Task #1892: Readding style without symlink

.gitattributes

@@ -232,6 +232,7 @@ CEP/DP3/AOFlagger/doc/site/img/rfigui-plotmenu.png -text
 CEP/DP3/AOFlagger/doc/site/index.html -text
 CEP/DP3/AOFlagger/doc/site/reading-mode.html -text
 CEP/DP3/AOFlagger/doc/site/strategy-example-a.html -text
+CEP/DP3/AOFlagger/doc/site/style.css -text
 CEP/DP3/AOFlagger/include/AOFlagger/CMakeLists.txt -text
 CEP/DP3/AOFlagger/include/AOFlagger/baseexception.h -text
 CEP/DP3/AOFlagger/include/AOFlagger/blaswrap.h -text

CEP/DP3/AOFlagger/doc/site/CHANGELOG

+Version 2.0.1
+2012-03-16	André Offringa <of...nga@astro.rug.nl>
+  * This release is a quick fix for a bug that caused a strategy read failure on machines with non-standard locales
+  * Bug fix: fixing bug causing strategy reader to malfunction with different locales (reported by Arpad Miskolczi)
+  * Bug fix: show an error box when a strategy fails to load instead of crashing
+  * Bug fix: complex plane plot was still using gnuplot -- now uses the internal plotter.
+  * Bug fix: fixed a bug that sometimes caused a crash after having resized the time-frequency diagram.
+  * Bug fix: building without gtkmm was not possible, patched by Marcel Loose.
+
 Version 2.0.0
 2012-03-08	André Offringa <of...nga@astro.rug.nl>
   * Main points of this release: no longer depence on pdfviewer & gnuplot for drawing plots and new tools for quality analysis. Strategy file format did not change, thus .rfis files from 1.5.0 can be opened without a problem in 2.0.0.
@@ -8,6 +17,7 @@ Version 2.0.0
   * New feature: Text along x,y,z axes of time-frequency plot can be manually set.
   * New feature: log-log distribution plot in rfigui, with various analysis possible (slope calculation, rayleigh fitter).
   * New feature: rfigui will now immediately ask which baseline to load, instead of loading the first baseline (requested by Raymond Oonk).
+  * New feature: you can now specify a MS on the commandline with the rfigui: "rfigui <ms>"
   * Bug fix: Baseline name disappeared in bottom status bar when moving mouse over time-frequency plot. Baseline name is now reported when mouse is moved outside time-frequency plot (requested by Raymond Oonk).
   * Bug fix: very large sets were not displayed correctly in the rfigui due to cairo limitations.
   * Bug fix: clicking on statistics button sometimes crashed the gui.

CEP/DP3/AOFlagger/doc/site/faq.html

@@ -25,10 +25,10 @@
 <li>I still have questions / contact info</li>
 </ul>
 <h3>Where should I start with reading documentation about the tools?</h3>
-<p>At present, there is not so much information on the RFI tools. If you
-are reducing LOFAR data, you should at least read the
+<p>If you are reducing LOFAR data, you should at least read the
 <a href="http://www.astron.nl/radio-observatory/lofar/lofar-imaging-cookbook">LOFAR imaging cookbook</a>.
-A first tutorial on the GUI can be found here:
+The NDPPP chapter contains also information about the "quality" tools that are included in the AOFlagger
+package. A first tutorial on the GUI can be found here:
 <a href="gui-tutorial.html">RFI gui tutorial</a>, and an example to
 optimize the default strategy here:
 <a href="strategy-example-a.html">Strategy optimization example</a>.
@@ -80,7 +80,7 @@ This depends on the channel resolution and frequency behaviour. Should be fine i
 <p><code>makeFLAGwritable &lt;MyObservation.MS&gt;</code></p>
 <p>This will take a few seconds to rewrite the flag column, after which you can run rficonsole.</p>
 <h3>Plotting does not work in the GUI</h3>
-<p>Plotting requires several programs:</p>
+<p>[update 2012-03: the GUI now uses an internal plotter, and this answer is probably no longer relevant]. Plotting requires several programs:</p>
 <ul>
 <li><a href="http://www.gnuplot.info/">Gnuplot</a>, version 4.2 or higher</li>
 <li>ps2pdf, which is part of the <a href="http://ghostscript.com/">Ghostscript</a> software</li>
@@ -102,10 +102,13 @@ part of the strategy with a newer strategy, you might be able to solve the probl
 <h3>Does rficonsole store e.g. the statistics in a log?</h3>
 <p>Since October 2010, RFI console uses the LOFAR logger, which in turn uses LogCplus. Standard logging configuration can be set up in a configuration file. The parameters <code>-nolog</code> and <code>-v</code> can be used to alter logging strategy. The standard unix program <code>tee</code> can be used to save the output to file while at the same time monitoring the standard output.</p>
 <h3>How does RFI console recognise RFI?</h3>
-<p>It estimates the astronomical signal and searches for statistical abnormalities that look like lines in the time/frequency plots. It has several tricks to enhance the speed. The following papers describe parts of the detection technique in detail:</p>
+<p>It estimates the astronomical signal and searches for statistical abnormalities that look like lines in the time/frequency plots.
+After initial detection, it applies a morphological algorithm to find likely contaminated samples.
+It has several tricks to enhance the speed. The following refereed papers describe parts of the detection technique in detail:</p>
 <ul>
-  <li><a href="http://adsabs.harvard.edu/doi/10.1111/j.1365-2966.2010.16471.x">Post-correlation radio frequency interference classification methods</a>, <em>MNRAS</em>, Volume 405, Issue 1, June 2010, pp. 155-167</li>
-  <li><a href="http://adsabs.harvard.edu/abs/2010arXiv1007.2089O">A LOFAR RFI detection pipeline  and its first results</a></li>
+  <li><a href="http://adsabs.harvard.edu/doi/10.1111/j.1365-2966.2010.16471.x">Post-correlation radio frequency interference classification methods</a>, <span class="journal">MNRAS</span>, Vol. 405, 1, June 2010, pp. 155-167</li>
+  <li><a href="http://adsabs.harvard.edu/abs/2010arXiv1007.2089O">A LOFAR RFI detection pipeline  and its first results</a>, <span class="journal">PoS, RFI2010</span>, March 2010.</li>
+	<li><a href="http://adsabs.harvard.edu/abs/2012A%26A...539A..95O">A morphological algorithm for improving radio-frequency interference detection</a>, <span class="journal">A&amp;A</span>, Vol. 539, A95, March 2012.</li>
 </ul>
 <h3>I still have questions / contact info</h3>
 <p>I love to have feedback in order to update this FAQ and get a grib on common problems. You can reach me on my e-mail address, <code>&lt;my-last-name&gt;@astro.rug.nl</code>, and my last name is offringa.</p>

CEP/DP3/AOFlagger/doc/site/index.html

@@ -5,9 +5,10 @@
 <body>
 <a href="http://www.astro.rug.nl/~offringa/">Offringa</a>-&gt;RFI software
 <h2>RFI software</h2>
-<p>This page describes the software to detect and mitigate radio frequency interference (RFI) in a radio measurement set. The main algorithms is described in the article "Post-correlation radio frequency interference classification methods" by Offringa et al, published in <a href="http://adsabs.harvard.edu/doi/10.1111/j.1365-2966.2010.16471.x">MNRAS, Volume 405, Issue 1, pp. 155-167</a>. Please acknowledge this paper in publications in which the software is used. </p>
+<p>This page describes the software to detect and mitigate radio frequency interference (RFI) in a radio measurement set. The main algorithms is described in the articles
+"<a href="http://adsabs.harvard.edu/doi/10.1111/j.1365-2966.2010.16471.x">Post-correlation radio frequency interference classification methods'</a>" (Offringa et al. 2010, MNRAS, Volume 405, Issue 1, pp. 155-167) and "<a href="http://www.aanda.org/index.php?option=com_article&access=doi&doi=10.1051/0004-6361/201118497&Itemid=129">A morphological algorithm for improving radio-frequency interference detection</a>" (Offringa et al. 2012, A&amp;A, Volume 539, Issue A95). Please acknowledge these papers in publications in which the software is used. The first one introduces the SumThreshold method and tests signal estimation methods, the latter introduces the Scale-invariant rank operator.</p>
 <p>I've made a "<a href="faq.html">Frequently Asked Questions</a>" page for the software, a short <a href="gui-tutorial.html">RFI GUI tutorial</a> and an <a href="strategy-example-a.html">example of how one can optimize the strategy</a>.</p>
-<p>Last release: version 2.0.0, 9 March 2012.</p>
+<p>Last release: version 2.0.1, 16 March 2012.</p>
 <p>Contents:</p>
 <ul>
 <li><a href="#introduction">Introduction</a></li>
@@ -25,6 +26,7 @@
 <p>The software is published under the GNU General Public License version 3.</p>
 <a id="download"><h4>Download</h4></a>
 <p>The latest version of the software can be downloaded here:</p>
+<ul><li>Download: <a href="AOFlagger-2.0.1.tar.bz2">AOFlagger-2.0.1.tar.bz2</a> (16 March 2012, <a href="CHANGELOG">changelog</a>)</li></ul>
 <ul><li>Download: <a href="AOFlagger-2.0.0.tar.bz2">AOFlagger-2.0.0.tar.bz2</a> (9 March 2012, <a href="CHANGELOG">changelog</a>)</li></ul>
 <ul><li>Download: <a href="AOFlagger-1.5.0.tar.bz2">AOFlagger-1.5.0.tar.bz2</a> (20 October 2011, <a href="CHANGELOG">changelog</a>)</li></ul>
 <ul><li>Download: <a href="AOFlagger-1.4.0.tar.bz2">AOFlagger-1.4.0.tar.bz2</a> (22 Juli 2011, <a href="CHANGELOG">changelog</a>)</li></ul>
@@ -33,7 +35,7 @@
 <ul><li>Download: <a href="AOFlagger-1.1.0.tar.bz2">AOFlagger-1.1.0.tar.bz2</a> (22 October 2010)</li></ul>
 <p>See the compilation instruction below.</p>
 <a id="installation"><h4>Installation</h4></a>
-<p>The package contains part of the LOFAR software tree. In contrast to the previous version, this version does no longer including external libraries: they need to be installed separately. Most astronomical workstations will have most of the libraries.</p>
+<p>The packages contain a part of the LOFAR software tree that contain the AOFlagger tools. Most astronomical workstations will have most of the required libraries.</p>
 <h5>Requirements</h5>
 <p>Below is a list of libraries that are required.</p>
 <ul>
@@ -43,11 +45,12 @@
 <li><a href="http://xmlsoft.org/">libxml</a>, used for saving scripts / configurations.</li>
 <li><a href="http://www.netlib.org/clapack/">CLAPACK</a>, for linear algebra, such as singular value decomposition.</li>
 <li><a href="http://heasarc.nasa.gov/fitsio/">CFITSIO</a>, for reading and writing FITS files.</li>
-<li>(the <a href="http://www.gnu.org/software/gsl/">GNU Science Library</a> is no longer required since version 1.2)</li>
+<li><a href="http://log4cplus.sourceforge.net/">Log4cplus</a>, for making log files. I was notified by Arpad Miskolczi that AOFlagger is not yet compatible with Log4cplus version 1.1.0, so use version 1.0.4 or earlier. </li>
+<li>(the <a href="http://www.gnu.org/software/gsl/">GNU Science Library</a> is not required for versions between 1.2 and 1.5)</li>
 <li>gtkmm (only for <tt>rfigui</tt> and other graphical programs)</li>
 </ul>
-<p>All the libraries are available as free and open software. The gtkmm libraries and headers are only required to compile the gui. If they are not present, cmake will warn about it, but will compile the console programs nevertheless.</p>
-<p>I would not encourage you to compile gtkmm yourself; it has many dependencies. Rather use your package manager (or ask your system administrator). Debian ships this library as "gtkmm-dev".</p>
+<p>All the libraries are available as free and open software. The gtkmm libraries and headers are required for the gui but not for the console binary. If they are not present, cmake will warn about it, but will compile the console programs nevertheless.</p>
+<p>I disencourage you to compile gtkmm yourself; it has many dependencies. Rather use your package manager (or ask your system administrator). Debian ships this library as "gtkmm-dev".</p>
 <p>Some other libraries have to be available on the system (but are generally available). The complete list: </p>
 <ul>
 <li>png library</li>
@@ -77,16 +80,20 @@ CMake will tell you when some of the files can not be found. If you need to spec
 <h5>rficonsole</h5>
 <p>The <tt>rficonsole</tt> program is the simplest way of executing a strategy. To flag RFI in a measurement set, type the following command:</p>
 <pre>./rficonsole &lt;path&#8209;to&#8209;ms&gt; [&lt;another&#8209;path&#8209;to&#8209;ms&gt; ...]</pre>
-<p>This will run the default flagging strategy, which has the best balance between flagging quality and speed. The specified filename should normally be a .MS directory containing an AIPS measurement set. You can type <tt>./rficonsole</tt> without parameters to get information about its command. Currently, the following page is returned:</p>
+<p>This will run the default flagging strategy, which has the best balance between flagging quality and speed. The specified filename should normally be a .MS directory containing an AIPS++/Casa measurement set. You can type <tt>./rficonsole</tt> without parameters to get information about its command. Currently, the following page is returned:</p>
 <pre>./rficonsole
-RFI strategy console runner
-This program will execute an RFI strategy as can be created with the RFI gui
-or a console program called rfistrategy, and executes it on one or several .MS
-directories.
-
-Author: Andr&eacute; Offringa (e-mail)
-
-Usage: ./rficonsole [-j &lt;threadcount&gt;] [-strategy &lt;file.rfis&gt;] &lt;ms1&gt; [&lt;ms2&gt; [..]]</pre>
+Usage: ./rficonsole [-v] [-j &lt;threadcount&gt;] [-strategy &lt;file.rfis&gt;] [-indirect-read] [-nolog] [-skip-flagged] &lt;ms1&gt; [&lt;ms2&gt; [..]]
+  -v will produce verbose output
+  -j overrides the number of threads specified in the strategy
+  -strategy specifies a possible customized strategy
+  -indirect-read will reorder the measurement set before starting, which is normally faster
+  -nolog will not use the LOFAR logger to output logging messages
+  -skip-flagged will skip an ms if it has already been processed by RFI console according
+   to its HISTORY table.
+  -uvw reads uvw values (some strategies require them)
+  -column &lt;NAME&gt; specify column to flag
+Execute 'rfistrategy' without parameters for help on creating RFIS strategies.
+</pre>
 <h5>rfistrategy</h5>
 <p>To customize the flagging process, you can run the rficonsole with an alternate strategy with the <tt>-strategy</tt> flag. You can create an <tt>.rfis</tt>-strategy file with the gui or with the rfistrategy command. rfistrategy is a console program. Run the rfistrategy command without parameters to get help:</p>
 <pre>./rfistrategy

CEP/DP3/AOFlagger/doc/site/style.css

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+
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