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	<title>The Telegraphic &#187; physics</title>
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	<link>http://blog.thetelegraphic.com</link>
	<description>Online home of Danny Price, University of Oxford</description>
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		<title>pyFitsidi &#8211; Python FITS IDI writing</title>
		<link>http://blog.thetelegraphic.com/2011/pyfitsidi-python-fits-idi-writing/</link>
		<comments>http://blog.thetelegraphic.com/2011/pyfitsidi-python-fits-idi-writing/#comments</comments>
		<pubDate>Wed, 18 May 2011 13:38:50 +0000</pubDate>
		<dc:creator>dan</dc:creator>
				<category><![CDATA[physics]]></category>
		<category><![CDATA[python]]></category>
		<category><![CDATA[scripts & stuff]]></category>

		<guid isPermaLink="false">http://blog.thetelegraphic.com/?p=243</guid>
		<description><![CDATA[I recently spent a few weeks at the Medicina Radiotelescope, Italy, working on getting data from a correlator into a format that CASA and AIPS could read. To do this, I made a python script to convert the data into a FITS IDI file. The FITS Interferometry Data Interchange Convention...]]></description>
			<content:encoded><![CDATA[<p><a href="http://blog.thetelegraphic.com/wp-content/uploads/2011/05/CygA.img_.png"><img class="alignleft size-thumbnail wp-image-245" title="CygA.img" src="http://blog.thetelegraphic.com/wp-content/uploads/2011/05/CygA.img_-150x150.png" alt="Cygnus A" width="150" height="150" /></a>I recently spent a few weeks at the Medicina Radiotelescope, Italy, working on getting data from a correlator into a format that CASA and AIPS could read. To do this, I made a python script to convert the data into a FITS IDI file.</p>
<p>The FITS Interferometry Data Interchange Convention (“FITS-IDI”) is a  set of conventions layered upon the standard FITS format to assist in  the interchange of data recorded by interferometric telescopes,  particularly at radio frequencies and very long baselines.</p>
<p><a href="https://github.com/telegraphic/pyfitsidi">pyFitsidi</a> is a collection of functions that create headers and data units that conform to the FITS-IDI convention. It was written primarily to convert data from a CASPER correlator into a format that can be imported into data reduction packages such as AIPS++ and CASA.</p>
<p>pyFitsidi is built upon <a href="http://www.stsci.edu/resources/software_hardware/pyfits">pyFITS</a> and <a href="http://numpy.scipy.org/">numpy</a>. Astronomical coordinate calculations are done with <a href="http://rhodesmill.org/pyephem/">pyEphem</a>, and the HDF file reading is done with <a href="http://www.pytables.org/moin">pyTables</a> (although you could use h5py also). HTML documentation (generated with sphinx), can be found in docs/_build/html, and there is also a PDF file.</p>
<h3>Links</h3>
<p>pyFitsidi @ Github<br />
<a href="https://github.com/telegraphic/pyfitsidi">https://github.com/telegraphic/pyfitsidi</a></p>
<p>Much more info on the FITS IDI convention can be found on its official page<br />
<a href="http://fits.gsfc.nasa.gov/registry/fitsidi.html">http://fits.gsfc.nasa.gov/registry/fitsidi.html</a></p>
<p>pyFitsidi uses pyFITS for file I/O, so its worth getting familiar with pyfits<br />
<a href="http://www.stsci.edu/resources/software_hardware/pyfits">http://www.stsci.edu/resources/software_hardware/pyfits</a></p>
<p>Finally, there are useful FITS resources at the NASA FITS website<br />
<a href="http://www.stsci.edu/resources/software_hardware/pyfits">http://fits.gsfc.nasa.gov/fits_home.html</a></p>
]]></content:encoded>
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		<item>
		<title>Oxford LyX Thesis Template</title>
		<link>http://blog.thetelegraphic.com/2010/oxford-lyx-thesis-template/</link>
		<comments>http://blog.thetelegraphic.com/2010/oxford-lyx-thesis-template/#comments</comments>
		<pubDate>Sun, 30 May 2010 14:28:17 +0000</pubDate>
		<dc:creator>dan</dc:creator>
				<category><![CDATA[LyX]]></category>
		<category><![CDATA[physics]]></category>
		<category><![CDATA[scripts & stuff]]></category>
		<category><![CDATA[Stickied]]></category>

		<guid isPermaLink="false">http://blog.thetelegraphic.com/?p=162</guid>
		<description><![CDATA[To celebrate the release of LyX 1.6.6, I thought I&#8217;d upload an Oxford Thesis Template for mathematics/physics/engineering, based on K. Gillow&#8217;s excellent LaTeX class. While it&#8217;s tailored to Oxford, with a few modifications I&#8217;m sure it could be used for any thesis. To get it working, you&#8217;ll  have to copy...]]></description>
			<content:encoded><![CDATA[<p><a href="http://blog.thetelegraphic.com/wp-content/uploads/2010/05/Oxford_University_Logo.jpg"><img class="alignleft size-thumbnail wp-image-207" title="Oxford_University_Logo" src="http://blog.thetelegraphic.com/wp-content/uploads/2010/05/Oxford_University_Logo-150x150.jpg" alt="" width="150" height="150" /></a>To celebrate the release of <a href="http://www.lyx.org">LyX 1.6.6</a>, I thought I&#8217;d upload an <a title="Oxford LyX Thesis Template" href="https://github.com/telegraphic/Oxford-LyX-Thesis-Template">Oxford Thesis Template</a> for mathematics/physics/engineering, based on K. Gillow&#8217;s <a href="http://www.maths.ox.ac.uk/help/faqs/latex/thesisclass">excellent LaTeX class</a>. While it&#8217;s tailored to Oxford, with a few modifications I&#8217;m sure it could be used for any thesis.</p>
<p>To get it working, you&#8217;ll  have to copy the <em>ociamthesis-lyx.cls </em>into your TeX installation, and copy the <em>ociamthesis-lyx.layout</em> to your LyX layout directory. Have a read of the readme.txt for further instructions. Finally, here&#8217;s an <a href="http://blog.thetelegraphic.com/wp-content/uploads/2010/05/thesis.pdf">example PDF</a>.</p>
<p>&nbsp;</p>
<p><strong>Update (May 2011):</strong> I have moved the files over to <a title="Oxford LyX Thesis Template @ GitHub" href="https://github.com/telegraphic/Oxford-LyX-Thesis-Template">Github</a>, to open it up to the world a little!</p>
<p><strong>Note:</strong> Some people have had issues with the  \maketitle, which comes about due to something to do with graphics in  child documents. It can be fixed by adding the line</p>
<pre>\usepackage{graphicx}</pre>
<p>to the preamble (go to the menu document &gt; settings &gt; LaTeX preamble).</p>
<p style="text-align: right;"><a title="Oxford thesis template - LyX" href="https://github.com/telegraphic/Oxford-LyX-Thesis-Template">Download  LyX template »</a></p>
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		<item>
		<title>Physics report with LyX + JabRef + Inkscape</title>
		<link>http://blog.thetelegraphic.com/2009/physics-report-with-lyx-jabref-inkscape/</link>
		<comments>http://blog.thetelegraphic.com/2009/physics-report-with-lyx-jabref-inkscape/#comments</comments>
		<pubDate>Mon, 17 Aug 2009 18:17:45 +0000</pubDate>
		<dc:creator>dan</dc:creator>
				<category><![CDATA[Miscellany]]></category>
		<category><![CDATA[physics]]></category>
		<category><![CDATA[scripts & stuff]]></category>

		<guid isPermaLink="false">http://blog.thetelegraphic.com/?p=143</guid>
		<description><![CDATA[To anyone doing an undergraduate degree in physics &#8211; download and learn to use these three programs: LyX: A frontend for LaTeX,  specially designed for people who don&#8217;t like LaTeX. You could consider it &#8220;training wheels for LaTeX&#8221;, but if you learn it well you&#8217;ll probably never need to learn...]]></description>
			<content:encoded><![CDATA[<p><img class="alignleft size-thumbnail wp-image-217" title="xkcd centrifuge" src="http://blog.thetelegraphic.com/wp-content/uploads/2009/08/xkcd-centrifuge-150x150.jpg" alt="No Mr Bond, I expect you to die.." width="150" height="150" />To anyone doing an undergraduate degree in physics &#8211; download and learn to use these three programs:</p>
<ul>
<li><a title="LyX: What you see is what you want" href="http://www.lyx.org">LyX</a>: A frontend for LaTeX,  specially designed for people who don&#8217;t like LaTeX. You could consider it &#8220;training wheels for LaTeX&#8221;, but if you learn it well you&#8217;ll probably never need to learn full-on LaTeX.</li>
<li><a title="JabREF reference manager" href="http://jabref.sourceforge.net/">JabREF</a>: A reference manager for making Bibtex bibliographies. It plays nice with LyX, and you can use it to organise all those papers you read just for fun.</li>
<li><a title="Inkscape" href="http://inkscape.org/">Inkscape</a>: A vector graphics program (SVG). Super useful for making diagrams to put into LaTeX. If you&#8217;re using LyX, the best option is to save your files as PDF when you want to insert them into LyX.</li>
</ul>
<p>These are all free, and cross-platform. Note that for LyX, you&#8217;ll need to download TeX as well. Just follow the instructions on the <a href="http://www.lyx.org/Download">lyx download page</a> and you should be fine. The only other thing you&#8217;ll need is a graphing program: I&#8217;d recommend Mathematica, MATLAB and OriginPro (note: not free).</p>
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		<item>
		<title>UWA Physics LyX Thesis template</title>
		<link>http://blog.thetelegraphic.com/2009/uwa-physics-lyx-thesis-template/</link>
		<comments>http://blog.thetelegraphic.com/2009/uwa-physics-lyx-thesis-template/#comments</comments>
		<pubDate>Mon, 17 Aug 2009 18:05:37 +0000</pubDate>
		<dc:creator>dan</dc:creator>
				<category><![CDATA[LyX]]></category>
		<category><![CDATA[physics]]></category>
		<category><![CDATA[scripts & stuff]]></category>
		<category><![CDATA[Stickied]]></category>

		<guid isPermaLink="false">http://blog.thetelegraphic.com/?p=137</guid>
		<description><![CDATA[In my honours at UWA (2008), I was the lone cowboy who decided to LyX instead of LaTeX. It saved me a shitload of time and LaTeX related anguish. As such, I thought I&#8217;d offer a UWA Thesis Template up to give a helping hand to anyone else who wants...]]></description>
			<content:encoded><![CDATA[<p><img class="alignleft size-full wp-image-212" title="logo_uwa" src="http://blog.thetelegraphic.com/wp-content/uploads/2009/08/logo_uwa.jpg" alt="" width="94" height="112" />In my honours at UWA (2008), I was the lone cowboy who decided to <a title="LyX: What you see is what you want" href="http://www.lyx.org">LyX </a> instead of LaTeX. It saved me a shitload of time and LaTeX related anguish. As such, I thought I&#8217;d offer a <a href="http://blog.thetelegraphic.com/wp-content/uploads/2009/08/UWA-Thesis.zip">UWA Thesis Template</a> up to give a helping hand to anyone else who wants to give LyX  a stab. In retrospect, there&#8217;s a few things I did dodgy along the way (I was pretty stressed out though, in my defense). Even so, I reckon it&#8217;ll be useful for some.</p>
<p>&nbsp;</p>
<p>A few hot tips:</p>
<ul>
<li>Press Ctrl + L to manually enter LaTeX, whenever you can&#8217;t do it out-of-the-box</li>
<li>Press Ctrl + M to enter maths mode</li>
<li>Learn all the maths shortcut key combinations (e.g. press Alt + M, then F to input a fraction)</li>
<li>Watch some youtube videos, <a href="http://www.youtube.com/watch?v=Wq9ti7GGHrs">like this one</a>, to help you get up to speed</li>
</ul>
<p>Good luck&#8230;</p>
<p style="text-align: right;"><a title="UWA thesis template - LyX" href="http://blog.thetelegraphic.com/wp-content/uploads/2009/08/UWA-Thesis.zip">Download LyX template »</a></p>
]]></content:encoded>
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		<item>
		<title>Anritsu VNA Python Script</title>
		<link>http://blog.thetelegraphic.com/2009/anritsu-vna-python-script/</link>
		<comments>http://blog.thetelegraphic.com/2009/anritsu-vna-python-script/#comments</comments>
		<pubDate>Tue, 26 May 2009 14:11:58 +0000</pubDate>
		<dc:creator>dan</dc:creator>
				<category><![CDATA[physics]]></category>
		<category><![CDATA[python]]></category>
		<category><![CDATA[Stickied]]></category>

		<guid isPermaLink="false">http://blog.thetelegraphic.com/?p=122</guid>
		<description><![CDATA[I spent a lot of time in the lab last month, taking measurements with an Anritsu 37xxxC series VNA. It would've taken me even longer if I hadn't made this little python script to control the VNA over GPIB.]]></description>
			<content:encoded><![CDATA[<p>I spent a lot of time in the lab last month, taking measurements with an Anritsu 37xxxC series VNA. It would&#8217;ve taken me even longer if I hadn&#8217;t made this little python script to control the VNA over GPIB. All it does it open a connection, grab the data off and then write it to a CSV file. The magic lines you need to know:</p>
<pre style="padding-left: 30px;"><span style="color: #da4332;">## Open a connection to the VNA</span>
VNA = visa.instrument("GPIB::06")

<span style="color: #da4332;">## Select a channel</span>
VNA.write("CH1")

<span style="color: #da4332;">## Get frequency data</span>
freq = VNA.ask_for_values("OFV")

<span style="color: #da4332;">## Get channel data</span>
S11 = VNA.ask_for_values("OFD")</pre>
<p>If you&#8217;re lazy just run the <a href="http://blog.thetelegraphic.com/wp-content/uploads/2009/05/grabData.py">grabData script</a> and voila. If you&#8217;re not, try editing the grabData() function to your needs and script away.</p>
<p>To get this to work, you&#8217;ll need <a href="http://www.python.org/">Python 2.5</a>, <a title="Python GPIB etc. support with pyVIsa" href="http://pyvisa.sourceforge.net/">pyVisa</a> and the relevant <a title="NI Instrument Driver Network" href="http://www.ni.com/devzone/idnet/">NI drivers</a> (488.2 and for me the ones for the UBS-GPIB thing). There&#8217;s some useful documentation on the <a href="http://www.us.anritsu.com/sitesearch/default.aspx?site=us_www_root&amp;q=37xxxc&amp;sort=date:D:L:d1&amp;filter=p">Anritsu site here</a>. Kudos to Oliver King for his help .</p>
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