections between the co-categories. All of the papers are clearly in physics.med-ph and all other categories are linked to that. The other lines in the network plots represent when a paper was simultaneously in more than two categories (e.g. medical physics, biophysics, and physics - data analysis).<br /><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;">
<!--<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgW5p8d7y19pSqcg4OQOiw8_tXTyXA35hVSk_pHrJXEz2YPql4NuOhUDMS9NoFYOfq-3okMOE1T5IFhTarvIirxcRyZKYSEA5KfDY6qj4UU_QV2nUKqaONzSI3A4mIBd1pHHx1hF_PA8grZ/s1600/network1-500px.png -->
<a href="https://www.dropbox.com/s/zuhb5jknql2q09t/network1.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgW5p8d7y19pSqcg4OQOiw8_tXTyXA35hVSk_pHrJXEz2YPql4NuOhUDMS9NoFYOfq-3okMOE1T5IFhTarvIirxcRyZKYSEA5KfDY6qj4UU_QV2nUKqaONzSI3A4mIBd1pHHx1hF_PA8grZ/s1600/network1-500px.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 3. Network graph of categories for papers submitted to physics.med-ph. Click for larger version.</td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;">
<!-- <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh01ZsYFD1lvOYl2M24-4dlIu-rJXSz13NRGIxaB4YMgfPwLTpr93v7l5PlOdAxGCUSzrHBBDyxYhYjgRljdfICxvkPv8rHeNOQrP69wgbvJXXhCFcOVZxU2AmJsgB2gwW9RZWMjXazc4th/s1600/network2-500.png" -->
<a href="https://www.dropbox.com/s/xeywnu1parsprka/network2labels2-large.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh01ZsYFD1lvOYl2M24-4dlIu-rJXSz13NRGIxaB4YMgfPwLTpr93v7l5PlOdAxGCUSzrHBBDyxYhYjgRljdfICxvkPv8rHeNOQrP69wgbvJXXhCFcOVZxU2AmJsgB2gwW9RZWMjXazc4th/s1600/network2-500.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 4. Network graph of categories for papers submitted to physics.med-ph. Click to view larger version with category labels on the nodes.</td></tr>
</tbody></table>
In Figure 4 the region near the center of the graph are the categories that are the most likely to be co-listed with other categories. As you might expect, the categories with a dense set of lines connecting them tend to also be the most frequently occurring categories, as seen in Figure 2. This is more easily seen in the <a href="https://www.dropbox.com/s/xeywnu1parsprka/network2labels2-large.png">larger version</a> of Figure 4 with category names. (click the above figure).
<br /><br />
As you can see the arXiv physics.med-ph category as a wide ranging and growing category for open access articles related to medical physics. It will be interesting to see how it fits in with the wider trends of funder mandates for open access and the general growing acceptance and demand for open access in out community.<br /><br />N.B. This arXiv meta-data is relatively easily pulled down and processed with Python tools using the arXiv API, going from XML to JSON to your computer screen at home!Royhttp://www.blogger.com/profile/14293477186383292023noreply@blogger.com3tag:blogger.com,1999:blog-1805856980450756766.post-56929053413623530352012-06-21T05:10:00.001+02:002012-06-21T05:10:51.337+02:00libdEdx 1.2.0 released - stopping powers for the masses!<span id="internal-source-marker_0.7839143734890968"></span><br />
Our master's student Jakob Toftegaard has been very busy lately, and we're now ready to release a new version of the <a href="http://libdedx.sf.net/">open-source stopping power library libdEdx</a> - <a href="https://sourceforge.net/projects/libdedx/files/">version 1.2.0</a>.<br />
<br />
<div>
Changes to the last version 1.0 are<br />
<ul>
<li><span style="background-color: white;">first of all: a new, nice and clean API. This breaks compatibility with 1.0, but we will do our best to avoid this happening again in the future. (We now have extensive use of structs, which can be extended with new members.)</span></li>
<li><span style="background-color: white;">generic ICRU table included, which combines ICRU49 and the revised ICRU73.</span></li>
<li><span style="background-color: white;">all four calculation modes in MSTAR are now supported, the default is that recommended by Helmut Paul.</span></li>
<li><span style="background-color: white;">aggregate state can be specified, following ICRU recommendations</span></li>
<li><span style="background-color: white;">I-values can be overridden for analytical functions (BETHE_EXT)</span></li>
<li><span style="background-color: white;"><dedx_tools.h> provides a bunch of new functions</dedx_tools.h></span></li>
<ul>
<li><span style="background-color: white;">calculate CSDA range</span></li>
<li><span style="background-color: white;">inverse range lookup - a given range will return required particle energy in CSDA approximation. (Yes, this is the feature you have been waiting for all your life!)</span></li>
<li><span style="background-color: white;">inverse dEdx lookup - a given stopping power will yield an energy (either high or low value, depending on what the user requested)</span></li>
</ul>
<li><span style="background-color: white;">version string of libdEdx can be accessed</span></li>
<li><span style="background-color: white;">memory leak fixes</span></li>
<li><span style="background-color: white;">typo fixes in material lists</span></li>
<li><span style="background-color: white;">code should now be thread-safe</span></li>
</ul>
And were just getting started!<br />
<br />
A <i>real gem</i> is our new web based frontend at <a href="http://dedx.au.dk/">http://dedx.au.dk</a> to libdEdx. Here you can lookup stopping power functions using various tables and energies, use it as a supplement to those from NIST. The website includes a nice plotting feature as well, where you can add multiple plots for comparison.<br />
<br />
The web frontend is still in beta-testing phase and may reside in this state for a long time. Any feedback is appreciated.<br />
<br />
We have a lot of plans regarding how to continue with this. In the next version of libdEdx we plan to include more features such as <br />
<ul>
<li><span style="background-color: white;">more Bethe-based stopping power functions such as</span></li>
<li><span style="background-color: white;">Bethe-Bloch</span></li>
<li><span style="background-color: white;">Bethe-Bloch-Barkas</span></li>
</ul>
We also would like to include additional stopping power programs such as ESTAR, ATIMA and SRIM (just the stopping power part, of course), yet the outcome will depend on the willingness of the respective authors to contribute.<br />
<ul>
<li><span style="background-color: white;">algorithms for nuclear stopping power</span></li>
<li><span style="background-color: white;">… and a surprise which we won’t reveal yet … :-)</span></li>
</ul>
Other contributors will be most welcome, the project is available on sourceforge for inspection.<br />
<br />
We greatly acknowledge our hero Helmut Paul for contributing to the development with very fruitful discussions and suggestions. We also acknowledge the permission from the ICRU to use their stopping power tables in libdEdx.<br />
<br />
Yet, we do not claim that the produced results are correct in any way, so any use of the data are on own risk. Nonetheless, if you DO find discrepancies, errors, misbehaviour of code, we would really appreciate if you tell us.<br />
<br />
Enjoy!<span style="background-color: transparent; font-weight: normal; vertical-align: baseline;"></span></div>
<img border="0" src="http://neptun.phys.au.dk/%7Ebassler/stat/w_ww4s.gif" />Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com1tag:blogger.com,1999:blog-1805856980450756766.post-30326614083566832222012-06-01T14:37:00.002+02:002012-07-10T21:33:54.847+02:00Don't Mention the WarLast year the Danish government announced that it will finance a national particle therapy facility together with some private funding agencies. Two applications were submitted for evaluation:<br />
<br />
<ul>
<li>The <a href="http://goo.gl/XouEv">Proposal for a Proton Therapy Center at Rigshospitalet</a> (located in <a href="http://en.wikipedia.org/wiki/Copenhagen">Copenhagen</a>)</li>
<li><a href="http://goo.gl/NQaJi">The Danish National Center for Particle Radiotherapy</a> (located in <a href="http://en.wikipedia.org/wiki/Aarhus">Aarhus</a>)</li>
</ul>
and of course there is a strong interest from each side to host this project. Naturally, since I am part of the <a href="http://www.phys.au.dk/aptg">Aarhus Particle Therapy Group</a>, I will right out admit I am naturally in favour of our project in Aarhus.<br />
<br />
The plan is now that an international expert commission is being setup by the ministry of health. That commission will then evaluate those two applications and give a suggestion where to place such a facility. <br />
<br />
If you compare those two applications, you will see that they both apply for a 3-gantry treatment facility. Copenhagen lock themselves on a cyclotron solution, where we in Aarhus are also open to a synchrotron based solution.<br />
<br />
Basically the differences can be summarized here:<br />
<br />
<table>
<tbody>
<tr> <td><b>Copenhagen</b></td> <td><b>Aarhus</b></td>
</tr>
<tr> <td>3 treatment rooms with 2 gantries </td> <td>3 treatment rooms with 2 gantries,<br />
+1 research room</td>
</tr>
<tr> <td>3rd gantry will be installed later</td> <td>3rd gantry will be installed later,<br />
a fourth treatment room with gantry can be added</td>
</tr>
<tr> <td>Protons</td><td>Protons</td>
</tr>
<tr> <td>Cyclotron</td><td>Cyclotron or Synchrotron</td>
</tr>
<tr> <td>1000 patients per year</td><td>1000 patients per year</td>
</tr>
</tbody></table>
<br />
<br />
So basically what we apply for is rather similar.<br />
<br />
What about the costs? If you compare those budgets, you will note that the prices of the equipment and the building are comparable too.<br />
<table>
<tbody>
<tr> <td><br /></td><td><b>Copenhagen</b></td> <td><b>Aarhus</b></td>
</tr>
<tr> <td>Equipment</td><td>450 mio. DKK </td><td>475 mio. DKK</td> </tr>
<tr> <td>Building</td><td>382 mio. DKK </td><td>295 mio. DKK</td> </tr>
<tr> <td>Supply systems and lines</td><td>195 mio. DKK </td><td>(incl. in building) </td> </tr>
<tr> <td>Purchase and demolition of Rockefeller Building</td><td>147 mio. DKK </td><td>(none) </td> </tr>
<tr> <td><i><b>Total</b></i></td><td><i><b>1174 mio. DKK </b></i></td><td><i><b>770 mio. DKK</b></i> </td> </tr>
<tr> <td>Optional 3rd gantry</td><td>(not mentioned) </td><td>75 mio. DKK </td> </tr>
</tbody></table>
<br />
Copenhagen need to build in the middle of the city, whereas we in Aarhus have a pristine green field adjacent to the <a href="http://www.dnu.rm.dk/english">New University Hospital</a>. This means that the expenses for the Copenhagen proposal are significantly higher than the Aarhus solution, since a building has to be demolished first (they have simply a lack of space in Copenhagen). The "supply lines" cover, as far as I heard, establishing extra power for the facility, please correct me if I am wrong here. The annual operational costs are also similar.<br />
<br />
There has been a few articles in the Danish press about the two applications. None of the Journalists managed to actually compare the two budgets, so basically the message was <a href="http://www.dagensmedicin.dk/nyheder/mediko-teknik/aarhus-dumper-pris-pa-partikelkanon/">that Aarhus offeres particle therapy at dumping prices</a>. Yeah right.<br />
<br />
In addition, I hear a lot of weird arguments, e.g. such a facility MUST be build in Copenhagen, since it is the capital city, and it has a proximity to the airport.<br />
<br />
Huh?<br />
<br />
How many of the existing facilities are located in capital cities? Lets pick some of the most famous ones: <a href="http://www.klinikum.uni-heidelberg.de/index.php?id=112189&L=en">HIT is in Heidelberg</a> (147.000 inhabitants, 1hours drive to next airport). <a href="http://p-therapie.web.psi.ch/">PSI is in Villingen</a>. <a href="http://www.skandionkliniken.se/">The Swedish facility is built in Uppsala</a>, and not Stockholm. Why is that so? These research institutions simply had the longest track record in terms of particle therapy! I don't get the point of the closeness of an airport either, since you can reach any point within a few hours in DK by car, and sorry guys... particle therapy is not that acute.<br />
<br />
Now, today this conflict took a very curious turn, as Copenhagen announced in <a href="http://www.dagensmedicin.dk/">Dagens Medicin</a> that they will <a href="http://www.dagensmedicin.dk/#dmPlus-access-anonymous">cut the price 75 %</a> (<i>login required to view link</i>). What is going on?<br />
It seems that Copenhagen suddenly decided to go for a single gantry facility by <a href="http://mevion.com/">Mevion</a>, formerly known as StillRiver. To me this looks like a very poor decision. The Mevion facility has been controversial for a long list of reasons. In <a href="http://informahealthcare.com/doi/abs/10.3109/0284186X.2011.582513">a scientific article by Schippers and Lomax</a> they list some of the issues with this facility:<br />
<br />
<ul>
<li>the very compact design of the cyclotron, may lead to large beam losses and resulting activation. </li>
<li>repetition frequency of synchrocyclotrons are typically 1kHz which limits applicability of the different pencil beam scanning methods.</li>
<li>There is no beam analysis and no magnets in the beam path, in other words an energy selection system is missing. This means that the beam will have a poor distal edge, always looking as if it traversed 25-30 cm of material, e.g. when treating head an neck cancers. This limits possible treatment planning techniques, such as patch fields.</li>
<li>Neutron contamination may be an issue, due to the proximity of the degrader, modulator and collimator(s). </li>
</ul>
To this, I might add that the construction of the prototype is still awaiting FDA approval, and we have not seen any data on how this machine operates. We are just in the middle of a never ending scandal about a couple of <a href="http://en.wikipedia.org/wiki/IC4">diesel IC4 trains</a> ordered from <a href="http://en.wikipedia.org/wiki/AnsaldoBreda">AnsaldoBreda</a> a decade ago, where the trains still are not functional and with a significant risk that they never will be. Billions of taxpayer money are lost here. Most Danes are therefore allergic to order unproven technology abroad.<br />
<br />
<i>Update: <a href="http://campaign.r20.constantcontact.com/render?llr=8gm8pjiab&v=0018sxp1v_8zeOFfqbPAzi0W6QFV1cCJsnPlWRa-qMpE4TYW1eNPpI4i0Bmc7StTt9nTSslXuCLeioufFa9E9iB5ZfXBmCjJc7p7NaR_PMDMw0%3D">Mevion just got their FDA approval.</a></i><br />
<br />
<i>Another update: it's a "Premarket Notification" and not a "New Device Approval". <a href="http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpmn/pmn.cfm?ID=39132">Read it here</a>. Thanks to <a href="http://www.scienceblog.dk/">Klaus Seiersen</a> for pointing this out.</i><br />
<br />
The recent article in Dagens Medicin does not even mention that cutting 75% of the price leads to a single-gantry facility, which means the patient numbers needs to be adjusted down, perhaps by 2/3rds.<br />
<br />
Finally, if you need three treatment rooms, then measured in costs per treatment room, a conventional solution is cheaper than the Mevion solution, according to Schippers. <br />
<br />
I am very astonished, it seems that Copenhagen just scored an own goal. However, I fear this may delay the decision process even more. In the end <b>this is about patients</b>, and if the money is there, we should not be satisfied with giving our patients the most inferior kind of proton therapy, and rely on unproven technology.<br />
<br />
<img border="0" src="http://neptun.phys.au.dk/%7Ebassler/stat/w_ww4s.gif" />Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com0Aarhus County, Denmark56.162939 10.20392156.092206000000004 10.045992499999999 56.233672 10.3618495tag:blogger.com,1999:blog-1805856980450756766.post-53072260745267216112012-01-22T22:01:00.006+01:002012-02-13T18:02:36.067+01:00The Quick and Dirty Guide for Parallelizing FLUKA<i>(Single PC version)</i><br />
<br />
Imagine you got a desktop or laptop PC with 4 or perhaps even 8 CPU cores available, and you want to run the Monte Carlo particle transport program <a href="http://www.fluka.org/">FLUKA</a> on it using all CPU cores.<br />
The FLUKA execution script <i>rfluka </i>however was designed to run in "serial" mode. That is, if you request to repeat your simulation a lot of times (say, 100) issuing the command <i>rfluka -N0 -M100 example</i>, each process is launched serially, instead of utilizing all available cores on your PC.<br />
<br />
A solution can be to use a job queuing system and a scheduler. Here, I'll present one way to do it on a <a href="http://www.debian.org/">Debian</a> based Linux system. <a href="http://www.ubuntu.com/">Ubuntu</a> might work just as well, since Ubuntu is very similar to Debian. A feature of the method presented here, is that it can easily be extended to cover several PCs on your network, so you can use the computing power of your colleagues when they do not use their PCs (e.g. at night). However, this post will try to make it very simple, namely set it just on your own PC. In less than 10 minutes you'll have it up and running...<br />
<br />
The idea is to use <a href="http://www.adaptivecomputing.com/products/torque.php">TORQUE</a> in a very minimal configuration. There will be no fuzz with <a href="http://www.clusterresources.com/pages/products/maui-cluster-scheduler.php">Maui</a> or similar schedulers, we will only use packages we can get from the Debian/Ubuntu software repositories.<br />
In order to be friendly to all the Ubuntu users out there, all commands issued as root are here prefixed with the "sudo" command. As a Debian user you can become root using the "su" command first. <br />
<br />
First install these packages:<br />
<br />
<pre>$ sudo apt-get install torque-server torque-scheduler
$ sudo apt-get install torque-common torque-mom libtorque2
</pre>and either<br />
<pre>$ sudo apt-get install torque-client
</pre>or<br />
<pre>$ sudo apt-get install torque-client-x11
</pre><br />
after installation we need to setup torque properly. I here assume that your PC hostname cannot be resolved by DNS, which is quite common on small local networks. You can test whether your hostname can be resolved by the "host" command. Assuming your PC has the name "kepler", you may get an answer like:<br />
<br />
<pre>$ host $HOSTNAME
Host kepler not found: 3(NXDOMAIN)
</pre><br />
this means you may need to edit the <i>/etc/hosts</i> file, so your PC can associate an IP number with your hostname. Debian like distros may have a propensity to assign the hostname to 127.0.1.1 which will <b>not</b> work with torque. Instead I looked up my IP number (which in my case is pretty static) using <i>/sbin/ifconfig</i>, and edited the <i>/etc/hosts</i> accordingly, using your favourite text editor (emacs, gedit, vi...)<br />
My <i>/etc/hosts</i> file ended up looking like this:<br />
<br />
<pre>127.0.0.1 localhost
#127.0.1.1 kepler.lan kepler
192.168.1.108 kepler
</pre><br />
If your hostname of your PC can be resolved, you can ommit the last line, but under all circumstances <i>you must</i> comment out the line starting with 127.0.1.1.<br />
<br />
<br />
Once this is done, execute the following commands to configure torque:<br />
<pre>$ sudo echo $HOSTNAME > /etc/torque/server_name
$ sudo echo $HOSTNAME > /var/spool/torque/server_name
$ sudo pbs_server -t create
$ sudo echo $HOSTNAME np=`grep proc /proc/cpuinfo | wc -l` > /var/spool/torque/server_priv/nodes
$ sudo qterm
$ sudo pbs_server
$ sudo pbs_mom
</pre><br />
(Update: If qterm fails, you probably have a problem with your /etc/hosts file. You can still kill the server with $killall -r "pbs_*".)<br />
<br />
Now let's see if things are running as expected:<br />
<pre>$ pbsnodes -a
kepler
state = free
np = 4
ntype = cluster
status = rectime=1326926041,varattr=,jobs=,state=free,netload=3304768553,gres=,loadave=0.09,ncpus=4,physmem=3988892kb,availmem=6643852kb,totmem=7876584kb,idletime=2518,nusers=2,nsessions=8,sessions=1183 1760 2170 2271 2513 15794 16067 16607,uname=Linux kepler 3.1.0-1-amd64 #1 SMP Tue Jan 10 05:01:58 UTC 2012 x86_64,opsys=linux
</pre><br />
and also<br />
<pre>$sudo momctl -d 0 -h $HOSTNAME
Host: kepler/kepler Version: 2.4.16 PID: 16835
Server[0]: kepler (192.168.1.108:15001)
Last Msg From Server: 279 seconds (CLUSTER_ADDRS)
Last Msg To Server: 9 seconds
HomeDirectory: /var/spool/torque/mom_priv
MOM active: 280 seconds
LogLevel: 0 (use SIGUSR1/SIGUSR2 to adjust)
NOTE: no local jobs detected
</pre><br />
Now setup a queue, which here is called "batch".<br />
<pre>$ sudo qmgr -c 'create queue batch'
$ sudo qmgr -c 'set queue batch queue_type = Execution'
$ sudo qmgr -c 'set queue batch resources_default.nodes = 1'
$ sudo qmgr -c 'set queue batch resources_default.walltime = 01:00:00'
$ sudo qmgr -c 'set queue batch enabled = True'
$ sudo qmgr -c 'set queue batch started = True'
$ sudo qmgr -c 'set server default_queue = batch'
$ sudo qmgr -c 'set server scheduling = True'
</pre><br />
[<i>update: you may want to increase walltime to 10:00:00 so jobs dont stop after 1 hour</i>] <br />
<br />
and start the scheduler:<br />
<pre>$ sudo pbs_sched
</pre><br />
The rest of the commands can be issued as a normal user (i.e. non-root).<br />
<br />
Let's see if all servers are running:<br />
<pre>$ ps -e | grep pbs
1286 ? 00:00:00 pbs_mom
1293 ? 00:00:00 pbs_server
2174 ? 00:00:00 pbs_sched
</pre><br />
Anything in the queue?<br />
<pre>$ qstat
$
</pre>Nope, it's empty.<br />
<br />
Lets try to submit a simple job<br />
<pre>echo "sleep 20" | qsub
</pre><br />
and within the next 20 seconds you can test, if its in the queue:<br />
<pre>$ qstat
Job id Name User Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
0.kepler STDIN bassler 0 R batch
</pre><br />
<br />
Great, now were ready to rock 'n roll! This is really a minimalistic setup, which just works. For more bells and whistles, check the <a href="http://www.clusterresources.com/torquedocs/index.shtml">torque manual</a>.<br />
<br />
All we need, is a simple FLUKA job submission script: <a href="http://neptun.phys.au.dk/%7Ebassler/FLUKA/scripts/rtfluka.sh">rtfluka.sh</a> <br />
<pre style="background: #ffffff; color: black;"><span style="color: dimgrey;">#!</span><span style="color: #007997;">/bin/bash</span>
<span style="color: dimgrey;">#</span>
<span style="color: dimgrey;"># how to use this</span>
<span style="color: dimgrey;"># change to directory with the files you want to run</span>
<span style="color: dimgrey;"># and enter:</span>
<span style="color: dimgrey;"># $ qsub -V -t 0-9 -d . rtfluka.sh</span>
<span style="color: dimgrey;">#</span>
<span style="color: dimgrey;">#PBS -N FLUKA_JOB</span>
<span style="color: dimgrey;">#</span>
<span style="color: #797997;">start</span><span style="color: #808030;">=</span><span style="color: #0000e6;">"</span><span style="color: #797997;">$PBS_ARRAYID</span><span style="color: #0000e6;">"</span>
<span style="color: #bb7977; font-weight: bold;">let</span> <span style="color: #797997;">stop</span><span style="color: #808030;">=</span><span style="color: #0000e6;">"</span><span style="color: #797997;">$start</span><span style="color: #0000e6;">+1"</span>
<span style="color: #797997;">stop_pad</span><span style="color: #808030;">=</span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: black;">`</span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: #bb7977; font-weight: bold;">printf</span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: black;"> </span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: #0000e6;">"%03i</span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: #0f69ff;">\n</span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: #0000e6;">"</span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: black;"> </span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: #797997;">$stop</span><span style="background: none repeat scroll 0% 0% rgb(255, 255, 232); color: black;">`</span>
<span style="color: dimgrey;">#</span>
<span style="color: dimgrey;"># Init new random number sequence for each calculation. </span>
<span style="color: dimgrey;"># This may be a poor solution.</span>
cp <span style="color: #797997;">$FLUPRO</span><span style="color: #40015a;">/random.dat</span> ranexample<span style="color: #797997;">$stop_pad</span>
<span style="color: #bb7977; font-weight: bold;">sed</span> -i <span style="color: #0000e6;">'/RANDOMIZE 1.0/c\RANDOMIZE 1.0 '</span><span style="color: #0000e6;">"</span><span style="color: #797997;">${RANDOM}</span><span style="color: #0000e6;">"</span><span style="color: #0000e6;">'.0 \'</span> example<span style="color: maroon; font-weight: bold;">.</span>inp
<span style="color: #797997;">$FLUPRO</span><span style="color: #40015a;">/flutil/rfluka</span> -N<span style="color: #797997;">$start</span> -M<span style="color: #797997;">$stop</span> example <span style="color: #44aadd;">-e</span> flukadpm3
</pre><br />
<i>Update: </i>Note that your RANDOMIZE card in your own .inp file must match the sed regular expression above, else you may repeat the exact same simulation over and over again... <br />
<br />
<br />
Let's submit 10 jobs:<br />
<pre>$ qsub -V -t 0-9 -d . rtfluka.sh
</pre><br />
And watch the blinkenlichts.<br />
<pre>$ qstat
Job id Name User Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
15-0.kepler FLUKA_JOB-0 bassler 0 R batch
15-1.kepler FLUKA_JOB-1 bassler 0 R batch
15-2.kepler FLUKA_JOB-2 bassler 0 R batch
15-3.kepler FLUKA_JOB-3 bassler 0 R batch
15-4.kepler FLUKA_JOB-4 bassler 0 Q batch
15-5.kepler FLUKA_JOB-5 bassler 0 Q batch
15-6.kepler FLUKA_JOB-6 bassler 0 Q batch
15-7.kepler FLUKA_JOB-7 bassler 0 Q batch
15-8.kepler FLUKA_JOB-8 bassler 0 Q batch
15-9.kepler FLUKA_JOB-9 bassler 0 Q batch
</pre><br />
Surely, this can be improved a lot, suggestions are most welcome in the comments below. One problem is for instance, that the random number seed is limited to a 16 bit integer, which only covers a very small fraction of the possible seeds for the RANDOMIZE card.<br />
<i>Update: </i>There is also a very small risk that the same seed occasionally is used twice (or more often). Alternatively one could just add a random number to a starting seed after each run. (Any MC random number experts out there?)<br />
<br />
Output data can be processed in regular ways, using <a href="http://www.fluka.org/flair/">flair</a>. <br />
Alternatively you may use some of the scripts in the <a href="http://sourceforge.net/projects/auflukatools/">auflukatools</a> package, which for instance can do the merging of USRBIN output with a single command. Auflukatools also includes <i>rtfluka.sh</i> as well as a CONDOR job submission script <i>rcfluka.py</i>, which is better suited for heterogenous clusters.<br />
<br />
Finally, here is a job script for <a href="https://svn.nfit.au.dk/trac/shieldhit">SHIELD_HITxxA</a>, (which is even shorter):<br />
<br />
<pre style="background: #ffffff; color: black;"><span style="color: dimgrey;">#!</span><span style="color: #007997;">/bin/bash</span>
<span style="color: dimgrey;">#</span>
<span style="color: dimgrey;"># how to use</span>
<span style="color: dimgrey;"># change to directory you want to run</span>
<span style="color: dimgrey;"># $ qsub -V -t 0-9 -d . rtshield.sh</span>
<span style="color: dimgrey;">#</span>
<span style="color: dimgrey;">#PBS -N SHIELD_JOB</span>
shield_exe -N<span style="color: #797997;">$PBS_ARRAYID</span>
</pre><br />
Enjoy!<br />
<br />
Totally unrelated: <a href="http://englishrussia.com/">englishrussia.com</a> just posted some nice pics from the <a href="http://en.wikipedia.org/wiki/Budker_Institute_of_Nuclear_Physics">Budker institute for Nuclear Physics</a> in Novosibirsk, Russia. Certainly worth visiting, have a look at: <br />
<a href="http://englishrussia.com/2012/01/21/the-budker-institute-of-nuclear-physics/">http://englishrussia.com/2012/01/21/the-budker-institute-of-nuclear-physics/</a><br />
:-) Heaps of pioneering accelerator technology was developed there, such as <a href="http://en.wikipedia.org/wiki/Electron_cooling">electron cooling</a>, the first collider, lithium lenses (e.g. for capturing antiprotons), and they supplied the conventional magnets for the beam transfer lines to the LHC at CERN. I visited the center many years ago but <a href="https://picasaweb.google.com/niels.bassler/AcceleratorsOfTheWorldNovosibirskRussia?authuser=0&feat=directlink">my pics are not as good</a>. :-/ The German <a href="http://de.wikipedia.org/wiki/Gersch_Izkowitsch_Budker">wiki about Budker</a> himself, is also worth reading.<br />
<br />
<div class="separator" style="clear: both; text-align: center;"></div><br />
<img border="0" src="http://neptun.phys.au.dk/%7Ebassler/stat/w_ww4s.gif" />Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com12Aarhus, Denmark56.162939 10.20392100000003756.1034075 10.130644000000038 56.2224705 10.277198000000036tag:blogger.com,1999:blog-1805856980450756766.post-88996441164176571772012-01-11T20:01:00.001+01:002012-01-16T01:08:20.232+01:00Visit at the Primary Standards Laboratory in SlovakiaThis post is not related to computing, but more to medical physics. Primary standards dosimetry laboratories (PSDL) are important for medical physicists, since they define fundamental quantities such as dose. If you buy some dosimeter, say, an ionization chamber, it is most likely calibrated at a PSDL (for ample amounts of money) or a secondary standards dosimetry laboratory (SSDL) which is linked towards a PSDL. <a href="http://www-naweb.iaea.org/nahu/dmrp/ssdl.asp">Not all countries have a PSDL or SSDL</a>, and some countries (like <a href="http://en.wikipedia.org/wiki/Slovakia">Slovakia</a> in this case) have both PSDL and a SSDL facilities. To my knowledge, Denmark quite recently got the SSDL status at the <a href="http://www.sis.dk/">National Institute for Radioprotection</a>.<br />
<br />
During summer vacation 2011, after finishing the run at CERN, <a href="http://opasnajazona.blogspot.com/2011/08/dresden-i-wave-of-capitalism.html">I had a rather messy tour across Europe</a> and also went to <a href="http://en.wikipedia.org/wiki/Bratislava">Bratislava</a> to visit some friends. Here I got the chance to get a tour of the Slovakian PSDL at the Metrological <span style="font-size: x-small;">(not to mistaken with the Meteological)</span> Institute. It is my second vist at a PSDL - a few years ago, I visited the PSDL at the <a href="http://www.npl.co.uk/">National Physical Laboratory</a> in the UK, but I only got crappy mobile phone pictures.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxeJhkuU2ZU4mGBZe7lN7pWX4PU8ZuDYGtSFOYo6lVcg8J2uWk8EoyedSX_2keTtnCLmgL6fOD0JP4mh7bYXlWBtUjIVFuCjlzvBg36TgUiioFgTA3eyWc2roswAWF_F1HBkScDQifFgE/s1600/DSC_0497.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxeJhkuU2ZU4mGBZe7lN7pWX4PU8ZuDYGtSFOYo6lVcg8J2uWk8EoyedSX_2keTtnCLmgL6fOD0JP4mh7bYXlWBtUjIVFuCjlzvBg36TgUiioFgTA3eyWc2roswAWF_F1HBkScDQifFgE/s400/DSC_0497.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The Metrological Institute of Slovakia, Bratislava.</td></tr>
</tbody></table><br />
The director of the institute, Jozef Dobrovodsky gave me a tour of the facility. They have a close cooperation with the NPL - most physicists working with particle therapy may have heard of proton dosimetry expert Hugo Palmans who works at NPL near London, but (quite conveniently) actually lives in Bratislava.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjx8YCzmjnkzwzN40kHjxrNPOY3g1gxPuiU2pIaHvmyeNUi-XWyjwnJB-7T0AHuSMBKzkfsvKsgMnMMPMYny78gs59KDcvkKzh7MS5soqhb9QbraYVa35kcZQuizR3JaVI80zox8lGZMVY/s1600/DSC_0511.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjx8YCzmjnkzwzN40kHjxrNPOY3g1gxPuiU2pIaHvmyeNUi-XWyjwnJB-7T0AHuSMBKzkfsvKsgMnMMPMYny78gs59KDcvkKzh7MS5soqhb9QbraYVa35kcZQuizR3JaVI80zox8lGZMVY/s400/DSC_0511.JPG" width="266" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Jozef and Hugo looking at Roos plane parallel ionization chambers from PTW, well suited for measuring depth-dose curves of pencil shaped ion beams.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsnM1RbqK_hIiN-REAoATyu4O3Lr9XQGk6JwjMJB2dqwgoy0UHp1JyYGhAc4-Le1nCGqK0JX-zKIz5xIUUazRhRBNvyEBhmNkhFG0OHBGeMmdb9fnM3U5kme7aHiPqtiHl3HairEbFOkY/s1600/DSC_0513.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="265" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsnM1RbqK_hIiN-REAoATyu4O3Lr9XQGk6JwjMJB2dqwgoy0UHp1JyYGhAc4-Le1nCGqK0JX-zKIz5xIUUazRhRBNvyEBhmNkhFG0OHBGeMmdb9fnM3U5kme7aHiPqtiHl3HairEbFOkY/s400/DSC_0513.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Outline of the facility.</td></tr>
</tbody></table>The facility has a Betatron, a <a href="http://en.wikipedia.org/wiki/Co-60">Cobalt-60</a> unit, a 320 kV X-ray unit, a <a href="http://en.wikipedia.org/wiki/Cs-137">Caesium-137</a> irradiator and a neutron vault with various neutron sources.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwgVzqJufnrGmAv1DgbjRhJzgTIcb1-IAUncaqpkI7gX4TzDAfrtin6virKysbkqA2s1ALXwIwaKtph9tVgqpUFZNNOoFSBREEXGSvue80-sUi2fxbMvg6jtw85JLQhkxODctxDWP3a_g/s1600/DSC_0518.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="265" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwgVzqJufnrGmAv1DgbjRhJzgTIcb1-IAUncaqpkI7gX4TzDAfrtin6virKysbkqA2s1ALXwIwaKtph9tVgqpUFZNNOoFSBREEXGSvue80-sUi2fxbMvg6jtw85JLQhkxODctxDWP3a_g/s400/DSC_0518.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Mock-up models of Cs-137 sources (these are NOT radioactive).</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOlXLtMxiq-mGLi02rN9LPLfC76DKuXExmvC5c8DH2p47Q4-UCakvTFjRiNryiCR_tx6ygHeo3rtXgnf-g73od6zH2lOq4i-jP6z9pS8RHpCSgAy-KXG0rx6wnNG95pzEWIWaX-fH7Qvo/s1600/DSC_0519.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="265" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOlXLtMxiq-mGLi02rN9LPLfC76DKuXExmvC5c8DH2p47Q4-UCakvTFjRiNryiCR_tx6ygHeo3rtXgnf-g73od6zH2lOq4i-jP6z9pS8RHpCSgAy-KXG0rx6wnNG95pzEWIWaX-fH7Qvo/s400/DSC_0519.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A part of the control room, with the very well known UNIDOS electrometer by PTW, <a href="http://willworkforscience.blogspot.com/2011/07/antiproton-radiotherapy-experiments-at.html">which I worked a lot with e.g. while at CERN</a>.</td></tr>
</tbody></table>Probably the most important room is where the Co-60 irradiator is kept. Co-60 has a long history serving as reference radiation for a wide range of dosimetric tasks. Beam quality is usualy expressed relative to Co-60 standard. However, Co-60 irradiators are getting rare. Radiation treatment with Co-60 is rather something seen in developing countries, at most hospitals they were replaced with megavolt linear accelertors, also for safety issues. (Messing with radioactive sources is always a bad thing and should be avoided). As a researcher, it gets increasingly difficult to get access to a proper reference radiation.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhl2HacHdprdEIjEd2DFlutg9L7poM_cJhADRYniTKZ0qRiSXXXH12bqG1swi1A41TFJdCKdOxiiEmD7n1qkWjbprUaAy3K9Jp4yVNxD9uAB0JG8iVAWaQeUzhJP6aBynnaLack04unqbg/s1600/DSC_0524.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhl2HacHdprdEIjEd2DFlutg9L7poM_cJhADRYniTKZ0qRiSXXXH12bqG1swi1A41TFJdCKdOxiiEmD7n1qkWjbprUaAy3K9Jp4yVNxD9uAB0JG8iVAWaQeUzhJP6aBynnaLack04unqbg/s400/DSC_0524.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The yellow box holds the Co-60 source, behind the tank an additional collimator is visible which can be mounted in front of the Co-60 unit.</td></tr>
</tbody></table><div class="separator" style="clear: both; text-align: center;"></div><br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh23xDmT1XImJHgLpKAed8a2gKpuOfj1iZR_XEzx3dbOdm5TrjrFhlY9R4L_-gztlGcWYLl2rbzKKegqj9uh8UAR-BGZiJHVdNhVUBxZm-srag50HGEYy31zPSl7JYi1bQtNPFSF7lV-i8/s1600/DSC_0523.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh23xDmT1XImJHgLpKAed8a2gKpuOfj1iZR_XEzx3dbOdm5TrjrFhlY9R4L_-gztlGcWYLl2rbzKKegqj9uh8UAR-BGZiJHVdNhVUBxZm-srag50HGEYy31zPSl7JYi1bQtNPFSF7lV-i8/s400/DSC_0523.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Co-60 irradiation room. The tank holds a Markus ionization chamber, and the dose-rate can be reduced by increasing the distance to the Co-60 irradiation unit.</td></tr>
</tbody></table>Next we took a look at the X-ray irradiation room. X-rays have lower energies than Co-60 and are made electrically and not from a radioactive source.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxZ_4I9fQ-6S9uQhfAd577hfWqcYjH1_DUiV751aFueoIZQ79NKzoq6ukgOVTZyHFZQNKcdBNMLPRmVlyByILOMjp49yHtJpMzvs4RMRj-JsHyJoHnFdfohPWnaT-A-C0dXZbsHQv-7Es/s1600/DSC_0537.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxZ_4I9fQ-6S9uQhfAd577hfWqcYjH1_DUiV751aFueoIZQ79NKzoq6ukgOVTZyHFZQNKcdBNMLPRmVlyByILOMjp49yHtJpMzvs4RMRj-JsHyJoHnFdfohPWnaT-A-C0dXZbsHQv-7Es/s400/DSC_0537.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Two X-ray sources are seen here, one in the background with wheels of various copper filers which can be positioned in the beam. Copper filters can remove characteristic lines of the X-ray spectrum, thereby flattening it. In front an X-ray diagnostic device is visible.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjnG1DEKgqwENkSC1O4hyphenhyphenANEMIRicoDrJaZ3boogSuC7Z1i6c6TagsQ06kcOVJzsEggM2G2vRJrFSgduXJZE9gP031l73lvoahpqZUfYtZ-F4Sb2PzrZoIrvAHangBQDGJ-2UFljomjXNA/s1600/DSC_0540.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjnG1DEKgqwENkSC1O4hyphenhyphenANEMIRicoDrJaZ3boogSuC7Z1i6c6TagsQ06kcOVJzsEggM2G2vRJrFSgduXJZE9gP031l73lvoahpqZUfYtZ-F4Sb2PzrZoIrvAHangBQDGJ-2UFljomjXNA/s400/DSC_0540.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">How to make 90 Volts. :)</td></tr>
</tbody></table><div class="separator" style="clear: both; text-align: center;"></div>Cs-137 provide a photon field at about half the energy of the MeV Co-60 photons.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVnIpLSjHr1FGVAnCF5hTmAjlsKdkVYQYxQpbVajxegVVtT1H0_xrR-exQCTmJQX24lD4AbBDXxmgvRrjKSUy21U820LGK1c9PcGHQwVYbv19CsRmJdLdEKJhy7m12nGtSZR0pyd2RItM/s1600/DSC_0550.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVnIpLSjHr1FGVAnCF5hTmAjlsKdkVYQYxQpbVajxegVVtT1H0_xrR-exQCTmJQX24lD4AbBDXxmgvRrjKSUy21U820LGK1c9PcGHQwVYbv19CsRmJdLdEKJhy7m12nGtSZR0pyd2RItM/s400/DSC_0550.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Cs-137 irradiation room.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEir38JWDTNJTBOPH8iEkiGShejYwtHv6HhnBekjPq15P6gfVQ6p7lGH6GPebGSVxHkII2y3Ltf0yTSqF2-mLv7AHyJLnS8tqKdGD1vyNhOd_edXRX0Dei9ykrJPHetKXLB7zUPy0OHvo1o/s1600/DSC_0549.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEir38JWDTNJTBOPH8iEkiGShejYwtHv6HhnBekjPq15P6gfVQ6p7lGH6GPebGSVxHkII2y3Ltf0yTSqF2-mLv7AHyJLnS8tqKdGD1vyNhOd_edXRX0Dei9ykrJPHetKXLB7zUPy0OHvo1o/s400/DSC_0549.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Cs-137 irradiator seen from the front. Aperture can slide to the right, exposing the room to the source.</td></tr>
</tbody></table>A real gem was their <a href="http://en.wikipedia.org/wiki/Betatron">Betatron</a>: it's a Czech construction, which can deliver both electron and photon beams. The betatron is an old design originally invented by the Norwegian Widerøe, who also invented the idea of drift tubes, widely used at almost any accelerator today. Betatrons (especially <i>functioning</i> betatrons) are a very rare sight today, most were replaced with LINACs long time ago. I once saw a betatron at the physics department of Freiburg in Germany, but it was not operational anymore. This one however is still functioning! (Look how clean and tidy it is... I am used to messy laboratories.)<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6GFO8URJz-irCMzpOUPQCqJClSZaSOVYImTjVEZuKuCjY0XuY7kqnbnQaASDOC9LK2j0cAJxrHkj96mem8O0AXR1Xoex2zVS7qizJNNCuHpOEaFKiWlkUTEN0JDdEWMKL3V33dmT3c68/s1600/DSC_0567.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6GFO8URJz-irCMzpOUPQCqJClSZaSOVYImTjVEZuKuCjY0XuY7kqnbnQaASDOC9LK2j0cAJxrHkj96mem8O0AXR1Xoex2zVS7qizJNNCuHpOEaFKiWlkUTEN0JDdEWMKL3V33dmT3c68/s400/DSC_0567.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Second time I ever see a betatron. Yay! :-)</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUSXciq63i4vRgFgE2wx41Wd1_BpmJIESAc9gZiL_9ovYwIpyMidlQI7nG3An3KvkXAdc9J4y1Rb1jAeWX-U6nwmsUEsI436DVomuS2IyxsHdlf1NvGkSc7DfZAxznTMk-eY3_7z05iao/s1600/DSC_0560.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUSXciq63i4vRgFgE2wx41Wd1_BpmJIESAc9gZiL_9ovYwIpyMidlQI7nG3An3KvkXAdc9J4y1Rb1jAeWX-U6nwmsUEsI436DVomuS2IyxsHdlf1NvGkSc7DfZAxznTMk-eY3_7z05iao/s400/DSC_0560.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">You can extract either photons or electrons on either side. This is the photon exit (I think).</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizCbVRnDluSg8RLxIa_vnCCdeJVk8ptpGL79xFap-vJnHeuSSDUeRbX1jTY6LTuPUdJ0_CzCkNO-TPVkvjhYPcyKZMAgyq3kUVYmFpC3DvUlOfLduBnDNEgHbgxy3FWPCm1llCbT-R35Q/s1600/DSC_0557.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizCbVRnDluSg8RLxIa_vnCCdeJVk8ptpGL79xFap-vJnHeuSSDUeRbX1jTY6LTuPUdJ0_CzCkNO-TPVkvjhYPcyKZMAgyq3kUVYmFpC3DvUlOfLduBnDNEgHbgxy3FWPCm1llCbT-R35Q/s400/DSC_0557.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">They even had a spare betatron tube, heavily tarnished by radiation damage to the glass.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEirpPRN4ND2EJmdgxMtcsBzCRy8KurmSmzPvmyOljPZw6YMNPKJLl6IAluREikl8ixiH6_oUQqavhM3BUDk-gzFIJcl-Hyzz7OOK5cKofNvaD9uBSEaomYvwaGjoD9HxtL6BVYBCWmpxg8/s1600/DSC_0553.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEirpPRN4ND2EJmdgxMtcsBzCRy8KurmSmzPvmyOljPZw6YMNPKJLl6IAluREikl8ixiH6_oUQqavhM3BUDk-gzFIJcl-Hyzz7OOK5cKofNvaD9uBSEaomYvwaGjoD9HxtL6BVYBCWmpxg8/s400/DSC_0553.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Control console for the betatron. Nice and sleek.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjG-08MObIpU3jwV7kQpGcd2gjCVSYSG_P81f-yvoyBlvfxzq9ZAg2DTtjFP6tVyrgFviPEK3O0LCJEmYVX-F1Fsn80D49EUbHw6w_4LEUoDlyhL7aswbEtnMXpLuF297ydj18JAFQ8v1k/s1600/DSC_0572.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjG-08MObIpU3jwV7kQpGcd2gjCVSYSG_P81f-yvoyBlvfxzq9ZAg2DTtjFP6tVyrgFviPEK3O0LCJEmYVX-F1Fsn80D49EUbHw6w_4LEUoDlyhL7aswbEtnMXpLuF297ydj18JAFQ8v1k/s400/DSC_0572.JPG" width="266" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Power supply and controls for the betatron. Many components are still genuine Czech, manufactured by TESLA.</td></tr>
</tbody></table>Finally we visited the neutron vault. Here they had three neutron irradiators: two different accelerator based sources and a range of radioactive neutron emitters. The neutron sources were kept in a cave in the floor shielded with lots of plastic material for neutron moderation/absorption. The sources they have are quite common. Some intense alpha source (Plutonium or Americium) mixed with some light material (Beryllium). A Californium source was also there which fissions spontaneously.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjP7wuxdagpkAfHM4YZLQgRUETOLfMJ_cAKCd-kzGP4Iw5X2Ysv9M1fbSMbTrNKMhY18g3Ufy0GUnK8Qey0wBTaNswU2M9zDZf7QsAelV8vauz_nL-rEgannaC15fbFrPVf0C8zG_KNMCg/s1600/DSC_0585.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjP7wuxdagpkAfHM4YZLQgRUETOLfMJ_cAKCd-kzGP4Iw5X2Ysv9M1fbSMbTrNKMhY18g3Ufy0GUnK8Qey0wBTaNswU2M9zDZf7QsAelV8vauz_nL-rEgannaC15fbFrPVf0C8zG_KNMCg/s400/DSC_0585.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Neutron vault. In the floor several neutron sources are kept, and can be raised out of the cave by the visible holder. I was a bit hesitant, when the scientist suddenly pulled a string, and the holder surfaced out of the neutron cave, as shown on this picture. “Is it empty?!” “Sure it's empty.”</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1BknEjO-64MhM73ZT1KbyVnQyvfHh6swc5kKAPSzJMywz3zAuNI_fyTOtsmImrzvGs81BynvFZ_q4EqsO4q2wviYfLLjgIOMktghbQvG7myN5G8FxyOo2t9SFYChMepOigq2qK3GuqoU/s1600/DSC_0591.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1BknEjO-64MhM73ZT1KbyVnQyvfHh6swc5kKAPSzJMywz3zAuNI_fyTOtsmImrzvGs81BynvFZ_q4EqsO4q2wviYfLLjgIOMktghbQvG7myN5G8FxyOo2t9SFYChMepOigq2qK3GuqoU/s400/DSC_0591.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This accelerator was very cute: protons accelerated towards a <a href="http://en.wikipedia.org/wiki/Tritium">tritium</a> target produces a neutron beam. The design of the high voltage terminal looks very much like the design found in the terminal of our <a href="http://opasnajazona.blogspot.com/2011/08/5-mv-van-de-graaff-accelerator.html">Van de Graaf KN machine in Aarhus</a>.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEipt5zGwdUszWbDQPerm5G-SmsOFt-eoI90kzwjFxZe1fLU3dA-Vvy4Pyg3qH30CJaTGLAVUyivNvrhAAqAYgQNaUiH9KA1q-GyFR4eouOAa9V8cbrvhnQHOBSX5LJCUnm4L3T-EeJj0JM/s1600/DSC_0594.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEipt5zGwdUszWbDQPerm5G-SmsOFt-eoI90kzwjFxZe1fLU3dA-Vvy4Pyg3qH30CJaTGLAVUyivNvrhAAqAYgQNaUiH9KA1q-GyFR4eouOAa9V8cbrvhnQHOBSX5LJCUnm4L3T-EeJj0JM/s400/DSC_0594.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The ion source can be seen in the middle.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgiDo9olROgRdIYlkHgLeJTWIo5g9Sqkipf4in12aYrjWNkEj_k4k-gkoEWRuHdn_5DOmpN_fuelSPcGbykJrBneoEi2ArcGW85PUwEScwOmqvfmzYIuXOJQecohHL3DRoCke2y0622OHQ/s1600/DSC_0596.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgiDo9olROgRdIYlkHgLeJTWIo5g9Sqkipf4in12aYrjWNkEj_k4k-gkoEWRuHdn_5DOmpN_fuelSPcGbykJrBneoEi2ArcGW85PUwEScwOmqvfmzYIuXOJQecohHL3DRoCke2y0622OHQ/s400/DSC_0596.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Beam is directed against a tritium metal hydride target, which is rotated to redistribute the dissipated power over a larger area. This produces a neutron beam, exiting to the lower left.</td></tr>
</tbody></table><br />
I always found acceletor technology very interesting, especially old designs where you easily can recognize what is going on (or not). If it is eastern-european design, it's just even more interesting, since they tend to look rather different and often show signs of various improvisations.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5BWykyM1ADEPJ2BaG7VqBMEsCUIfBHNVBzTnHx3lEHlBBVhQs6Kai9Rjs6oPmEhrZvRPBP8FROtsG20VwWnAgcEwV_SgATShynoVyrK1OYlbaQltC0A2HGUn88ZPC3EcNwjxWEA-t4Jc/s1600/DSC_0603.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5BWykyM1ADEPJ2BaG7VqBMEsCUIfBHNVBzTnHx3lEHlBBVhQs6Kai9Rjs6oPmEhrZvRPBP8FROtsG20VwWnAgcEwV_SgATShynoVyrK1OYlbaQltC0A2HGUn88ZPC3EcNwjxWEA-t4Jc/s400/DSC_0603.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This is some Russian accelerator based neutron source. However, it was not really used if I remember correctly, and unfortunately I didn't pick up all the details about it.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiENPIcXRzxO49q4SpeiLAAPSyipVrksCesfjPrzE_R33eTjY1jPlSUIMNzA4WVwrJcLCcJTX5OSmQ6vQ1EFpSmxLefFCCORGTiRqYY1XRu6fZCcn7t6YXtt7tRzl5gf3SUqNY_j9HJIDA/s1600/DSC_0605.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiENPIcXRzxO49q4SpeiLAAPSyipVrksCesfjPrzE_R33eTjY1jPlSUIMNzA4WVwrJcLCcJTX5OSmQ6vQ1EFpSmxLefFCCORGTiRqYY1XRu6fZCcn7t6YXtt7tRzl5gf3SUqNY_j9HJIDA/s400/DSC_0605.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">I was once told that its very characteristic for Russian accelerator systems, that the vacuum tubes are fixed with 4 screws only.</td></tr>
</tbody></table><br />
This concludes our little tour at the irradiation facilities of the primary standard lab in Bratislava. Thanks to Hugo Palmans and Jozef Dobrovodsky for the tour!<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8FNVswMqNVMxzmTgw5pPfB_fSdhC8BE1xFxiL4nFdZKb1GueyE77IUg_KSYIWak5pLkjwTFtg3KJSlEvwNJMnxkEnBWCVczTmUMM7JClYc5g91Z4VAidq8_oxIgF8lbe1FLfcoEdDWrE/s1600/DSC_0806.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8FNVswMqNVMxzmTgw5pPfB_fSdhC8BE1xFxiL4nFdZKb1GueyE77IUg_KSYIWak5pLkjwTFtg3KJSlEvwNJMnxkEnBWCVczTmUMM7JClYc5g91Z4VAidq8_oxIgF8lbe1FLfcoEdDWrE/s400/DSC_0806.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">An antiproton and a proton dosimetry researcher meet. No annihilation, but some sort of a bound state, clearly sharing common goals and interests.</td></tr>
</tbody></table><br />
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<img border="0" src="http://neptun.phys.au.dk/%7Ebassler/stat/w_ww4s.gif" />Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com4Bratislava, Slovakia48.1462386 17.1072618000000648.017060599999994 16.937350300000059 48.2754166 17.277173300000062tag:blogger.com,1999:blog-1805856980450756766.post-57527159479155309132011-07-30T18:00:00.007+02:002011-10-03T18:57:21.776+02:00Cloud computing in medical physics*: A snapshot - July 2011<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgbDPa8DAm9N5pcJECXSQ0nnYIxd60liy3UpBNOIP3O3XUHckczwJoEc2TiAhU32TcnCoSQr16GDvQwiJlbLN2_gAjsN8B4h9k5qElhgBUhsZzLYTmg4S4dJgQTGX33k476boAE5alJ9QBj/s1600/cloud_computing_icon1.png"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5635178838556415698" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgbDPa8DAm9N5pcJECXSQ0nnYIxd60liy3UpBNOIP3O3XUHckczwJoEc2TiAhU32TcnCoSQr16GDvQwiJlbLN2_gAjsN8B4h9k5qElhgBUhsZzLYTmg4S4dJgQTGX33k476boAE5alJ9QBj/s200/cloud_computing_icon1.png" style="cursor: hand; cursor: pointer; float: right; height: 140px; margin: 0 0 10px 10px; width: 200px;" /></a>
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These days if you do almost anything with a computer hooked up to the internet, you’ve probably heard the term “cloud computing”. Well I’m here to tell you that cloud computing actually does mean something and that it is something useful for medical physics! In this post I’m going to take a quick look at the current state of cloud computing research in medial physics and how it got there.</div>
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First things, first, what do I mean by cloud computing? Cloud computing generally refers to scalable computing resources, such as data storage, CPU time, or software access, offered over the internet with a pay-as-you-go pricing scheme (and sometimes free). This service can be provided at a few levels: raw server level access (infrastructure as a service, IaaS), pre-configured systems for specific tasks (platform as a service, PaaS), and software as a service, SaaS, e.g. Gmail or Dropbox. The interesting thing about cloud computing is that, suddenly, anyone armed with a network connection, a credit card, and a little know-how can have access to an unprecedented amount of computing resources. This opens up a huge number of computing possibilities for medical physicists, among others.</div>
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Starting in the second half of 2009, our research group at the University of New Mexico, the <a href="http://cs.unm.edu/~compmed/PTG">UNM Particle Therapy Group</a>, started investigating using IaaS-style cloud computing as the basis for massively parallel medical physics calculations (read, very fast, large calculations). Our very first results, demonstrating proof-of-concept with proton beam calculations on a “virtual Monte Carlo cluster” of nodes running on Amazon.com’s EC2 service were presented at the XVIth ICCR conference in Amsterdam in May, 2010. We presented a poster of our second set of results at the AAPM annual meeting in July, 2010 and then posted a paper to the arXiv titled “Radiation therapy calculations using an on-demand virtual cluster via cloud computing” <a href="http://arxiv.org/abs/1009.5282">http://arxiv.org/abs/1009.5282</a> (Sept. 2010). </div>
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It has been exciting to see the reactions to our posters, talks, and arXiv print, with most physicists immediately seeing the potential benefits offered by the new levels of access to computing resources offered by cloud computing services. Even more exciting is to see the projects subsequently launched by other medical physics researchers.</div>
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So what’s happening now?</div>
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<ul>
<li>Chris Poole, et al (Queensland Univ. of Tech.) posted a note to the arXiv titled “Technical Note: Radiotherapy dose calculations using GEANT4 and the Amazon Elastic Compute Cloud” <a href="http://arxiv.org/abs/1105.1408">http://arxiv.org/abs/1105.1408</a> (May, 2011)</li>
<li>Chris Poole also posted code used in that project to <a href="http://code.google.com/p/manysim/">http://code.google.com/p/manysim/</a> (May, 2011)</li>
<li>UNM held a <a href="http://www.cs.unm.edu/~compmed/workshop2011/">workshop</a> that included tutorials on using cloud computing for medical physics calculations. Sponsored in part by Amazon.com. (May, 2011)</li>
<li>UNM launched a cloud computing webpage in conjunction with the workshop: <a href="http://www.cs.unm.edu/~compmed/PTG/cloud.html">http://www.cs.unm.edu/~compmed/PTG/cloud.html</a> (May, 2011)</li>
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<ul>
<li>At least *seven* cloud computing abstracts at the AAPM/COMP 2011 meeting</li>
<li><a href="http://www.aapm.org/meetings/2011AM/PRAbs.asp?mid=59&aid=15504">McCloud: Toward 10 Million Monte Carlo Primaries in 5 Minutes for Clinical Use</a></li>
<li><a href="http://www.aapm.org/meetings/2011AM/PRAbs.asp?mid=59&aid=15512">Monte-Carlo Simulation in a Cloud Computing Environment with MapReduce</a></li>
<li><a href="http://www.aapm.org/meetings/2011AM/PRAbs.asp?mid=59&aid=15871">Toward Real-Time Monte Carlo Simulation Using a Commercial Cloud Computing Infrastructure</a></li>
<li><a href="http://www.aapm.org/meetings/2011AM/PRAbs.asp?mid=59&aid=16866">Toward Web-Based Real-Time VMAT and IMRT Inverse Planning Using Cloud Computing</a></li>
<li><a href="http://www.aapm.org/meetings/2011AM/PRAbs.asp?mid=59&aid=16961">Fast and Reliable Cone-Beam CT Reconstruction Using Cloud Computing</a></li>
<li><a href="http://www.aapm.org/meetings/2011AM/PRAbs.asp?mid=59&aid=15049">Cloud Computing for Interventional Fluoroscopy Dose Assessment</a></li>
<li><a href="http://www.aapm.org/meetings/2011AM/PRAbs.asp?mid=59&aid=16502">The Compute Cloud, a Massive Computing Resource for Patient-Independent Monte Carlo Dose Calculations and Other Medical Physics Applications</a></li>
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Compared to our single abstract at AAPM last year, you could claim there has been an “exponential explosion” in interest in cloud computing in medical physics since we presented our first results in 2010! Does this mean we’ll see 50 abstracts in 2012 mentioning cloud computing? (Two points does not a trend make?? ;) )</div>
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I look forward to seeing where this new technology will take our field.</div>
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*I’m really leaving off all of the (mostly commercial) cloud-based PACS and related radiology software and services. Some of these are mentioned in our paper on the <a href="http://arxiv.org/abs/1009.5282">arXiv</a>.</div>
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<img border="0" src="http://neptun.phys.au.dk/~bassler/stat/w_ww4s.gif" />Royhttp://www.blogger.com/profile/14293477186383292023noreply@blogger.com12tag:blogger.com,1999:blog-1805856980450756766.post-17141355513097029792011-07-01T21:54:00.008+02:002011-07-03T02:34:17.291+02:00Antiproton Radiotherapy Experiments at CERNIn this moment we have a week of antiproton beam at CERN for radiobiology and dosimetry experiments. The main experiment is to measure the relative biological effectiveness (RBE) of antiprotons. As an endpoint we use clonogenic survival of V79 Chinese hamster cells (in vitro).<br />
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What makes this experiment so complicated, is :<br />
<ul><li>we only have narrow beam geometry available at CERN</li>
<li>antiprotons are rare, we only get app. 1 Gy / hour</li>
<li>beam is highly pulsed, i.e. a 500 nanosecond spill every 90 seconds.</li>
</ul>Therefore, we invest a lot of effort in performing precise dosimetry with multiple redundant systems. This is a long story, which I will tell more about another time. Here, let me just show a few pictures...<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8634pgtCU7RXGoxbGWWMFdUg-222JC8O4dR6icrBjoPO1Y4FYts1YX_gB7esU3y93SrAfN105quef8rQ2nAH4OtewtE5pJvD3Xz9AJvEoW4lWSN_IuA7zOkdjvjOvmCctP-7myFALc94/s1600/DSC_0949.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8634pgtCU7RXGoxbGWWMFdUg-222JC8O4dR6icrBjoPO1Y4FYts1YX_gB7esU3y93SrAfN105quef8rQ2nAH4OtewtE5pJvD3Xz9AJvEoW4lWSN_IuA7zOkdjvjOvmCctP-7myFALc94/s400/DSC_0949.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The antiproton beam line with a water phantom for dosimetry.</td></tr>
</tbody></table>The entire experiment is located in an experimental zone at the antiproton decelerator (AD) at CERN. We share our zone with the AEgIS people, who want to find out if antiprotons fly up or down in the gravitational field of the earth. :)<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEWGyVEbkKQrLTw0Gqv0EfVu2XZba7WQoT6YnxdsHfqorL_0Wus9yYdZQLNW36pxHB_-6iwOHgKkOc1MVH7riMvXKXC_ytV2qaEdR9q9w3iMVVBcb5p87apf1CdDf5fcGEycOMzX9a8RA/s1600/DSC_0940.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEWGyVEbkKQrLTw0Gqv0EfVu2XZba7WQoT6YnxdsHfqorL_0Wus9yYdZQLNW36pxHB_-6iwOHgKkOc1MVH7riMvXKXC_ytV2qaEdR9q9w3iMVVBcb5p87apf1CdDf5fcGEycOMzX9a8RA/s400/DSC_0940.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Franz-Joachim Kaiser messing with the water phantom. Behind him the AEgIS beam line.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjisc3Odg-9koJmaxmgGdwrz4NC8HlyN3Z3Lo8c05z_uG1RwzQTpIIMfZB0r6nOgDkyqyffbCwAR1mqYoJ9nYHXleLoQyr-XdvnbwxxdLmtJdvmUrw_f1y62EkimPKPNO6W-Ie2kohGpis/s1600/DSC_0950.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjisc3Odg-9koJmaxmgGdwrz4NC8HlyN3Z3Lo8c05z_uG1RwzQTpIIMfZB0r6nOgDkyqyffbCwAR1mqYoJ9nYHXleLoQyr-XdvnbwxxdLmtJdvmUrw_f1y62EkimPKPNO6W-Ie2kohGpis/s400/DSC_0950.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Three ionization chambers (ICs) are visible here, from the left to the right: a custom made "Advanced Roos" chamber, a Markus chamber and the MicroLion liquid ionization chamber. All by <a href="http://www.ptw.de/">PTW</a>.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiT6kF2MpD8xdBtCEryBPqUjWi2S0PlJ2B_ZydSIBwmRU6XJDU7ThllkOO83RVsIuflPCou9uO0C-yR9qVBY7vYaEXkP080BTPAsDuhgnZxeHp09yhDz-yVzOp7jZ3xDJsTpsHiAYi4WVc/s1600/DSC_0939.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiT6kF2MpD8xdBtCEryBPqUjWi2S0PlJ2B_ZydSIBwmRU6XJDU7ThllkOO83RVsIuflPCou9uO0C-yR9qVBY7vYaEXkP080BTPAsDuhgnZxeHp09yhDz-yVzOp7jZ3xDJsTpsHiAYi4WVc/s400/DSC_0939.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Gafchromic EBT film irradiated with antiprotons. Beam spot is about 1 cm FWHM. The narrow beam geometry makes us very vulnerable to positioning errors...</td></tr>
</tbody></table><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUriVA0gCQmfRQExu8aOcYvKBl2Si5hsHnwM7wlDkFrNsj_dGcOBABHB-5NLqTst7XaOGjCfZEQiQQj9SL41X1GQvrXr4MwmbUOKuEH3ckdc_bmttxfcIjXmqgoDDm4JXb8xOK4Poi96U/s1600/DSC_0931.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUriVA0gCQmfRQExu8aOcYvKBl2Si5hsHnwM7wlDkFrNsj_dGcOBABHB-5NLqTst7XaOGjCfZEQiQQj9SL41X1GQvrXr4MwmbUOKuEH3ckdc_bmttxfcIjXmqgoDDm4JXb8xOK4Poi96U/s400/DSC_0931.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">... and therefore we also monitor the beam from spill to spill with a Mimotera detector.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLZt2c166WRTMO6btpsxhgvDJ-xBmDKP70SUa4a-vEV_EG6AsUoq6jYiYgBgudGebFXwmarkQWbsUPg9JzqAXHIZXsUqERCqa-s4aJIAsqns-8U8XwTCOFwDMR9ckMdBr8JL35v0Jnles/s1600/DSC_0938.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLZt2c166WRTMO6btpsxhgvDJ-xBmDKP70SUa4a-vEV_EG6AsUoq6jYiYgBgudGebFXwmarkQWbsUPg9JzqAXHIZXsUqERCqa-s4aJIAsqns-8U8XwTCOFwDMR9ckMdBr8JL35v0Jnles/s400/DSC_0938.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">We are usually 2-4 people on a shift. Tonight I will do the night shift with Franz-Joachim (to the left). Stefan will leave soon. Usually, I would do night shifts with Roy Keyes, but he couldn't be here this year. </td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6W7LNnrTwwnUmx3kjkxPMSE7S6cIfBt_Tli_r2b7cgEvQuryNLS-K4PVuVRrV1v-WNhWu5kCabnUPQOr6kwZ_PsiMTam47Evfs9ue6Az12Cpg1LpykOvfvo3h3_hRE23u2jyP8c2tBno/s1600/DSC_0928.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6W7LNnrTwwnUmx3kjkxPMSE7S6cIfBt_Tli_r2b7cgEvQuryNLS-K4PVuVRrV1v-WNhWu5kCabnUPQOr6kwZ_PsiMTam47Evfs9ue6Az12Cpg1LpykOvfvo3h3_hRE23u2jyP8c2tBno/s400/DSC_0928.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">I build this little box for the experiment: it interfaces the antiproton decelerator with the printer port of our data acquisition computer. No need for expensive IO cards or fancy LabView. Basically it is just some TTL logic and optocouplers. On the server side, a daemon listens to the parallel port if a new spill of antiprotons is coming in.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhB2r70L-KB8hQHzisS0zulRnsqMgYW5_lY1WJByqplSxJXU4b6-QMTxMEJt9IgJqBPqyGKXgzxQ_Y-t6w3qAMAVSDluvnD4Ul-6qzBSy-12BksZvgywhsUdifk3VG3sPXxOxe6ZHhxgpU/s1600/DSC_0930.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhB2r70L-KB8hQHzisS0zulRnsqMgYW5_lY1WJByqplSxJXU4b6-QMTxMEJt9IgJqBPqyGKXgzxQ_Y-t6w3qAMAVSDluvnD4Ul-6qzBSy-12BksZvgywhsUdifk3VG3sPXxOxe6ZHhxgpU/s400/DSC_0930.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Once triggered, the server takes care to read out all data systems, such as beam current transformers, ionization chamber and scintillators.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1FkfmXYGVPVbLKrQ_rR8NdUY_wMazTylWR8m1QFRTaTnWlj9vdtuaztUHOTbHlV43CcoCKE0yJ6YTl2aQz3Ipwj5wTplUqRmce0zdx4kCgkc7KlpgWDqnvIre_mVuBEwfT27pIVcsYns/s1600/DSC_0936.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1FkfmXYGVPVbLKrQ_rR8NdUY_wMazTylWR8m1QFRTaTnWlj9vdtuaztUHOTbHlV43CcoCKE0yJ6YTl2aQz3Ipwj5wTplUqRmce0zdx4kCgkc7KlpgWDqnvIre_mVuBEwfT27pIVcsYns/s400/DSC_0936.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Client programs, here running on the laptop to the left, can connect to the server, and change various settings of the readout procedure.</td><td class="tr-caption" style="text-align: center;"><br />
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</tbody></table><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhl-jAK4_p2wL9nPqwJTTPDniWB8j_YlB0LRAYDjlnO7iCL3JTTvaBDUFTH1xlmpTYF-v0lQzjbqHudaKCbLUXNWANaCKsHYKVMP6jR37uXtvcLjJJLGyTnxa1YQFsMzTCCuLHCrThZTH8/s1600/DSC_0977.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhl-jAK4_p2wL9nPqwJTTPDniWB8j_YlB0LRAYDjlnO7iCL3JTTvaBDUFTH1xlmpTYF-v0lQzjbqHudaKCbLUXNWANaCKsHYKVMP6jR37uXtvcLjJJLGyTnxa1YQFsMzTCCuLHCrThZTH8/s400/DSC_0977.JPG" width="400" /></a></div><br />
Again, this is home-brew. Earlier, the data acquisition was some <a href="http://en.wikipedia.org/wiki/Ncurses">libncurses</a> based stuff, this year is the first time we had a traditional GUI for the client and a clear client/server separation. I wrote the client in C++/<a href="http://qt.nokia.com/">QT4</a> and compiled it for linux and win32. Stefan did a package for mac. Server is pure C, linux only. Sometimes, I think the most valuable course I had when I was a student at our Physics department in Aarhus, was a C-programming course. (And that course was only offered once! What a shame!)<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQqIuA7V0Tz_GgpZ2Xz_gPnu335FKA696tJLVEiCrOSVVi1HHufUGX5D8JeOXx834rBlxMN2Ct8p1ps_45phyphenhyphenj_LsZaU11nWj31BUIzbGN_-ERozEPp7FDQQknuB6ylxhwp74IRBTtGEk/s1600/DSC_0982.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQqIuA7V0Tz_GgpZ2Xz_gPnu335FKA696tJLVEiCrOSVVi1HHufUGX5D8JeOXx834rBlxMN2Ct8p1ps_45phyphenhyphenj_LsZaU11nWj31BUIzbGN_-ERozEPp7FDQQknuB6ylxhwp74IRBTtGEk/s400/DSC_0982.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Fiona from the Belfast QUB group is in charge of the film scans, and making sure there are enough sweets for all of us.</td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTgk1Ijf4FuYNYU0T6xrBfiJG99WnrE9i_OwhjQ1n-KD_YDwCu4uM_U2E0RZ6MN3_CV45JoZORpXLwzBsFsHJvIWn5gwF9v06C05hCIF04Nkb3ODZFdgpPycBn4iF05R7xzkVIfBpT5nA/s1600/DSC_0956.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTgk1Ijf4FuYNYU0T6xrBfiJG99WnrE9i_OwhjQ1n-KD_YDwCu4uM_U2E0RZ6MN3_CV45JoZORpXLwzBsFsHJvIWn5gwF9v06C05hCIF04Nkb3ODZFdgpPycBn4iF05R7xzkVIfBpT5nA/s400/DSC_0956.JPG" width="266" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Entire experimental zone in the AD hall, seen from above, where our non-existant counting hut would be..</td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9U0ZzuIgRVVITIYznhTQKNCErvSVM-DjhBHjLAb3QGSxPz6iv8Su8Xh7afW_xrnkJ6nIlGF4pHAwuglm45NWQnFLtv3Aeg7brpf8fdUILVnBdTPkZuaNh6JL_6WEVChnVpXtqFmdxJX8/s1600/DSC_0958.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9U0ZzuIgRVVITIYznhTQKNCErvSVM-DjhBHjLAb3QGSxPz6iv8Su8Xh7afW_xrnkJ6nIlGF4pHAwuglm45NWQnFLtv3Aeg7brpf8fdUILVnBdTPkZuaNh6JL_6WEVChnVpXtqFmdxJX8/s400/DSC_0958.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A bit off topic, but just over our heads, there is a positron beam line, which delivers the positrons to the anti-hydrogen "bottle" of ATRAP. Positrons go from the right side to the left. </td></tr>
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<tr><td style="text-align: center;"><br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgP7wWw6TUSY8KKEFMd6_lJbsBl8Y9kIlM69mzRyMl4LkjikQZtpMokke-1ZSZWhc25uqv8lvubVEXBtErQk3thiPkW5ZLlPFP5F1jgnCaJRXXTwmya6vY9G9dilnLqNCyLms9QtmH8RgM/s1600/DSC_0946.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgP7wWw6TUSY8KKEFMd6_lJbsBl8Y9kIlM69mzRyMl4LkjikQZtpMokke-1ZSZWhc25uqv8lvubVEXBtErQk3thiPkW5ZLlPFP5F1jgnCaJRXXTwmya6vY9G9dilnLqNCyLms9QtmH8RgM/s400/DSC_0946.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Me, checking up on things... :-) I think this is the 8th or 9th time I am working at the ACE experiment. </td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5opppU-5wOkSWxBOu8cXwj6RXcPI58Y2oEm1nB894UPeJD4UPZpNbM8_xrmJwf9t7bf58QaaWzXENP0BlLOCPwV3QxdsRkxMi4TqPoQURxERfTFiaQoEK8cy3CW89kKjzseM44BZbw_g/s1600/DSC_1008.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5opppU-5wOkSWxBOu8cXwj6RXcPI58Y2oEm1nB894UPeJD4UPZpNbM8_xrmJwf9t7bf58QaaWzXENP0BlLOCPwV3QxdsRkxMi4TqPoQURxERfTFiaQoEK8cy3CW89kKjzseM44BZbw_g/s400/DSC_1008.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Alanine is one of the most reliable solid state dosimeters for such exotic beams such as antiprotons. Here a stack of pellets is prepared for irradiation.</td></tr>
</tbody></table><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqBpUD8s6wphhiHilROXT9ZujKRp5yfGzxPq6oA_1A8zT0B0Fgi_d0RcZsYfgW0BNXTBdBAO2RmmmYRudRcHqjtk9ZA9gUan8a5VTefPyWm3YeOzBdI1oHl6AROrSwOoPuG8FM9E8-pPs/s1600/DSC_1010.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqBpUD8s6wphhiHilROXT9ZujKRp5yfGzxPq6oA_1A8zT0B0Fgi_d0RcZsYfgW0BNXTBdBAO2RmmmYRudRcHqjtk9ZA9gUan8a5VTefPyWm3YeOzBdI1oHl6AROrSwOoPuG8FM9E8-pPs/s400/DSC_1010.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Once the pellets have been irradiated with antiprotons, they are shipped for read out to our collaborators at the National Physical Laboratory (NPL) in Teddington, UK.. (The NPL serves also as a primary standard lab for radiation quantities.)</td></tr>
</tbody></table><br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiroHxI8-TrDtXfX7qk0Kdjemyg7aLJGnGeimL5KYmuAS9IjjWn3AmOVrqkEG2RSWeyOSn11go9PnyXRpHDPRZitui-dlZ1HgqhHSn6wLd0iT1_m2o_JxpkZ-GL0oZA2md3TuvL_mbcX8c/s1600/DSC_0985.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiroHxI8-TrDtXfX7qk0Kdjemyg7aLJGnGeimL5KYmuAS9IjjWn3AmOVrqkEG2RSWeyOSn11go9PnyXRpHDPRZitui-dlZ1HgqhHSn6wLd0iT1_m2o_JxpkZ-GL0oZA2md3TuvL_mbcX8c/s400/DSC_0985.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Alright then.. :/</td></tr>
</tbody></table><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFIgcmaZ8rTCP6W1n0ziChvNQn8neespp2FpFyIkReOa978s761rSA_y0IpCgVvfU4Je4bYrm0E6XwB_inb9JuX6YYLVzWZ71VqJAz0Mdg2u5Qe6gehyphenhyphenT_3mpzFtqqYozf1IcDt2Trknk/s1600/DSC_1003.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFIgcmaZ8rTCP6W1n0ziChvNQn8neespp2FpFyIkReOa978s761rSA_y0IpCgVvfU4Je4bYrm0E6XwB_inb9JuX6YYLVzWZ71VqJAz0Mdg2u5Qe6gehyphenhyphenT_3mpzFtqqYozf1IcDt2Trknk/s400/DSC_1003.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Recursively posting this blog entry.</td></tr>
</tbody></table>More pictures <a href="https://picasaweb.google.com/niels.bassler/2011CERN">here</a>.<br />
<br><br />
<img border="0" src="http://neptun.phys.au.dk/~bassler/stat/w_ww110703.gif">Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com4tag:blogger.com,1999:blog-1805856980450756766.post-74938264856584875932011-04-27T01:44:00.001+02:002011-04-27T02:39:33.126+02:00The Monte Carlo Race 2011We saw earlier <a href="http://willworkforscience.blogspot.com/2010/10/monte-carlo-programs-in-particle.html">how different cars</a> (and a box of Lego) could fit the description of various Monte Carlo particle transport codes. Every year there is the prestigious <a href="http://en.wikipedia.org/wiki/Monaco_Grand_Prix"><i>Monaco Grand Prix</i></a> race (according to Wikipedia, I must stress, I am absolutely not into cars!), and this race passes the famous <a href="http://en.wikipedia.org/wiki/Monte_carlo">Monte Carlo</a> region with its casino.<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://upload.wikimedia.org/wikipedia/commons/thumb/c/cc/Monaco_680.JPG/800px-Monaco_680.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="http://upload.wikimedia.org/wikipedia/commons/thumb/c/cc/Monaco_680.JPG/800px-Monaco_680.JPG" width="400" /></a></div><br />
<br />
What you may not be aware of is the little known, sister event called the <i>Monte Carlo Grand Prix</i>, the year long publishing competition of Monte Carlo codes. I’m going to give you a run down of the latest results. Get a seat in the grandstand and plugin your ear plugs!<br />
<br />
<br />
Monte Carlo codes are surging in radiotherapy treatment planning. For a course at the Aarhus University Hospital I had to give <span style="font-size: xx-small;">[footnote1]</span> a little review of MC codes in radiotherapy. Inspired by a talk given by <a href="http://www.eurados.org/meeting2008/Workshop/15-Spezi.pdf">Emiliano Spezi</a> I did a little study done using the <a href="http://apps.isiknowledge.com/">ISI web of knowledge</a> which clearly shows this trend:<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdJuc1RJvbyfqXGPPzp6Ksf0B6RtYDtsi4lp1sNY2rWjGrwMf-UfJ5YqmgMLi69CCRe44U3a-Pz2JaXNoOweOa50elkiUBYcffoVrVr-DqBAH6rsNA1dqhvgm_Dndt8bG8dTLu1en-TP0/s1600/mc_publ_year.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="316" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdJuc1RJvbyfqXGPPzp6Ksf0B6RtYDtsi4lp1sNY2rWjGrwMf-UfJ5YqmgMLi69CCRe44U3a-Pz2JaXNoOweOa50elkiUBYcffoVrVr-DqBAH6rsNA1dqhvgm_Dndt8bG8dTLu1en-TP0/s400/mc_publ_year.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Number of publications on “Monte Carlo Treatment Planning”. Data for 2011 are still incomplete for obvious reasons.</td></tr>
</tbody></table>For a real race we of course need several competitors. In addition to the <a href="http://www.geant4.org/geant4/">Geant4</a>, <a href="http://www.fluka.org/">FLUKA</a> and <a href="http://www.inr.troitsk.ru/shield/index.html">SHIELD-HIT</a> cars, we will have a few new participants joining the race!<br />
<br />
From the country of <i>The United States of America</i> there are the two participants, <b>MCNP</b> and <b>MCNPX</b> developed in the secret labs of the Bombs-R-Us factory (a.k.a. <i>Los Alamos</i>), now released to the public (with a few exclusions) against a modest fee. MCNP helps physicists transporting neutrons as well as photon and electrons. The grand old MNCP brings along its more recent offspring MCNPX which also can transport heavy ions!<br />
<br />
Just of north of the US, the <i>Canadian National Research Council</i> funded the development of <b>EGS4/EGSnrc</b> and as a courtesy to our medical minded people <b>BEAMnrc</b> was developed which is particularly suited for simulations of linear accelerators for radiation therapy. Rumours say that this nifty product is based on US technology from University of Wisconsin, ‘traitors’ some might argue, I’d say this is a remarkable example of pan American friendship!<br />
<br />
The <i>Japanese</i> people, known for their industrial know-how, diligence and incomprehensible machine translated manuals contribute with this gemstone of technology: the <b>PHITS</b> multi purpose particle transport vehicle... sorry... code, maintained by the <i>Japanese Atomic Energy Agency</i>! Jovial attitude to technology breeds wonderful gadgets, often decades ahead of what eventually will appear in Europe.<br />
<br />
Finally, and being among us for a while are the diligent efforts of our European friends in <i>University of Barcelona in Spain</i>. Hola <b>PENELOPE</b>! PENELOPE can transport photons and electrons, evil tongues may even say much faster and smoother than our Canadian opponents. Let the masses judge how well they perform on the curved streets of Monaco.<br />
<br />
Anyway, the race started many years ago and is still going on, let us see the current results:<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsOViJytEaIPMNXOo9jY8AAF_1A9HgJ1lZsBjlX8k4u_Hs8b2noXR6baAI-FOnpJlX8nWyj24J4gJ3QXSdmyRLpL90BMnuDn4FXqJwWPkjpVHcfmlH-WqcgMCOyiLapuK16o8wzS-rnuA/s1600/mc_publ_year2.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="260" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsOViJytEaIPMNXOo9jY8AAF_1A9HgJ1lZsBjlX8k4u_Hs8b2noXR6baAI-FOnpJlX8nWyj24J4gJ3QXSdmyRLpL90BMnuDn4FXqJwWPkjpVHcfmlH-WqcgMCOyiLapuK16o8wzS-rnuA/s400/mc_publ_year2.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Number of publications on various MC codes (not restricted to therapy planning)</td></tr>
</tbody></table><br />
Clearly <i>MCNP</i> has been roaring through the Mediterranean streets long before computers became mainstream and when 1 MByte was still an unbelievable amount of memory. It would have been a dull race, if <i>EGS4</i> had not slowly appeared on the horizon. <i>Geant4</i> was not conceived of when <i>FLUKA</i> already had an early start. Both Geant4 and FLUKA are developed at CERN, which makes their performance particularly exciting. <i>Geant3</i> does not even appear here, it had a trauma from an earlier rally - it might recover, but bones tend to heal slowly at that age.<br />
<br />
The fiery tempered Spanish <i>PENELOPE</i> and the latest ace from the United States <i>MCNPX</i> entered the rally roughly at the same time, and here the race gets really exciting! Let us take a closer look at the last 10 years. All codes are surging, so I will plot it relative to the total amount of publications per year:<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEix8828SPpaJJIwTBqcSnCKQL6utjCpZ9XcsDSvsMq_E5gQNb6q6aRRYTQUTABTmqZT4W7JISgbv6uI4UvaIL-9mjkPhADDAuMnNUMJyowwaxjuQo06yArsoujEk2tvlLMHHIyHdd5Dwuw/s1600/mc_publ_year3.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="216" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEix8828SPpaJJIwTBqcSnCKQL6utjCpZ9XcsDSvsMq_E5gQNb6q6aRRYTQUTABTmqZT4W7JISgbv6uI4UvaIL-9mjkPhADDAuMnNUMJyowwaxjuQo06yArsoujEk2tvlLMHHIyHdd5Dwuw/s400/mc_publ_year3.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The Monte Carlo Particle Transportation Grand Prix, during last 10 years.</td></tr>
</tbody></table><br />
<br />
It’s clearly a close race between the elderly and not-so-elderly codes. <i>MCNP</i> is clearly losing against its younger offspring <i>MCPNX</i> which also offers heavy ion transport. However, it is difficult to hide that MCNPX is loosing towards <i>Geant4</i>. The good news for MCNP is that it will be merging the MCNPX code base so it will get a boost of sorts! The success of Geant4 is truly amazing! Even if Geant4 cars are complicated, DIY affairs, the possibility to have total freedom with modding your car, giving it personal style, seems to attract a solid customer base.<br />
<br />
<i>FLUKA</i> clearly shows a remarkably constant relative user base, going steady, going strong. But woo-hoo... whats happening with <i>EGS4</i>? The medical physicists came out of their closet declaring themselves as <i>BEAMnrc</i> users, and EGS4 is superseded by <i>EGSnrc</i>... 2011 could be one of the last years we hear of EGS4, but no-one will really miss it, we’ve got EGSnrc and BEAMnrc.<br />
<br />
Trailing still is <i>PHITS</i>. PHITS users have still not published this year (2011) at the time writing these lines, but obviously I would not be surprised if it suddenly might come into play. Hopefully Japanese physicists will find time to catchup after they fix their issues with their nuclear power plants.<br />
<br />
Where are the Russians? I can see smoke coming up on the horizon somewhere behind, I hope it is not a fire, but just a demonstration of the new engine. I am confident the Russian mechanics (with some aid from their friends in Aarhus :-) are working on it, and we soon will see fast <i>SHIELD-HIT</i> Niwas with whining tires and roaring physics engines in the curved streets of Monte Carlo.<br />
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The race isn’t over yet, and frankly I am not sure if it is supposed to end at all... but what can be said, some codes will prevail, others may lag and eventually disappear from the race.<br />
<br />
See you next year at the Monte Carlo rally 2012 - readers are welcome to place their bets for 2012 below !<br />
<br />
<br />
<br />
<span style="font-size: xx-small;">[footnote1]</span><br />
<span style="font-size: xx-small;">“You have to give a 5 ECTS course in dosimetry.” Yeah right, I thought, it took me almost 4 months to prepare and run it, do all the exams (400 pages + external reviewer), no time for research whatever, looking forward for the day when it was all over. What followed? Research? Guess again: more teaching!</span>Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com0tag:blogger.com,1999:blog-1805856980450756766.post-28210224404914732772011-03-21T03:00:00.007+01:002011-03-21T04:42:32.526+01:00The "ideal" Monte Carlo user interface<div style="text-align: justify;">If you have read many of our posts, you probably know that radiation Monte Carlo software plays a large role in both Niels' and my research efforts. Niels wrote an insightful and entertaining <a href="http://willworkforscience.blogspot.com/2010/10/monte-carlo-programs-in-particle.html">overview</a> of the available Monte Carlo engines relevant for particle therapy. I'm going to talk about one of the things that most MC users have surely thought about or at least been frustrated by: user interfaces.</div><br /><div style="text-align: justify;">I'll start by making a disclaimer. Monte Carlo for radiation / particle transport is <i>not a simple problem</i>. It takes many person years worth of effort to produce a codebase that gives reasonable results. This post is mostly my musings about some ideal user interface. I am the proverbial beggar who also wants to be a chooser :)</div><br /><div style="text-align: justify;">Most interaction with MC programs is performed by creating input files of some sort (in Geant4 these are called macro files and can function in largely the same way). Usually these input files allow you to set the majority of important parameters relevant to your simulation (e.g. beam parameters, target geometry, detector geometry, scoring parameters, etc). While initially cryptic (see Fluka and MCNP input files), these text input files are extremely flexible and can be generated programatically or with a GUI. The problem of course, is that your typical input file format is not very intuitive, designed to be machine parsible, rather than human friendly. And as all new MC users know, input files and their syntax are one of the major hurdles in getting up and running.</div><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSsX9Qu2GQb7g6fSf0d5Ic1KSsxzp0-rGhvg9zh375RwQM3ablpNrp2iLL7jOirrd-Z6Y9gI30LQLg9od7ySB01DJL2_7qQvtY4KaArHCL2lnzsWqIAxWY6Vu7ni-jiiyH5_qom5nkAP3R/s1600/Fluka-input.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 212px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSsX9Qu2GQb7g6fSf0d5Ic1KSsxzp0-rGhvg9zh375RwQM3ablpNrp2iLL7jOirrd-Z6Y9gI30LQLg9od7ySB01DJL2_7qQvtY4KaArHCL2lnzsWqIAxWY6Vu7ni-jiiyH5_qom5nkAP3R/s400/Fluka-input.png" border="0" alt="" id="BLOGGER_PHOTO_ID_5586353614956106130" /></a><div style="text-align: center;"><span class="Apple-style-span">A Fluka input file</span>.</div><div><br /><div style="text-align: justify;">So what would the ideal MC user interface look like? Radiation physics users of MC engines want to irradiate something and score some quantity. For medical physics users, that usually means irradiating a human or water phantom and scoring dose or fluence. To me the obvious interface for MC codes would be identical to 3D CAD (computer-aided design).</div><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://upload.wikimedia.org/wikipedia/commons/c/cd/Bearing_freecad.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 500px; height: 388px;" src="http://upload.wikimedia.org/wikipedia/commons/c/cd/Bearing_freecad.png" border="0" alt="" /></a><div style="text-align: center;"><span class="Apple-style-span">The open source <a href="http://free-cad.sourceforge.net/">FreeCAD</a> CAD program.</span></div></div><div><br />A 3D CAD style interface would put you directly in the geometry of the simulation world. Build your target from simple shapes or import existing geometries (e.g. DICOM files), graphically designate your beam source, type, and direction, and set up your detector geometries. More importantly, you would be able to manage your simulation end-to-end in the interface.<br /><br /><div style="text-align: justify;">It can be argued that 3D CAD is as hard or harder to learn than a given MC engine. My approach for a user interface would be to expose the minimum useful controls, making advanced options discoverable through menus and configurable with shortcuts.</div><br /><div style="text-align: justify;">The follow-up disclaimer is that 3D CAD is also <i>not an easy problem</i>, so we are unlikely to see this soon. In fact many of the MC programs can import geometries from CAD programs (see <a href="http://theis.web.cern.ch/theis/simplegeo/">SimpleGeo</a>), but I'm unaware of any that have attempted to fully integrate a CAD-style GUI as a primary user interface.</div><br /><div style="text-align: justify;">What's your ideal Monte Carlo user interface? Leave us a comment and let us know.</div></div>Royhttp://www.blogger.com/profile/14293477186383292023noreply@blogger.com2tag:blogger.com,1999:blog-1805856980450756766.post-33541006265234966642011-03-14T00:45:00.000+01:002011-03-14T00:45:14.284+01:00How to Produce AntiprotonsBoth Roy and I work on the <a href="http://users-phys.au.dk/hknudsen/ad4homepage.html">AD-4/ACE</a> project at <a href="http://www.cern.ch/">CERN</a> where we investigate <a href="http://en.wikipedia.org/wiki/Antiproton">antiprotons</a> as candidate particles for use in cancer therapy. We have about one week of beam time every year where we conduct radiobiological and dosimetric experiments at the beam line in a very interdisciplinary team consisting of physicists, radiobiologists and radiation oncologists from more than 10 universities and university hospitals.<br />
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CERN is the only place in the world, where we have a antiproton beam at sufficiently *low* energy, that is, around 100 MeV which corresponds to a range of ~10 cm in water. The <a href="http://en.wikipedia.org/wiki/Lhc">LHC</a> is not involved in the production at all. In fact, for antiproton production only a relatively small amount of the CERN complex is used. However, the production is still very cumbersome. First a high energy proton beam must be made. This happens at the <a href="http://en.wikipedia.org/wiki/Proton_Synchrotron">Proton Synchrotron</a> (PS), the old workhorse of CERN. It was inaugurated by our great Dane Niels Bohr in 1959.<br />
The proton beam is accelerated up to 26 GeV, and then dumped into a target followed by a so-called magnetic horn.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgx26QbRpjl6RB-q42uf1g37_3D_t_TxrJfFKouOq8AFRSeVb3QQ9trBh3QWqdQn5q1pLjg6LVrJqKlieZKCqcnT7DIpSu3T54cxFxraDIrYu9ywgxv9Gfyi8MPnB_KRUHhAiHiaJu3Q38/s1600/7905091.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="213" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgx26QbRpjl6RB-q42uf1g37_3D_t_TxrJfFKouOq8AFRSeVb3QQ9trBh3QWqdQn5q1pLjg6LVrJqKlieZKCqcnT7DIpSu3T54cxFxraDIrYu9ywgxv9Gfyi8MPnB_KRUHhAiHiaJu3Q38/s320/7905091.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Antiproton production target.</td></tr>
</tbody></table><mag horn="" pic=""><br />
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Basically, it is an air cooled iridium target. When the beam is dumped, two protons are converted into three protons and an antiproton. During the dump a powerful current is sent along the beam axis, which generates a magnetic field, keeping as many antiprotons as possible on axis. Immediately after the target there is a “lithium lens” (a Russian invention), which tries to capture even more of the very precious antiprotons. The created antiprotons have a very high energy of several GeV and are then captured by the <a href="http://en.wikipedia.org/wiki/Antiproton_decelerator">Antiproton Decelerator</a> (AD). It then takes more than 80 seconds for the beam to slow down. The deceleration is actually not the time consuming issue, but rather shaping the beam, making it small and narrow, so antiprotons are not lost during the deceleration process.<br />
This is realized using <a href="http://en.wikipedia.org/wiki/Stochastic_cooling">stochastic cooling</a>. Along with <a href="http://en.wikipedia.org/wiki/Electron_cooling">electron cooling</a> (which was invented by <a href="http://en.wikipedia.org/wiki/Budker">G.I. Budker</a>, and is widely applied), this will remove energy from the transverse movements of the antiprotons, thereby reducing the <a href="http://en.wikipedia.org/wiki/Beam_emittance">emittance</a> of the beam.<br />
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Yesterday (while following <a href="http://twitter.com/#%21/Dean_of_Science">Dag Rune Olsens twitter account</a>) I learned that <a href="http://en.wikipedia.org/wiki/Simon_van_der_Meer">Simon van der Meer</a>, inventor of stochastic cooling - and winner of the Nobel Prize, died on 4 March 2011.<br />
From our last antiproton run at CERN I have a large amount of video material of technicians working at the AD, which also demonstrates antiproton production and stochastic cooling of the resulting beam. Check out the excerpt below:<br />
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<iframe allowfullscreen="" frameborder="0" height="330" src="http://www.youtube.com/embed/j9E7-8LTi-Q" title="YouTube video player" width="540"></iframe><br />
And yes, of all those computers, only one of them was running <a href="http://en.wikipedia.org/wiki/Windows_1.0">windows</a>. :)<br />
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At 1:49 you can see the AD hall. The antiproton decelerater is under that ring of concrete. Those large coils at the far end, which can be seen at 1:54, are delay coax cables which “short circuit” the AD ring across the middle.<br />
At 2:00 you see the bullseye of the production target and at 2:20 the 26 GeV proton beam hits the target as the antiprotons are made. These are slowed down, and the oscilloscope shows how emittance is reduced by stochastic cooling. The beam is then stepwise ramped down to 126 MeV, and cooled in between those steps. Finally the 126 MeV antiproton beam is extracted.<br />
(I plan to produce more videos about the AD-4/ACE experiments, but currently <a href="http://www.kdenlive.org/">kdenlive</a> crashes frequently and corrupts my project files. It took me almost one entire day to edit those 4 min of video.)<br />
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Here is another video which shows the construction of the antiproton production target and the collector. The white cylindrical object behind the target is the lithium lens.<br />
<cern acol=""></cern></mag><br />
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<mag horn="" pic=""><cern acol=""><a href="http://cdsweb.cern.ch/record/1063081">http://cdsweb.cern.ch/record/1063081</a><br />
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This is one of the “hottest” sites at CERN. Things are designed to require minimal human intervention. Here is a very old video of how a faulty magnet had to replaced near the production target. People have to plan each step in advance before they enter the zone.<br />
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<cern acol="" vid=""><a href="http://cdsweb.cern.ch/record/1171261">http://cdsweb.cern.ch/record/1171261</a><br />
</cern></cern></mag>Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com4tag:blogger.com,1999:blog-1805856980450756766.post-85876195882220284762011-02-21T19:52:00.013+01:002011-02-22T00:11:11.089+01:00Notes from the 2011 Geant4 Winter Course Tutorial<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwn3Hst-dd6okn_7gUAtwGOXWK5QqGaT8ZrwOykOWaa5iGJ0g5fO_egvnGsqExjZcT0EgY3JlNeGVJzOP3EbgVz3WwTGG4pePJWPKjvGaK3n0Yuxpi0bb_isMX_PCUGabFyNVla7qaq9Nk/s1600/Geant4-sign1.jpg"><img style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 320px; height: 222px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwn3Hst-dd6okn_7gUAtwGOXWK5QqGaT8ZrwOykOWaa5iGJ0g5fO_egvnGsqExjZcT0EgY3JlNeGVJzOP3EbgVz3WwTGG4pePJWPKjvGaK3n0Yuxpi0bb_isMX_PCUGabFyNVla7qaq9Nk/s320/Geant4-sign1.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5576227511003722434" /></a><br />In January I traveled to Texas A&M University in College Station, TX, USA to attend the<a href="http://geant4.slac.stanford.edu/TAMU2011/Agenda.html"> Geant4 Winter Course Tutorial</a> to brush up on my Geant4 skills. Here are some of my impressions from the tutorial. The tutorial was from 10-14 January and, despite being in Texas, was on the cold side. Though hosted by the Texas A&M Dept. of Nuclear Engineering, the tutorial itself was held in the main auditorium of the Texas A&M Institute for Preclinical Studies (TIPS). There were about 100 attendees from all over the world, with a sizable fraction from A&M.<div><br />So what goes on at one of these tutorials? As described in Niels' earlier <a href="http://willworkforscience.blogspot.com/2010/10/monte-carlo-programs-in-particle.html">post</a> about the different Monte Carlo "codes", Geant4 is not a program, per se, but rather a toolkit, primarily consisting of a set of C++ libraries and data files. The tutorial was aimed at bringing Geant4 newbies and post-newbies up to speed and slightly beyond. To accomplish this, we attended classes for five days in the stadium style auditorium with lectures covering a myriad of topics. Each day had one or two "hands on" sessions, in which we'd work through examples and have our questions answered. In many ways, the hands on sessions were the most useful, because of the one-on-one help. The actual exercises may not have been terribly useful, but having the time to ask questions with laptop-at-the-ready was when things came together. I certainly asked a few questions that were completely unrelated to the tutorial (but not unrelated to my research!) (Thanks again Sebastian!). The other thing I found extremely helpful was simply having time to discuss things with the Geant4 developers and other users. On the last day there were break-out sessions for medical physics, high energy physics, and on DNA damage. I attended the medical physics session with about 30 other people.<br /><br />Other random notes:<br /><ul><li>The attendees were a good mix of medical physics, nuclear applications, high energy physics, and others.</li><li>I met a number of people involved with proton therapy projects as well as a post-doc from Wayne State working on their re-commissioned fast neutron therapy project.</li><li>To keep small animals outside of TIPS, they had several poisonous plastic rocks outside the building (yes, really).</li><li>We got a nice tour of TIPS, which included seeing the "most powerful" PET/CT scanner in existence.</li><li>Catering by Jason's Deli all week</li><li>Possibility of using cloud computing for distributed Geant4 was mentioned in a lecture by Asai. This is a subject of one of my projects (see <a href="http://arxiv.org/abs/1009.5282">arXiv:1009,5282v1 [physics.med-ph]</a>).</li><li>Looked a lot like a web surfing conference.</li></ul><div><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXR56z0pgkL2ZLtmlpXmJwSxCtwt-exENdFv919Tmkfnzul-E7yA5XyW-sUCAvFFXXhEYxotBZyogWkBag3Sw1hXXm_V2OzVcVFbXttYdYjwctcAhDY4HFNXLiRfRNH7CLVkJEOQX8c800/s1600/poison_rock1.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 200px; height: 114px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXR56z0pgkL2ZLtmlpXmJwSxCtwt-exENdFv919Tmkfnzul-E7yA5XyW-sUCAvFFXXhEYxotBZyogWkBag3Sw1hXXm_V2OzVcVFbXttYdYjwctcAhDY4HFNXLiRfRNH7CLVkJEOQX8c800/s200/poison_rock1.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5576227689736936706" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg79xd229Oi-h0e7Q9HZY19uC5slj0Gn7hzqrmXX722y6vFPuqVj3QFOyCht3fmrxxBVZ73ky0pLQ8wY7ewRh8wFHs2KZNWaD7UwhoSen-QiRht0u_09aHElcag9rWq02JEylWdCvRwUcU2/s1600/PETCT1.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 200px; height: 178px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg79xd229Oi-h0e7Q9HZY19uC5slj0Gn7hzqrmXX722y6vFPuqVj3QFOyCht3fmrxxBVZ73ky0pLQ8wY7ewRh8wFHs2KZNWaD7UwhoSen-QiRht0u_09aHElcag9rWq02JEylWdCvRwUcU2/s200/PETCT1.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5576228018196390258" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_voOEHAuA60Rwub1d2hMve_L_Zmo-stDZvtRwqyVws4XhuMvALMiaLRt2dCgGKvuRYO3MhgtdOiyVlvoEdqtE9bpZvb6wFjw3yvmU0rXqWxzuzL28O0DLZigM0yd3SCR9VVmv4A1F2zz9/s1600/websurfing1.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 200px; height: 116px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_voOEHAuA60Rwub1d2hMve_L_Zmo-stDZvtRwqyVws4XhuMvALMiaLRt2dCgGKvuRYO3MhgtdOiyVlvoEdqtE9bpZvb6wFjw3yvmU0rXqWxzuzL28O0DLZigM0yd3SCR9VVmv4A1F2zz9/s200/websurfing1.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5576228080546973954" /></a><br /></div>Overall it was a good tutorial. We learned that we were taking some wrong (or at least more difficult) paths in our code. Certainly Geant4 is a vast topic and a tutorial like this can be very helpful, if only to meet the right people for when you need to ask questions.</div>Royhttp://www.blogger.com/profile/14293477186383292023noreply@blogger.com2tag:blogger.com,1999:blog-1805856980450756766.post-30759779228256226162011-01-31T01:01:00.000+01:002011-01-31T01:01:14.911+01:00Making Bubbles: The Particle Way<a href="http://www.bubbletech.ca/">BTI BubbleTech Industries</a> manufacture neutron detectors intended for personal dosimetry. Theses devices contain a polymer gel holding very small droplets of a superheated gas. When a neutron interacts with these superheated droplets, a phase transition happen from liquid phase to gas phase expanding the volume dramatically - a bubble appears.<br />
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The video below demonstrates how such a detector responds to a (weak) Americium-Beryllium neutron source:<br />
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<iframe allowfullscreen="" class="youtube-player" frameborder="0" height="390" src="http://www.youtube.com/embed/cyKbwv8GbN4" title="YouTube video player" type="text/html" width="480"></iframe><br />
<br />
The activity of the AmBe source was 2.64E+4 neutrons per second. The detectors we had were calibrated against <a href="http://www.icrp.org/publication.asp?id=ICRP%20Publication%2060">ICRP-60 </a>in terms of dose equivalent, according to BTI. The sensitivity of the particular detector shown in the video above was about 0.7 bubbles / µSv dose equivalent.<br />
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The detectors come with an integrated piston which repressurizes them, so they can be reused, however not indefinitely. We used our detectors rarely, and kept them refrigerated. However, after two years the encapsulation/pressurization system leaked.<br />
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The bubble detectors can be bought with varying sensitivity ranges and BTI even offers a set of detectors which are sensitive above a varying energy threshold. Deconvoluting the counts in each detector of this set will yield a coarse energy spectrum, in e.g. 6 energy bins.<br />
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We have used the these bubble detectors in our antiproton beam line at CERN in order to get a coarse measure of the amount of fast neutrons emitted from the antiproton annihilation. We used both the personal dosimeter type and the BDS spectrometer.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNv-v1Rdwke_4LyJS1zgr7rzSVY26QaaD2kqOlu5j1BwzeGEyfBMFwvk1KC4iLvt7Gut8d__lI8441HtLkRrwlz-p5ftt4j6-ZbL1iYkQaPlhwebC9Kgowac73upQlk_UfMSVX6qB8AA4/s1600/ace_bubble.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="265" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNv-v1Rdwke_4LyJS1zgr7rzSVY26QaaD2kqOlu5j1BwzeGEyfBMFwvk1KC4iLvt7Gut8d__lI8441HtLkRrwlz-p5ftt4j6-ZbL1iYkQaPlhwebC9Kgowac73upQlk_UfMSVX6qB8AA4/s320/ace_bubble.jpg" width="320" /></a><br />
The picture above show how multiple personal dosimeter detectors are places at a certain distance from the annihilation vertex.<br />
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Unfortunately we had some trouble interpreting the results from the spectrometer. The BDS spectrometer counts seemed to be simply unphysical and a spectrum could not be deconvoluted. The readings from the personal dosimeter also seemed to be off by an order of magnitude.<br />
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After some investigations we started to suspect that these bubble detectors were not only sensitive to fast neutrons, but also to charged particles, such as protons. From the antiproton annihilation we do get a similar amount of protons and a threefold multiplicity of energetic pions, which have a long range, far beyond the position of the bubble detectors.<br />
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<a href="http://dx.doi.org/10.1016/j.nimb.2006.05.020">A paper in NIM B</a>, which was published a few years ago by us, lists our findings. Basically we conclude that the sensitivity (# of neutrons per bubble) is quite comparable to that for protons, and perhaps a bit less for pions. The proton part we could test at our storage ring, <a href="http://www.isa.au.dk/">ASTRID</a>, which we have in the basement of our Physics Department in Aarhus.<br />
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In the video you are about to see, we extract a few million protons at about 50 MeV from the synchrotron. The bubble detector here is immersed in a water bath.<br />
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<iframe allowfullscreen="" class="youtube-player" frameborder="0" height="390" src="http://www.youtube.com/embed/EKp2hNEFpjI" title="YouTube video player" type="text/html" width="480"></iframe><br />
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The range of the protons are clearly visible. A distinct Bragg peak does not really form, the effect is primarily related to nuclear interaction cross sections.Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com0tag:blogger.com,1999:blog-1805856980450756766.post-48706096936581392692011-01-14T07:02:00.023+01:002011-01-19T20:04:08.527+01:00Open access, medical physics, and arXiv.org<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://upload.wikimedia.org/wikipedia/commons/thumb/2/25/Open_Access_logo_PLoS_white.svg/200px-Open_Access_logo_PLoS_white.svg.png"><img style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 128px; height: 200px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisn4RdU0xfGrYOcqNGsHyLIVvbDMGeLdFiql3WJlXI5YcVW6b2zryyhDSm058T0ZypOsjFJRJ622gg3z2CnvqAIM7w0wlt3b9g2lHyvnm-phRokpId5oxc1wuUf3gE6aVm0MIz7MXOpvfZ/s200/200px-Open_Access_logo_PLoS_white.svg.png" border="0" alt="" id="BLOGGER_PHOTO_ID_5563971566541654866" /></a><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: 100%; font-family: 'Times New Roman'; "><div style="margin: 0px;color:black;"><span id="internal-source-marker_0.4126536201220006" style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap; font-family: Arial; "></span><span style="font-family:arial;">If you read research papers, chances are you’ve heard the term open access. In this post I’m going to talk about what open access is, the state of open access in medical physics, and what medical physicists can do if they want to make their work open access using sites such as arXiv.org. The quick summary is: the primary obstacle to open access in medical physics is adoption by authors. Most journals are already on-board in important ways. If you want to make your medical physics publications open access, you probably can and I encourage you to do so.</span><br /><br /><span style="font-family:arial;">According to our friends at Wikipedia, </span><a href="http://en.wikipedia.org/wiki/Open_access_%28publishing%29"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">open access</span></a><span style="font-family:arial;"> is “unrestricted online access to articles published in scholarly journals”. Open access is generally placed into two categories: “Green” open access and “Gold” open access. Green access is defined as author “self-archiving”, when the author places a copy of a paper on their own site or on an e-print server. Gold access is free access provided directly by journals.</span><br /><br /><span style="font-family:arial;">No-fee access has many benefits for researchers. For medical physics, these benefits are potentially greater than for other fields, due to the fact that medical physicists are found in a wide variety of settings with varying levels of paid journal access (i.e. universities, community hospitals, small clinics, etc). Even being located at a large university with a large medical center, I have personally run into access barriers. For example, I can only access Medical Physics with my personal subscription; for a time the library subscribed to the Red Journal, but not the Green Journal; the university has no love for Radiation Protection Dosimetry whatsoever. In the current economic climate I’m not optimistic that institutional subscriptions will be on the increase. Ultimately, open access offers availability of information to all regardless of institutional affiliation or budget. (Also, I hate messing with proxies... :) )</span><br /><br /><span style="font-family:arial;">While open access is strongly established in some disciplines, particularly physics, computer science, math, and earth science, medical physics seems to have lagged behind the curve greatly, especially in self-archiving.</span><br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://upload.wikimedia.org/wikipedia/commons/9/94/OA_by_Discipline.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 260px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVW5sM_SVndA4cXhjjjZOkG-arREYX1K2marwXiUQu_xrUPQW514aqZzSFogjiMV4OmCf2z_G8Jks14kbpuTjizZC_-EXwL4kNQ0G_z7J02XuAb3VPj6Fj5t6GiZtluTva9a-bE9v0_4fI/s400/OA_by_Discipline.png" border="0" alt="" id="BLOGGER_PHOTO_ID_5563973922960855042" /></a><br /></div><div style="text-align: center;"><span style="font-size:78%;"><span style="font-family:arial;">“The availability of gold and green OA copies by scientific discipline. The disciplines are shown by the gold ratio in descending order, rather than in alphabetical order.” CCA 3.0. Björk B-C, Welling P, Laakso M, Majlender P, Hedlund T, Gudnason G.</span></span><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;font-size:78%;"> </span><span style="font-size:78%;"><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011273"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">doi:10.1371/journal.pone.0011273</span></a><br /></span></div><br /><span style="font-family:arial;">The above plot from Björk et al. shows the percentage of publications that are made open access in different disciplines. In some sub-disciples of physics, such as high energy physics, the rate of self-archiving is up to 100%. For reasons unknown to me, medical physicists have not embraced open access, despite the supportive polices of medical physics journals (see lists below). I suspect that medical physicists are largely ignorant of the journals’ policies. If medical physicists want to provide open access to their work, they have options to both self-archive (green) or publish in open access journals directly (gold). </span><br /><br /><span style="font-weight: bold;font-family:arial;">arXiv.org</span><br /><span style="font-family:arial;">In 1991, high energy physicists began self-archiving their publications on a site called the <a href="http://arxiv.org/">arXiv</a> (that X is supposed to be like a Greek “chi”). Since then, the arXiv has expanded to cover all of physics, as well as other fields, such as mathematics and computer science. As the leader in physics self-archiving, the arXiv is a logical destination for medical physicists to post their papers. In fact, the arXiv has a <a href="http://arxiv.org/list/physics.med-ph/recent">medical physics category</a>. Currently, the medical physics category of the arXiv has very low activity relative to the number of medical physics articles published that are eligible to be posted. (I plan to investigate the posting rates in a future blog post.) While the activity is low, it is encouraging to see prominent medical physics researchers, such as <a href="http://arxiv.org/find/all/1/all:+AND+steve+jiang/0/1/0/all/0/1">Steve Jiang</a> (UCSD) and <a href="http://arxiv.org/find/all/1/all:+AND+thomas+bortfeld/0/1/0/all/0/1">Thomas Bortfeld</a> (MGH/Harvard), posting articles. (Thanks!) In fact, one tiny area of medical physics that seems to be very well covered on the arXiv is <a href="http://www.google.com/search?q=gpu+arxiv+med-ph#q=site:arxiv.org+med-ph+gpu&">GPU based calculations</a> in medical physics. That’s probably due to Jiang’s group leading the way in posting their publications.</span><br /><br /><span style="font-weight: bold;font-family:Arial;">Medical journals</span><br /><span style="font-family:Arial;">While medical physics journals all allow self-archiving to servers such as arXiv.org, medical journals related to medical physics seem to be much less enthusiastic about open access (see the list for details). The Elsevier journals allow pre-prints and self-hosted archiving, but the main radiology journals have open access “hostile” policies. The one thing that has seemed to crack journals such as those from RSNA is government mandates. One example is the recent rule requiring NIH funded research publications to be made available as open access on PubMed Central within 12 months of initial publication. This rule has had a wide ranging effect on journals and led to much discussion. Funding agencies in other countries have instituted similar rules.</span><br /><br /><span style="font-family:Arial;"><span style="font-weight: bold;">What does this all mean for you?</span><br /><ol><li style="list-style-type: decimal;">If you’ve published in medical physics journals, you can probably <span style="font-weight: bold;">make your work open access right now</span> by posting your articles to <a href="http://arxiv.org/user/login">arXiv.org</a>.</li><li style="list-style-type: decimal;">If you are planning to submit an article to a journal, you should read the journal’s copyright policy <span style="font-weight: bold;">before submitting and before posting</span> a pre-print (or post-print). Some journals have very strange policies, unfortunately, and this has to be taken into account when submitting for publication.</li></ol></span><span style="font-family:Arial;">I encourage authors to strongly consider making their work open access, either by self-archiving to the arXiv or publishing in one of the gold access journals. Ultimately, the arXiv is just an example of an e-print repository, but it seems to be the best choice for now. If, for example, a dedicated medical physics repository were created and critical mass were achieved, the papers on the arXiv could be stored there as well. I haven’t discussed the concerns some people have with open access (see the Wikipedia </span><a href="http://en.wikipedia.org/wiki/Open_access_%28publishing%29"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">entry</span></a><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">). If there is interest, I might talk about that in another post.</span><br /><br /><span style="font-weight: bold;font-family:Arial;">Journal policies</span><br /><span style="font-family:Arial;">Below I will list the current (Jan. 2011) policies of the journals (as far as I can tell, UAYOR, YMMV, IANAL, etc). You can find out more information about the open access policies of these journals and others by using the <a href="http://www.sherpa.ac.uk/romeo/">SHERPA/RoMEO</a> tool.</span><br /><br /><span style="font-family:Arial;">The state of open access in medical physics journals:<br /><ul><li style="list-style-type: disc;">Medical Physics</li><ul><li style="list-style-type: circle;">Posting to e-print archives permitted with slight restrictions.</li><li style="list-style-type: circle;"><a href="http://www.medphys.org/documents/copyright.pdf">Medical Physics copyright policy [PDF]</a> (Item 4)</li></ul><br /><li style="list-style-type: disc;">Physics in Medicine and Biology (IOP)</li><ul><li style="list-style-type: circle;">Posting to e-print archives permitted with slight restrictions.</li><li style="list-style-type: circle;"><a href="http://authors.iop.org/atom/help.nsf/LookupJournalSpecific/WebPermissionsFAQ~**">PMB copyright policy</a> (Items 12, 13, 17)</li></ul><br /><li style="list-style-type: disc;">Journal of Applied Clinical Medical Physics</li><ul><li style="list-style-type: circle;">Gold access</li></ul><br /><li style="list-style-type: disc;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Journal of Medical Physics</span></li><ul><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Gold access</span></li></ul><br /><li style="list-style-type: disc;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">BMC Medical Phyics</span></li><ul><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Gold access</span></li><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Almost no activity</span></li></ul><br /><li style="list-style-type: disc;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Journal of Radiation Oncology Informatics</span></li><ul><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Gold access</span></li><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">New journal, low activity</span></li></ul><br /><li style="list-style-type: disc;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">BMC Medical Imaging</span></li><ul><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Gold access</span></li><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Low activity</span></li></ul><br /><li style="list-style-type: disc;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Radiation Protection Dosimetry (OUP)</span></li><ul><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Posting pre-prints with several restrictions</span></li><li style="list-style-type: circle;"><a href="http://www.oxfordjournals.org/access_purchase/self-archiving_policya.html"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Self-archiving policy A</span></a><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;"> - </span><a href="http://www.oxfordjournals.org/access_purchase/self-archiving_policyb.html"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Policy B</span></a><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;"> - </span><a href="http://www.oxfordjournals.org/access_purchase/publication_rights.html"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">publication rights</span></a><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;"> - </span><a href="http://www.oxfordjournals.org/news/2008/08/04/nih_deposits.html"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">NIH policy</span></a><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;"> - </span><a href="http://www.oxfordjournals.org/for_authors/repositories.html"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Other funding agencies</span></a></li></ul></ul><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">The state of open access in medical journals related to medical physics:</span><br /><ul><li style="list-style-type: disc;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Red and Green journals (Elsevier)</span></li><ul><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Posting pre-prints on archives OK (not considered prior publication)</span></li><li style="list-style-type: circle; font-style: normal; text-decoration: none; vertical-align: baseline;font-family:Arial;font-size:11pt;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Post-prints to public archives not allowed, except:</span></li><li style="list-style-type: circle; font-style: normal; text-decoration: none; vertical-align: baseline;font-family:Arial;font-size:11pt;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">Self-archiving on own site or institutional archive OK with slight restrictions</span></li><li style="list-style-type: circle;"><a href="http://www.elsevier.com/wps/find/supportfaq.cws_home/electronicpreprints"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">http://www.elsevier.com/wps/find/supportfaq.cws_home/electronicpreprints</span></a></li></ul><br /><li style="list-style-type: disc;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">RSNA journals</span></li><ul><li style="list-style-type: circle;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">No archiving(?), except for NIH funded papers (12 month embargo)</span></li><li style="list-style-type: circle; font-style: normal; text-decoration: none; vertical-align: baseline;"><a href="http://www.rsna.org/publications/rsnarights/faq.cfm"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">http://www.rsna.org/publications/rsnarights/faq.cfm</span></a></li><br /></ul><li style="list-style-type: disc;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">American Journal of Roentgenology</span></li><ul><li style="list-style-type: circle; font-style: normal; text-decoration: none; vertical-align: baseline;"><span style="font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">No archiving(?), except for NIH funded papers (assumed)</span></li><li style="list-style-type: circle; font-style: normal; text-decoration: none; vertical-align: baseline;"><a href="http://www.arrs.org/uploadedFiles/ARRS/Publications/cta.pdf"><span style="font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;font-family:Arial;">http://www.arrs.org/uploadedFiles/ARRS/Publications/cta.pdf</span></a><br /></li></ul><br /><span style="font-family:Arial;"><li>Radiation Oncology (BMC)</li><ul><li style="list-style-type: circle;">Gold access</li></ul></span></ul></span></div></span>Royhttp://www.blogger.com/profile/14293477186383292023noreply@blogger.com8tag:blogger.com,1999:blog-1805856980450756766.post-87366802750937648782011-01-05T20:45:00.001+01:002011-01-05T20:47:39.186+01:00libdEdx version 1.0 releasedVersion 1.0 of <a href="https://sourceforge.net/apps/trac/libdedx/">libdEdx</a> is now available at <a href="https://sourceforge.net/projects/libdedx/files/">sourceforge.net</a> <br />
<br />
List of features:<br />
<ul><li>ICRU 49 date tables for protons and Helium ions (PSTAR, ASTAR)</li>
<li>MSTAR for <b>heavy ions</b></li>
<li>ICRU 73 with and without the erratum for water target</li>
<li>A <b>Bethe</b> implementation for any ion, including <b>Linhard-Sørensen</b> equation for low energies</li>
<li>Support for <a href="https://sourceforge.net/apps/trac/libdedx/wiki/libdedx_material_list"><b>278 ICRU target</b> materials</a>, i.e. the complete ESTAR material table, all with default I-values for the Bethe equation</li>
<li>I-values can be overridden for elements</li>
<li>Automatic application of <b>Bragg's additivity rule</b>, if requested target material does not exist in default table for e.g. MSTAR.</li>
<li>Detailed documentation, and multiple example files</li>
<li>CMAKE based installer, with uninstall target.</li>
<li><b>getdedx</b> as a frontend command line program for querying the library</li>
<li>Two modes of operation: <b>simple</b> for lazy programmers and <b>fast</b> for e.g. MC codes. </li>
<li><b>GPL</b> license (non-GPL versions available upon request)</li>
</ul><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiT-QDhqy17Bx1Gn_LUq7z-ieeqR_DHmC8crSo7-7b6VNsAe2P1BuQf7AiMXfEfvsR83HJ6vnzBBYWdsqfRuRZNi3uM58FLbjvc0GCBWvdSlXlQCYwxYG03NCFWU3K8d3MYhmNA0nvVxd0/s1600/Screenshot+-+01052011+-+08%253A18%253A44+PM.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiT-QDhqy17Bx1Gn_LUq7z-ieeqR_DHmC8crSo7-7b6VNsAe2P1BuQf7AiMXfEfvsR83HJ6vnzBBYWdsqfRuRZNi3uM58FLbjvc0GCBWvdSlXlQCYwxYG03NCFWU3K8d3MYhmNA0nvVxd0/s400/Screenshot+-+01052011+-+08%253A18%253A44+PM.png" width="398" /></a></td><td style="text-align: center;"><br />
</td><td style="text-align: center;"><br />
</td></tr>
<tr><td class="tr-caption" style="text-align: center;">How to use libdEdx, simplest possible example.</td><td class="tr-caption" style="text-align: center;"></td></tr>
</tbody></table><div class="separator" style="clear: both; text-align: center;"></div><br />
Demonstration of command line program <b>getdedx</b>. 100 MeV protons using PSTAR on water:<br />
<br />
<pre>Usage: getdedx program_id Z icru_target_id energy.
bassler@kepler:~$ getdedx 2 1 276 100
100.000000 MeV/u HYDROGEN ions on WATER target using PSTAR
dEdx = 7.286E+00 MeV cm2/g
</pre><br />
Carbon ions on alanine target, using ICRU 73:<br />
<br />
<pre>bassler@kepler: getdedx 5 6 105 400
400.000000 MeV/u CARBON ions on ALANINE target using ICRU73
Bragg's additivity rule was applied,
since compound ALANINE is not in ICRU73 data table.
dEdx = 1.068E+02 MeV cm2/g
</pre><br />
For reporting bugs and feature request, you can use our <a href="https://sourceforge.net/apps/trac/libdedx/report/6">trac ticket system</a> or drop us an email.Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com2tag:blogger.com,1999:blog-1805856980450756766.post-47960315915196322092010-12-30T23:48:00.000+01:002010-12-30T23:48:10.416+01:00Happy new year...... and a few wishes for 2011: <br />
<br />
<b><a href="http://libdedx.sourceforge.net/">libdEdx</a></b>: I hoped I could announce first official release of the stopping power library before 2011. Unfortunately, there are a few minor problems with the Bethe implementation which Jakob wanted to fix first. It is almost done...<br />
Just to give an idea what's coming up: libdEdx 1.0 will probably be a Linux-only release and we most likely won't include <a href="http://physics.nist.gov/PhysRefData/Star/Text/ESTAR.html">ESTAR</a> tables. Good news are that PSTAR, ASTAR, MSTAR and the ICRU 73 (old and new) tables seem to work. The entire ESTAR ICRU material composition table is supported, so if the user of the library calls a non-standard compound, Braggs additivity rule is automatically applied according to the stochiometric compositions defined by ICRU (<a href="http://sourceforge.net/apps/trac/libdedx/wiki/libdedx_material_list">see list here</a>).<br />
The Bethe-equation implementation allows the user to override the mean exitation potential for elements. Also, an uninstall target is now provided in the CMake configuration.<br />
If you can't wait for the 1.0 release of libdEdx you may test revision 85 in the SVN repository which is quite close to something functioning.<br />
Enough said about that.<br />
<br />
So, regardning the current status of <b><a href="http://aptg-trac.phys.au.dk/shieldhit">SHIELD-HIT10A</a></b>: The main developer and maintainer Prof. Nikolaj Sobolevsky from <a href="http://www.inr.ru/">INR</a> Moscow visited us again in Aarhus for a month (a few pictures to be added later). Basically, we discussed the changes from 08 to 10A, the fitting of nuclear models to recently published experimental data and the development framework in general. More importantly, we try to encourage a clearer road map for <a href="http://www.inr.ru/shield/">SHIELD-HIT</a>. In particular, this involves <i>settling on a clear license model</i> and terms of use. This process is ongoing and takes time, but surely we still see SHIELD-HIT filling a gap which neither <a href="http://www.fluka.org/">FLUKA</a> or <a href="http://geant4.cern.ch/">Geant4</a> fills when it comes to combining ease-of-use while still having access to the source code. Stay tuned for more on this.<br />
<br />
Now for something completely different: Since <a href="http://willworkforscience.blogspot.com/"><b>this blog</b></a> (<-- beware of the recursion) quite unintentionally has turned more or less into a blog on topics in <i>computing</i>, <i>medical physics</i> and <i>particle therapy</i>, I have invited a fellow blogger <a href="http://www.unm.edu/%7Eroy/">Roy Keyes</a> from University of New Mexico (Albuquerque) to contribute. Roy and I have shared many night shifts at <a href="http://www.cern.ch/">CERN</a> running our <a href="http://www.phys.au.dk/%7Ehknudsen/ad4homepage.html">antiproton experiments</a>.<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisLdR3PrTcpmIDzLnTrmooDfqawxzQYAkfRajvjJandsquoU2BJIf-vWXNoTFRDHE6KAqQFxXA_aJuhMrase1dYFn2XfeMTXjppaQbz5uNcJQ3J0Wl6kcqNITnhSv9YgUx-jvWr-1uSZQ/s1600/roy_niels_.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="181" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisLdR3PrTcpmIDzLnTrmooDfqawxzQYAkfRajvjJandsquoU2BJIf-vWXNoTFRDHE6KAqQFxXA_aJuhMrase1dYFn2XfeMTXjppaQbz5uNcJQ3J0Wl6kcqNITnhSv9YgUx-jvWr-1uSZQ/s320/roy_niels_.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Roy Keyes' (to the left) inexhaustible repository of real life anecdotes helped me to stay awake during the long night shifts at CERN October 2011. Thanks, Roy. Everyone, say hi to Roy...</td></tr>
</tbody></table>Common work topics are also Monte Carlo simulations, mostly FLUKA, which UNM is running in the <a href="http://aws.amazon.com/ec2/">Amazon cloud</a> (awesome idea!). In addition, Roy works on an open source DICOM-RT viewer <a href="http://code.google.com/p/dicompyler/">dicompyler</a>. Dicompyler resembles in many ways my <a href="http://aptg-trac.phys.au.dk/pytrip">PyTRiP</a> project, which is supposed to be a versatile python visualization tool for the heavy ion treatment planning program <a href="http://bio.gsi.de/DOCS/TRiP98/PRO/DOCS/trip98.html">TRiP</a>, including a GUI. Probably these projects will merge at some point and take over the world. Again, more on this later.<br />
<br />
BTW: You can meet Roy in a <a href="http://www.youtube.com/watch?v=oSbfpmcv_nY">little test video</a> I made about the CERN antiproton experiments. Alas, since <a href="http://www.kdenlive.org/">kdenlive</a> crashes big time in the current version at project loading, I never made it further than the intro and gave up the editing. I'll have to wait until kdenlive is updated in Debian testing repo. But I got looooots of wonderful footage, including details of antiproton production and french speaking technicians fixing dead synchrotrons! :-)<br />
<br />
Plenty of plans, only little time, but surely this blog will become much more lively 2011. With these words, I wish you all a happy new year!<br />
<br />
Cheers,<br />
Niels<br />
<br />
P.S.: Future non-work related blog entries from my side will be published on <a href="http://opasnajazona.blogspot.com/">http://opasnajazona.blogspot.com</a>. (The similarity to a nuclear waste dump is not coincidental.)Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com1tag:blogger.com,1999:blog-1805856980450756766.post-76057029494905511632010-11-29T21:00:00.002+01:002010-11-30T03:25:57.648+01:00The Stopping Power of Frozen WaterIn my <a href="http://willworkforscience.blogspot.com/2010/11/one-stopping-power-library-to-rule-them.html">last blog entry</a> I commented on stopping powers of fast ions in medical physics, and announced the <a href="http://libdedx.sf.net/">libdEdx</a> library. (Stopping powers describe the energy loss of fast charged particles in material, thereby transferring energy to the target matter.) Stopping powers directly relate to the deposited dose, but there are plenty of more subtle effects where they may or may not have a profound influence:<br />
<ul><li>Range of ions in matter. Often the mean excitation energy (not to be confused with the ionization potential or w value...) in the <a href="http://en.wikipedia.org/wiki/Bethe_formula">Bethe-equation</a> is used as a macroscopic fitting parameter for the range of ions. Effects such as an primary particle dependent I-value are reported, even this is unphysical. Discussion is going on what the I-value for water actually is covering the 75 to 85 eV interval. <a href="http://physics.nist.gov/PhysRefData/Star/Text/PSTAR.html">PSTAR</a> claims 75 eV. More recent studies seem to agree on a value close to 80 eV.<br />
</li>
<li>Ionization chambers rely on a solid assertion of stopping power ratios, since these detectors measure dose to air. In order to translate this to dose to water, you should know the particle spectrums and the stopping power ratio of water to air (see e.g. <a href="http://www.google.com/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fwww.inca.gov.br%2Fpqrt%2Fdownload%2FTRS_398_v_Abr_2004.pdf&rct=j&q=iaea%20trs-398&ei=k_rzTJO7LciVOvXgpccK&usg=AFQjCNG_hu01TcpaqypnqUpY61ksh_8HIg&cad=rja">IAEA TRS-398</a> dosimetry protocol, so far one of the best out there, even though it has its flaws...) Or, you can use a parametrization, as Armin tries to show in our recent yet unpublished paper (<a href="http://arxiv.org/pdf/1010.5356">pre-print</a>).<br />
</li>
<li>Detector and biology response models such as the Katz or LEM model rely on the stopping power of ions. How large these effects are, is still to be investigated, and is something we want to look at using <a href="http://libdedx.sf.net/">libdEdx</a> and <a href="http://libamtrack.dkfz.org/libamtrack/index.php/Main_Page">libamtrack</a>.</li>
</ul>There may be many more applications, whereas the first two mentioned here are quite well researched. Frustrating enough, if you have to calculate e.g. the stopping power ratios for a given particle spectrum, you have to rely on the ICRU49 (PSTAR/ASTAR) table and the ICRU73, and they are not calculated consistently. Ok, the errors may be minor for practical dosimetry purposes, but thinking of primary standard laboratories such as <a href="http://www.ptb.de/index_en.html">PTB</a> in Braunschweig or <a href="http://www.npl.co.uk/">NPL</a> in London who try to increase the precision at least one order of magnitude, you may get into difficulties.<br />
<br />
How can this be, don't we have a large data base on experiments for various ions on various targets? Well, yes, for some ion/target combination, but not for all of them. Peter Sigmund from University of Southern Denmark, (now Professor Emeritus), once showed a very nice matrix of combinations at our 4th Danish Workshop, where all the experimental gaps are.<br />
Even worse is the situation for compounds, here no or very little data are available. <br />
<br />
So, we decided to take this up a the <a href="http://www.partikelterapi.dk/index.php?option=com_content&task=view&id=38&Itemid=57">5th Danish Workshop on Particle Therapy</a>, in order to sort out the field, and give the research some direction.<br />
This brings me back to the title of this blog entry: The workshop was scheduled to take place tomorrow (30th November) in Aarhus, but exactly due to the stopping power of frozen water, we had to cancel it. Several key persons were stuck in various airports and could not make it because of snowstorms.<br />
<br />
Now... this massive amount of snow in Aarhus at this time of the year is not common, and frankly, I wonder if I am going to make it to work tomorrow. Instead, I would like to invite you - dear reader of this blog - to stop a few minutes with me and silently enjoy the scenery below, accompanied with a piece of J.S. Bach.<br />
<object height="385" width="480"><param name="movie" value="http://www.youtube.com/v/RlzhUBkqqwo?fs=1&hl=en_US"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/RlzhUBkqqwo?fs=1&hl=en_US" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object>Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com0tag:blogger.com,1999:blog-1805856980450756766.post-47104141146823714142010-11-07T13:26:00.004+01:002011-01-04T13:55:05.366+01:00One Stopping Power Library to Rule Them All: libdEdx<a href="http://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29">Stopping powers</a> describe the energy loss of charged particles traversing matter. In particle therapy, stopping powers are an essential ingredient for calculating the dose distribution of ion beams.<br />
<br />
A direct way of calculating the stopping power is using the <a href="http://en.wikipedia.org/wiki/Bethe_formula">Bethe equation.</a> However, this equation requires a good knowledge of the ionization potential (in particle therapy jargon: "the I-value") and for compounds this value is pretty ill researched. The I-value can be found experimentally, but there are only few experimental data available for compounds relevant for particle therapy, such as various tissue types and even for water. Our postdoc. Armin Lühr has recently submitted a paper where he takes a closer look on these issues which is available on the archive: <a href="http://arxiv.org/abs/1010.5356">http://arxiv.org/abs/1010.5356</a><br />
<br />
Several programs provide stopping powers, either as analytic calculations or inter/extrapolated experimental data. The list below may be incomplete, but these are the codes I have been in touch with so far:<br />
<ul><li><a href="http://physics.nist.gov/PhysRefData/Star/Text/ESTAR.html">ESTAR</a>: for electrons. (Fortran77)</li>
<li><a href="http://physics.nist.gov/PhysRefData/Star/Text/PSTAR.html">PSTAR</a>: for protons. (Fortran77)</li>
<li><a href="http://physics.nist.gov/PhysRefData/Star/Text/ASTAR.html">ASTAR</a>: for alpha particles (Fortran77)</li>
<li><a href="http://www.exphys.uni-linz.ac.at/Stopping/MstarWWW/MSTARInstr.htm">MSTAR</a>: for alpha particles and heavier ions up to Z=18. Basically MSTAR is scaling ASTAR data, where the scaling factors are fitted to experimental data. (Fortran77)</li>
<li><a href="http://www-linux.gsi.de/%7Eweick/atima/">ATIMA</a>: code developed by <a href="http://www.gsi.de/">GSI</a>. (Java wrapping a Fortran core)</li>
<li><a href="http://www.srim.org/">TRIM/SRIM</a>: Application which can simulate any ion on any compound.</li>
</ul>And various tables provided by the <a href="http://www.icru.org/">ICRU</a>:<br />
<ul><li>ICRU 49: proton data and alphas, equivalent with PSTAR/ASTAR.</li>
<li>ICRU 73: ions heavier than helium, old version</li>
<li>ICRU 73: new version after errata, quite similar to MSTAR, even if calculated differently.</li>
</ul>and in summary they don't agree too well at lower energies (say below 10 MeV/u).<br />
<br />
Nonetheless: from an application developer point of view this leaves you in a dilemma of choosing the proper code for your application, and most likely we will see more updates, since the issues are not solved yet with the erratum of the ICRU73.<br />
<br />
In addition, from a technical point of view most stopping power codes are not written in convenient ways which allows a clean integration into your application. This is a common thing which happens when physicists develop code: the code will always be optimized to work nicely on the developers computer and fulfill their specific needs. Platform portability, an API, and install scripts following de-facto standards are mostly absent.<br />
<br />
This is why we started the development of <a href="http://sourceforge.net/projects/libdedx/">libdEdx</a>.<br />
<br />
libdEdx is meant to be a platform independent stopping power library which contains multiple tables to choose from, and can be extended with additional algorithms/tables. Currently libdEdx includes ESTAR,PSTAR,ASTAR,MSTAR and ICRU73 data as well as an implementation of the Bethe-equation akin to that found in <a href="http://aptg-trac.phys.au.dk/shieldhit">SHIELD-HIT</a>.<br />
The material database is based on the extensive ICRU set found in the ESTAR table, and using Braggs additivity rule libdEdx can extend the MSTAR/ICRU73 data set to cover the ESTAR material list.<br />
<br />
libdEdx comes along with an installer based on <a href="http://www.cmake.org/">cmake</a>, and the first official release should be able to run on <a href="http://en.wikipedia.org/wiki/Windows_1.0">Windoze</a> just as well as Unix/Posix/Linux compliant platforms.<br />
<br />
Surely, <a href="http://geant4.cern.ch/">Geant4</a> also offers a range of stopping power tables to choose from, but you do not want to install entire Geant4 just to access the stopping power values. <br />
<br />
Our bachelor student Jakob Toftegaard (who very conveniently has a background in physics and computer science) did most of the coding. A very early experimental pre-release is available on sourceforge, but if you want to experiment with it and even contribute you can also grab the most recent version from the <a href="http://sourceforge.net/projects/libdedx/develop">SVN repository</a>.<br />
<br />
P.S.: Armin and David will present libdEdx on the <a href="http://www.ki.se/MC2010">MC2010 conference</a> in Stockholm on the 9th to the 12th November. Posters can be found <a href="http://phys.au.dk/research/aptg/resources/">here</a>.Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com1tag:blogger.com,1999:blog-1805856980450756766.post-28394977567932390102010-10-06T22:30:00.007+02:002010-10-08T12:57:02.194+02:00Monte Carlo Programs in Particle Therapy Research<i>- a note on software design.</i> <br />
<br />
In my research, I use Monte Carlo particle transport codes a lot in order to simulate the interactions of a particle beams with matter. There are several of these particle transport codes which are available for free, but if I have to simulate ions heavier than protons, then there are only few codes available which are capable of simulating the physics processes at clinical relevant energies. The four most common codes are <a href="http://www.fluka.org/">FLUKA</a>, <a href="http://geant4.cern.ch/">Geant4</a>, <a href="https://mcnpx.lanl.gov/">MCNPX</a> and <a href="http://www.inr.troitsk.ru/shield/index.html">SHIELD-HIT</a>. <br />
<br />
Each of these transport codes have their scope of applicability, advantages and disadvantages. Here, in our research group <a href="http://www.phys.au.dk/aptg">APTG</a> we work with FLUKA, Geant4 and SHIELD-HIT. In fact, we are actively developing the SHIELD-HIT code (visit our <a href="http://aptg-trac.phys.au.dk/shieldhit">SHIELD-HIT developer page</a>). Recently, I had a discussion with a colleague (and non-programmer) where I wanted to clarify why we put so much effort into SHIELD-HIT, now that basically all functions are more or less available in FLUKA or can be build in Geant4. I found it difficult to explain him the reasons.<br />
<br />
That is why I came up with the idea of comparing the particle transport codes with cars. I am not particularly fond of cars, on the contrary, but in the spirit of particle transportation (pun intended) I could not resist the temptation.<br />
<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiLBjrXJzpvxdNnM4SFnxaV1F-Yj0rg99moHjSiojV94uRuypdXoXIeuo1-n19cqHzpKiuQHSltGXR-N8ouQa2Gj2qX57oorcu5GT8VfVyNibrs3fI7JZ3jqJwhYN3i7rMFFSZCL1b2UP0/s320/Volkswagen-Passat_1973_800x600_wallpaper_02.jpg" style="margin-left: auto; margin-right: auto;" width="320" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A FLUKA car, Fortran 77 style.</td></tr>
</tbody></table>A <a href="http://www.fluka.org/">FLUKA</a> car would be a regular car which does the job it is supposed to do. Imagine VW Passat or whatever. If you enter such a car for the first time, it will take you less than 10 seconds to orient yourself, since things are as expected: clutch, throttle, brakes etc.. If you forget to fasten your seat belt, you will get an error message which tells you exactly what is wrong. If you need some extras which goes beyond the standard equipment, you can add them yourselves (by the FLUKA user routines), although the developers limit what you can attach to your car. You are not allowed to touch the engine at all, the developers tune it for you to best possible performance.<br />
FLUKA is closed source, and black-box like. If something fails with the engine (the physics models inside FLUKA), and this happens very rarely, you should take the car to repair ( = notifying the developers). Only the developers have access to the engine interior, and can fix it. While they do this, you realize that the interior may look rather old fashioned (the source is written in Fortran 77), and imagine it might be difficult to maintain, but the developers are experts, and have worked with it for many years. No reason to change this, as long as the engine runs smoothly and you still can find the special gasoline for the car (= a Fortran 77 compiler, deprecated on many newer Linux distributions).<br />
If you want to publish benchmarks against other cars (other codes or experimental data), you must first talk back to the developers, and they want to assure that you have been operating the car right. (Unlike removing the brakes, then publishing how the car crashed.) The FLUKA car is increasingly popular, since it has a steep learning curve, is easy to run and the driver does not need to know how the engine is working.<br />
<br />
<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgK9lCdt-m4UowMfboD4AkpTeFXS3cWe9eq4GJeT1z6HxAUy19LTdiG8U6KLBfUBS0ssTnTalXe1bi0iRHaKQ5rpyUNS1A-EC5euQb_VM-ESrbVOZExILM6xscy2PEa1LiHwz8TRS_ldhE/s320/MindstormsCollection-c.jpg" style="margin-left: auto; margin-right: auto;" width="320" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A Geant4 car. Geant4 provides you all the pieces you need to build a car. ANY car.</td></tr>
</tbody></table><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgK9lCdt-m4UowMfboD4AkpTeFXS3cWe9eq4GJeT1z6HxAUy19LTdiG8U6KLBfUBS0ssTnTalXe1bi0iRHaKQ5rpyUNS1A-EC5euQb_VM-ESrbVOZExILM6xscy2PEa1LiHwz8TRS_ldhE/s1600/MindstormsCollection-c.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"></a></div><a href="http://geant4.cern.ch/">Geant4</a> is not a car. It is a large box of <a href="http://en.wikipedia.org/wiki/Lego">Lego</a> where you - in principle - can build your own car. We are not talking about normal standard Lego bricks, but the most fancy kind of them, Lego Technic C++ style bricks! If you ever have programmed in C++ and played with Lego, you know that equally to Lego you can also attach these code bricks in ways which they are not really supposed to (<a href="http://en.wikipedia.org/wiki/Weak_typing">weak typing</a>). Installing the Lego bricks in your laboratory may require some expert knowledge.<br />
No-one has ever build a Lego based car similar to the FLUKA car, where you just step in, start the engine and go places. But there is no doubt, given infinite resources, you can build yourself a Ferrari, if you want. You can build a diamond inlaid SUV if such things turns you on. In principle anything is possible, but you need a lot of good developers and plenty of time. No research group has access to indefinite money supplies (or time), so instead research groups using Geant4, focuses on their specific needs. For instance, a famous research group in Boston have developed an engine (doing protons), which works well for their specific needs. In Japan a group is working on a special vehicle, lets say a Caterpillar (think <a href="http://geant4.cern.ch/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch08s03.html#sect.VisDrv.Mocren">gMocren</a> is a part of this), which eventually can do specialized tasks (treatment planning with ions). That is fine, but if you want to adapt it to your own needs which goes beyond the application originally was designed for, it can again be quite some task and requires a good deal of programming knowledge. (Assuming you get the source code at all. If you get it, you still need to understand what is going on).<br />
Perhaps some group has already developed higher level parts such as a carburetor and a light generator which are available to other researchers, yet they are not obliged to give these parts away. Geant4 is not GPL.<br />
<br />
<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqwhtGo94aGq3NmANGa_drLtDnrECO5SBzRACzgtU9X_uUmMufENPqvuW6JzxTJjncFL56l9OoruWZIm7uNS-eBibIWfRnM_97D8zUHFTOxNzi1xp7kMyXW0pZnwBNO6f00Z7J9eS9OfY/s320/niva.jpg" style="margin-left: auto; margin-right: auto;" width="320" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A SHIELD-HIT type car. Note, the driver found the light switch.</td></tr>
</tbody></table><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqwhtGo94aGq3NmANGa_drLtDnrECO5SBzRACzgtU9X_uUmMufENPqvuW6JzxTJjncFL56l9OoruWZIm7uNS-eBibIWfRnM_97D8zUHFTOxNzi1xp7kMyXW0pZnwBNO6f00Z7J9eS9OfY/s1600/niva.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"></a></div><a href="http://www.inr.troitsk.ru/shield/index.html">SHIELD-HIT</a> is a russian <a href="http://en.wikipedia.org/wiki/Lada_Niva">Niva</a>. Well, not precisely a regular Niva. At first glance you think, this is a normal car, not unlike a FLUKA car. You have to get a special contract with the code owners at <a href="http://www.inr.ru/">INR</a> before you may access the car.<br />
Once you got it, you feel confident you can run this car effortlessly. However, as soon as you get inside, you realize something is very different. First of all you need three different keys to start the engine. The clutch is mounted on the steering wheel, the light switch is hidden under the seat, and if you need to do left turns, you must configure the car to do so before you start it. You need an English speaking Russian to tell you all this, because essential parts of the manual is written in Russian, and the manual itself is incomplete, only covering the light switch part.<br />
If you look on the engine, you again realize it has lot in common with the FLUKA engine (SHIELD-HIT is also written in Fortran 77, and the geometry parser is also CG).<br />
The key difference to the FLUKA car is, if something is broken, you are allowed (or even encouraged) to repair it yourself. Clear error messages or other indications of what is wrong, are seldom. You may simply have operated your Niva wrong, of there may be a real bug in the engine. But you do have access to the source code - and this enables you to do all the modification you want in the code. If you know exactly what you want, this is actually a big advantage. Imagine yourself stranded in a village in the middle of Siberia, you will be happy you drive a Niva. When your Niva is fixed, the car runs smoothly - just as smooth as a FLUKA car or a custom Geant4 based "forward going vehicle" would do. And the Niva is tolerant to various gasoline types (you can compile with g77, gfortran, ifort etc...)<br />
<br />
So, our MSc student <a href="http://owww.phys.au.dk/main/person/uk/individ/u051747.shtm">David</a> has invested a lot of time in building the next generation Niva, the Niva version 2.0 (currently also known as <a href="http://aptg-trac.phys.au.dk/shieldhit">SHIELD-HIT10A</a>). It is supposed still to resemble a regular car but with improved user friendliness . The clutch and light switch are moved to more intuitive positions. Only one key should be necessary for starting the engine. And, as I mentioned in an <a href="http://willworkforscience.blogspot.com/2010/09/cyrillic-letters-in-latex.html">earlier blog-post</a> I am currently preparing an English manual for the new Niva 2.0.<br />
<br />
David is also benchmarking the Niva 2.0 and overhauling the engine (meaning, better parameters for the physics models matching the recently released experimental data by E. Hättner). Finally, the Niva 2.0 will feature a lot of new features which are not readily available in any other Monte Carlo particle transport vehicle, such as air conditioning and cup holders (one for each passenger).<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhyJhVUvsMXhjZqzJduP2PMaEdMmTb7l3TG1LNJC07DbbM27qfBYBb1VAtRr-imHnEZDyBYeHpgEQ3T5vbjK2c6EuRv2qKhISwFpjwHipgPcmyDaGCFCAU-twUwbDxLP_Ptywq_7qFXQx8/s1600/images.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"></a></div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" height="207" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghaLsTu8UxySiuMgjG2fS2SCPLgnzi57huZkvzTDELv4xcDRGVn95J2eH2zqeul-kHjUoCY6b0vWZFDhWD_S_WxVw0z46qE8Ua21ed3vv2w1DmrMQbqckIPruYYESBhbdXmHEZixqTvTo/s320/66.jpg" style="margin-left: auto; margin-right: auto;" width="320" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">SHIELD-HIT10A, aka Niva 2.0. Fortran 77 style artwork is still visible despite of the upgrade. (APTG developer impression).</td><td class="tr-caption" style="text-align: center;"><br />
</td><td class="tr-caption" style="text-align: center;"><br />
</td></tr>
</tbody></table><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghaLsTu8UxySiuMgjG2fS2SCPLgnzi57huZkvzTDELv4xcDRGVn95J2eH2zqeul-kHjUoCY6b0vWZFDhWD_S_WxVw0z46qE8Ua21ed3vv2w1DmrMQbqckIPruYYESBhbdXmHEZixqTvTo/s1600/66.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"></a></div>Now, let us assume, when David finishes his MSc February 2010, he would like to do a PhD project involving a pair of windscreen wipers and a light generator.<br />
He has three codes to choose from. Of course, we all like playing with Lego. Lego is fun, and someone has already developed a Lego light generator ... so we only need to build the windscreen wipers, and off we go, doing a lot of research. (I really get carried away now.)<br />
Alternatively David could choose to continue to work with the Niva 2.0. As a side effect the Niva will be upgraded with windscreen wipers which may benefit the continuation of the SHIELD-HIT project. Not as much fun as working with Lego, but probably as useful. Personally, I'd hit it, but working with Fortran77 is really demotivating. Especially if the code is full of GOTO statements.<br />
Finally we have the choice of working with FLUKA. Perhaps this is the easiest, but in my opinion a bit dull since we are not contributing with much new on the developer side of the code.<br />
<br />
There will be more of the <a href="http://aptg-trac.phys.au.dk/shieldhit">Niva 2.0</a> at the <a href="http://ki.se/ki/jsp/polopoly.jsp?d=34132&l=en">MC2010 conference in Stockholm</a>, where David will present his work (either poster or talk, we don't know yet).<br />
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<i><b>Come and meet us!</b></i>Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com5tag:blogger.com,1999:blog-1805856980450756766.post-53736788376600440292010-10-05T00:35:00.004+02:002010-10-05T00:48:07.025+02:00Pretty Good Privacy and EvolutionThis year, the danish government forced all its internet users to use the "<a href="http://nemid.info/">NemID</a>" solution for digital communication between the several public institutions, banks etc. The NemID concept is based on regular asymmetric encryption with a public and secret key pair. The developers of NemID realized very wisely that a significant amount of users (if not the majority) won't be capable of storing their secret key safely on their respective computers running <a href="http://en.wikipedia.org/wiki/Windows_1.0">windows</a>.<br />
<br />
The solution is that a private company "<a href="https://danid.dk/export/sites/dk.danid.oc/da/om_danid/">DanID</a>", contracted by the danish government, stores the secret key for the user (imagine this happening in Germany!), and any interaction is realized with a java based login portal and a <a href="http://en.wikipedia.org/wiki/Transaction_authentication_number">TAN</a> list.<br />
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Without commenting on the trustworthiness of "DanID", this solution obviously does not integrate with typical Linux mailers such as <a href="http://projects.gnome.org/evolution/">Evolution</a>.<br />
<br />
Therefore, my colleague <a href="http://neptun.phys.au.dk/">Bjarne Thomsen</a> recently urged me (multiple times, thanks) to encrypt / sign my emails using <a href="http://www.gnupg.org/">gpg</a>. Last time I did this was in 2004, but I must admit I cannot remember where I stored my old secret key (it is probably lost), and the revocation file is probably also gone. So, I had to start again from scratch. Here is the recipe:<br />
<br />
Fist generate a new key pair. I was very paranoid, and closed down any closed source processes which I do not trust (skype, flash, google earth ...), while generating this key.<br />
<br />
<code>$ gpg --gen-key</code><br />
<br />
Let it be valid for 2 years, you will probably loose your secret key, forget your pass phrase and/or your revocation file sooner or later, and there is no way you can delete keys from the key server.<br />
You can also choose between <a href="http://en.wikipedia.org/wiki/Rsa">RSA</a> and <a href="http://en.wikipedia.org/wiki/Digital_Signature_Algorithm">DSA</a>/<a href="http://en.wikipedia.org/wiki/ElGamal_encryption">ElGamal</a> signing/encryption. I chose RSA, for no specific reason. For the bit length the default is 2048, but I chose 4096 bit, which should be safe until year 2030. <br />
<br />
You will get a response akin to:<br />
<br />
<code>pub 4096R/xxxxxxxx 2010-10-04 [expires: 2012-10-03]</code><br />
<br />
where the <code>xxxxxxxx</code> value is your public key identifier.<br />
<br />
Next, you submit your public key to the key server:<br />
<br />
<code>$ gpg --keyserver pgp.mit.edu --send-keys xxxxxxx</code><br />
<br />
And finally I recommend you generate the aforementioned revocation file.<br />
<br />
<code>$ gpg --output revoke.asc --gen-revoke xxxxxxxx</code><br />
<br />
Anyone who has this file can revoke your key. You can print the file on paper and store it a safe place, if you wish. <br />
<br />
So, now you are ready to go. Fire up evolution, go to your mail account setup. There is a tab which says "Security". In this tab there is a place where you can enter your secret key ID. Don't worry, your key identifier is not secret in that sense, the actual key is protected with your pass phrase.<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgk8NEQGmM4VYOfn_o9mViy2uD4MraftVWmSCo4m7Ls__krsTe0GW41zwqhvdo_JGIKuPnNzSSZjiZXXPldsDj1jhKlmrEAxPo1sQEsHE0UCKHqx_HeH35lW1JBFIQkZllXGInJvmkGf1U/s1600/Screenshot+-+10042010+-+11:01:08+PM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgk8NEQGmM4VYOfn_o9mViy2uD4MraftVWmSCo4m7Ls__krsTe0GW41zwqhvdo_JGIKuPnNzSSZjiZXXPldsDj1jhKlmrEAxPo1sQEsHE0UCKHqx_HeH35lW1JBFIQkZllXGInJvmkGf1U/s320/Screenshot+-+10042010+-+11:01:08+PM.png" width="313" /></a></div><br />
Now you are able to send signed emails. Evolution will ask for a pass phrase when accessing your key.<br />
<br />
But you probably also want to send encrypted emails. In order to do so, you need to import the public key of the recipient. Evolution does not do this automatically, this is a very old bug in evolution which still has not been fixed, see <a href="https://bugs.launchpad.net/evolution/+bug/259665">#259665</a>.<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6U4QOCvnP_uMcDpeuxiakwuNyHbpWZOlvVYqCxEpKUsfWLS-VTNe12f2T-GwqYIbtuM9aZG3i1ws3mD1QVHlvtBNzZsOZBaDfdJN40n4L2KWWnJCt_I4cRuDrQ8IumO447AnB8kyDwy0/s1600/Screenshot+-+10042010+-+11:04:31+PM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="195" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6U4QOCvnP_uMcDpeuxiakwuNyHbpWZOlvVYqCxEpKUsfWLS-VTNe12f2T-GwqYIbtuM9aZG3i1ws3mD1QVHlvtBNzZsOZBaDfdJN40n4L2KWWnJCt_I4cRuDrQ8IumO447AnB8kyDwy0/s320/Screenshot+-+10042010+-+11:04:31+PM.png" width="320" /></a></div><br />
Instead, you must manually import the recipients public key. I look up the recipients key id on a key server, such as this one: <a href="http://pgp.mit.edu/">http://pgp.mit.edu/</a><br />
<br />
<code>$ gpg --keyserver pgp.mit.edu --recv-keys xxxxxxxx</code><br />
<br />
If you are sure you got the right key, sign it:<br />
<code>$ gpg --sign-key xxxxxxxx</code><br />
<br />
Ideally, you meet the person and exchange they key (e.g. at <a href="http://en.wikipedia.org/wiki/Key_signing_party">key-signing party</a>)<br />
<br />
If you need to sign against a specific secret key, use:<br />
<code>$ gpg --default-key xx(yoursecretkeyID)xx --sign-key xx(keyIDtobesigned)xx</code><br />
<br />
List your keys with:<br />
<code>$ gpg --list-keys</code><br />
<br />
<br />
Tadaaa, now you can encrypt the mails in evolution. Note that the email addresses of the public key and the recipient you mail the key to must match.<br />
<br />
If you ever need to revoke your key, do:<br />
<code>$ gpg --output revoke.asc --gen-revoke xxxxxxxx<br />
$ gpg --import revoke.asc<br />
$ gpg --keyserver pgp.mit.edu --send-keys xxxxxxxx</code><br />
<br />
<br />
Oh yes, and here is my ASCII armored <a href="http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x3B2A28E300F8644F">public key</a>:<br />
<pre><span style="font-size: x-small;">-----BEGIN PGP PUBLIC KEY BLOCK-----
Version: SKS 1.1.0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=L/Hy
-----END PGP PUBLIC KEY BLOCK-----</span></pre>Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com0tag:blogger.com,1999:blog-1805856980450756766.post-58932967025788552382010-09-26T14:26:00.000+02:002010-09-26T14:26:47.423+02:00Cyrillic letters in LaTeXCurrently, I am writing a manual for a Russian Monte Carlo particle transport code <a href="http://www.inr.ru/shield/">SHIELD-HIT</a>. LaTeX is just perfect for this purpose due to its vast amount of capabilities while still, say, "forcing" the user to be well structured and use a clean layout and formatting.<br />
<br />
Unlike some years ago, most Linux distributions are now running in a UTF-8 environment, and most applications endorse UTF-8, which I think is a blessing for international minded spirits such as myself. LaTeX documents can be in UTF-8, without the use of awkward escape characters such as <code>\"u</code> for an ü.<br />
<br />
But LaTeX and dvips still need to have the appropriate fonts installed. The aforementioned manual may contain text in Cyrillic letters, so my header is formatted this way:<br />
<code><br />
\documentclass[a4paper,english,russian,10pt]{book}<br />
\usepackage[utf8]{inputenc} % make weird characters work<br />
\usepackage[T2A,OT1]{fontenc} % enable Cyrillic fonts<br />
\usepackage{amsmath}<br />
\usepackage{amssymb}<br />
...<br />
</code><br />
<br />
Most editors such as emacs or gedit will recognize the character encoding for you: <br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQ8ab__WbTvMhb5QL3eTFUrd9dm6wdh7C5yy8s8ovmq0lfa7U_pE9WL8KMA2iw5qWGQ_Fg23VENZGGjKM9RWZVcurFIznk2NuD2K1PdDlb9UDbfPA8c8auDATx5TxxYiWmzefyBdtrCWU/s1600/utf8_emacs.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQ8ab__WbTvMhb5QL3eTFUrd9dm6wdh7C5yy8s8ovmq0lfa7U_pE9WL8KMA2iw5qWGQ_Fg23VENZGGjKM9RWZVcurFIznk2NuD2K1PdDlb9UDbfPA8c8auDATx5TxxYiWmzefyBdtrCWU/s400/utf8_emacs.png" width="400" /></a></div>However, emacs is also sensitive to the <code>\usepackage[utf8]{inputenc}</code> line in the .tex file, presumably this is a feature coming along with the <i>auctex</i> package. If you specify something which is inconsistent with the character encoding of the file, you will have a terrible mess.<br />
<br />
Compiling the .tex file, I was confronted with an error:<br />
<code><br />
...<br />
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)))<br />
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty<br />
<br />
! Package fontenc Error: Encoding file `t2aenc.def' not found.<br />
(fontenc) You might have misspelt the name of the encoding.<br />
...<br />
</code><br />
Ok, so I looked into synaptic what file provides the <i>t2aenc.def</i>. But synaptic did not return any results. Then I searched for the "T2A" font. According to synaptic, this is provided by the "cm-super" package. But after installing the 60 MB package the error still persisted.<br />
<br />
The trick was to install the <i>texlive-lang-cyrillic</i> package. Then the .tex file could be compiled. This is rather unintuitive, since there is no mentioning of the <i>t2aenc.def</i> file in the <i>texlive-lang-cyrillic</i> package.<br />
<br />
Next step is to convert the .dvi file to a PDF file. If you do not have the <i>cm-super</i> package installed, you may end up with:<br />
<code><br />
~/Projects/shieldhit/trunk/doc/tex$ dvipdf ShieldHIT_Manual.dvi <br />
dvips: Font tctt0800 not found, using cmr10 instead.<br />
dvips: Design size mismatch in font tctt0800<br />
dvips: Checksum mismatch in font tctt0800<br />
dvips: ! invalid char 246 from font tctt0800<br />
</code><br />
<br />
and a rather empty .pdf file. The <i>cm-super-minimal</i> package may be insufficient, In my case I had to install the full <i>cm-super</i> package.<br />
<br />
Conclusion: UTF-8 is good for you, it makes life easier and more enjoyable. So use it whenever you can. :-)Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com0tag:blogger.com,1999:blog-1805856980450756766.post-4417655260776073772010-09-24T20:08:00.004+02:002010-09-25T00:21:35.910+02:00Yet another ssh wonder: SSHFS<a href="http://fuse.sourceforge.net/sshfs.html">SSHFS</a> is a file system which is capable of mounting remote filesystems locally on a computer if the remote system can be accessed by ssh.<br />
<br />
This is a very interesting alternative to NFS or Samba based filesystems. First of all, it can be operated entirely from userspace, which is cool. Contrary to NFS, any user can mount any remote directory he or she has access to via ssh.<br />
<br />
There are no locking issues with SSHFS, which makes it robust and free of the infamous "NFS stale handles". The speed is inferior to NFS and not recommended for intensive use, but it is perfect for occasional work.<br />
<br />
On Debian you merely need to install the sshfs package and its dependencies, e.g.: (as root)<br />
<br />
<code>$ apt-get install sshfs</code><br />
<br />
Then you need to add all the users to the fuse group. E.g. the user bassler can be added:<br />
<br />
<code>$ adduser bassler fuse</code><br />
<br />
after this, you must logout of the system (entirely, yes. Like exiting your X session, and logging in again. Just closing and opening the terminal window wont be sufficient).<br />
That's it.<br />
<br />
Now the (non-root) user you have added to the fuse group can mount remote directories:<br />
<br />
<code>$ sshfs example.com:/remote/directory /local/directory</code><br />
<br />
Unmounting can be realized with<br />
<br />
<code>$ fusermount -u /local/directory</code><br />
<br />
What I still miss, is an automount solution.Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com0tag:blogger.com,1999:blog-1805856980450756766.post-79540443374180539092010-09-16T23:17:00.000+02:002013-09-06T01:21:00.207+02:00Downloading a youtube video and extract audioEver played a game of the <a href="http://en.wikipedia.org/wiki/S.T.A.L.K.E.R.:_Shadow_of_Chernobyl">STALKER</a> series? I am not all that fond of ego shooters, but I enjoy movies made by the russian director <a href="http://en.wikipedia.org/wiki/Andrei_Tarkovsky">Tarkovsky</a>, and the STALKER triology is based upon his famous movie of the same name. You can find plenty of <a href="http://www.youtube.com/watch?v=XbRfDSTaIiQ">movie snippets on YouTube</a>.<br />
<br />
Anyway, I also came across <a href="http://www.youtube.com/watch?v=6QpAMzTCDpg">this little benchmark test</a> (yeah, there is no visible difference between DirectX10 and 11, but that's not the point here), which had a very catchy tune. A few visitors ask where the music was taken from, but no one replied. Now, it can be rather difficult to search for an instrumental piece of music on the net, when all you have got is the music.<br />
<i>Update:</i> Or you may find the tune <a href="http://youtu.be/ZqV-raQXTzE">in another vid</a>, and actually get a reply. The track above is Dream Catchers by A.L.N.P.S.V from the Tunguska Chillout Grooves vol. 1.<br />
<br />
So I searched for a way of somehow extracting the audio in a .ogg file. All my attempts (even trying to use some sort of audio capture) failed, until my friend <a href="http://www.oz9aec.dk/">Alexandru Csete</a> told me about <a href="http://bitbucket.org/rg3/youtube-dl/downloads">this nifty python script</a> which can download youtube videos.<br />
<br />
Unpacking it, and executing it from command line<br />
<br />
<code>$ ./youtube-dl http://www.youtube.com/watch?v=6QpAMzTCDpg<br />
</code><br />
which returns a .mp4 file. The audio channel can now be extracted with ffmpeg:<br />
<br />
<code>$ ffmpeg -i 6QpAMzTCDpg.mp4 -vn -acodec vorbis -aq 50 audio.ogg<br />
</code><br />
The "-vn" option tells ffmpeg to ignore the video part. If the "-acodec vorbis" is not specified, the audio had some aac format, which e.g. my mobile phone is not capable of handling, so this had to be stated explicitly. <br />
<br />
I spent some time to figure out the quality setting. First I tried "-ab 64000" setting, but somehow ffmpeg did all the encoding at about 60 kpbs irrespectively of the -ab setting. The default settings were pretty bad, and especially in this example you can easily hear losses. (If you listen to the faint woodwind-like sounds close to 5:30 you hear they are almost gone on lower quality setting.) Using the "-aq 50" option I got a good result.<br />
<br />
I checked with the "file" command to see what format the audio was:<br />
<br />
<code>$ file audio.ogg <br />
audio.ogg: Ogg data, Vorbis audio, stereo, 44100 Hz, ~0 bps<br />
</code><br />
Apparently the file command cannot recognize the bps correctly. <br />
<br />
I also tried to convert to mp3 format, but even if I had installed the "lame" library, ffmpeg refused to find it. I did not pursue this further, since I am actually quite happy with the ogg/vorbis format.Anonymoushttp://www.blogger.com/profile/13613098782917752267noreply@blogger.com2