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  <info>
    
    <name>scripts</name>
    <version>Sept 2009</version>
    <title>
      <long>Scripting ds9</long>
    </title>
    <history>
      <entry day="21" month="September" year="9" who="liz">
	Original version
	<!-- scripted version of contours thread //-->
     </entry>
     </history>
  </info>

  <text>
    <overview>

      <synopsis>
        <p>
	  Scripting with ds9 can be done in several ways:  by invoking
	  the GUI with a number of command-line options or via
	  the <a href="http://hea-www.harvard.edu/RD/xpa/index.html">XPA
	  messaging system</a>.   A third option, Simple Application
	  Messaging Protocol (SAMP), is introduced but not included in
	  the examples.
	</p>

	<p>
	  To illustrate how to script ds9, we
	  repeat the <a href="../contour/index.html">contours example</a>
	  with both methods,.  The examples use Chandra data from an
	  observation of the galaxy cluster Abell 2142 (ObsID 5005).  
	</p>
      </synopsis>
    </overview>

    <sectionlist>

      <section id="commandline">
        <title>Command-line Scripting</title>

	<p>
	  The ds9 Reference Manual
	  has <a href="../../ref/command.html">an extensive list of
	  the available command line options</a>.  The most important 
	  thing to note is that the commands are executed one at a
	  time in the order they are listed.   
	</p>

	<p>
	  To create contours on a data image:
	</p>

<screen>
unix% ds9 acisf05005N002_evt2.fits -bin about 3800 3800 -bin factor 2 \
    -scale log -cmap b \ 
    -contour yes -contour limits 1 100 \
    -contour smooth 5 -contour nlevels 6 -contour save ds9.con &amp;
</screen>

        <p>
	  This command line produces <figlink id="clcontour"/>.
	</p>

	 <figure id="clcontour">
	   <title>Command line: x-ray data with contours</title>
	   <description>Diffuse emission with
	   contours overlaid; a point source is visible in the upper
	   left corner of the image.</description>  
	   <bitmap format="png">contour.png</bitmap>
	 </figure> 

        <p>
	  The options direct ds9 to:
	</p>

	<list type="1">
	  <li><tt>-bin about 3800 3800</tt> : center the image display at (x,y)=(3800,3800)</li>
	  <li><tt>-bin factor 2</tt> : bin the data by a factor of 2</li> 
	  <li><tt>-scale log</tt> : set the display to log scale</li> 
	  <li><tt>-cmap b</tt> : use the "b" colormap</li>
	  <li><tt>-contour yes</tt> : display contours</li> 
	  <li><tt>-contour limits 1 100</tt> : set the minimum and maximum contour limits</li>
	  <li><tt>-contour smooth 5</tt> : set contour smoothness to "5"</li>	  
	  <li><tt>-contour nlevels 6</tt> : create six contour levels</li> 
	  <li><tt>-contour save ds9.com</tt> : save the contours to the file "ds9.con"</li> 
	</list>

	<p>
	  If you wish to add options to the command line after it has
	  been processed, the whole command must be run again from the
	  beginning.  It is, however, possible to interact with
	  the ds9 GUI that has been created.  For instance, instead of
	  including the "<tt>-bin about 3800 3800</tt>" modifier, the
	  image could be recentered in ds9 interactively.
	</p>

	<p>
	  The following command line builds on the previous example by
	  retrieving a DSS image and copying the contours to the new
	  frame:
	</p>

<screen>
unix% ds9 acisf05005N002_evt2.fits -bin about 3800 3800 -bin factor 2 \
    -scale log -cmap b \ 
    -contour yes -contour limits 1 100 \
    -contour smooth 5 -contour nlevels 6 -contour copy \
    -dsssao A2142 -cmap grey -contour paste \
    -frame first -match frames wcs &amp;
</screen>

	<p>
	  The resulting image is shown in <figlink id="clcontourdss"/>.
	</p>

        <figure id="clcontourdss">
	  <title>Command line: x-ray and optical data with contours</title>
	  <description>The x-ray data is in the left frame and the
	    optical data is in the right frame; both have the x-ray
	    contours displayed on the data.</description>
	  <bitmap format="png">contourdss.png</bitmap>
	</figure> 

	<p>
	  The options which have been added from the previous command
	  line are:
	</p>

	<list type="1">
	  <li><tt>-contour copy</tt> : copy the x-ray contours</li>
	  <li><tt>-dsssao A2142</tt> : retrieve a DSS image of A2142
	  from the DSS-SAO server (there are also a "dsseso" and
	  "dssstsci" options)</li>
	  <li><tt>-cmap grey</tt> : use the "grey" colormap in the DSS frame</li>
	  <li><tt>-contour paste</tt> : paste the x-ray contours onto
	  the optical data</li>
	  <li><tt>-frame first</tt> : select the first ds9 frame</li>
	  <li><tt>-match frames wcs</tt> : match the WCS of the DSS
	  frame to the current (x-ray) frame</li>
	</list>

	<p>
	  At this point, we can end the ds9 session or modify the
	  display interactively via the ds9 GUI.
	</p>


      </section>

      <section id="xpa">
        <title>XPA Scripting</title>

	<p>
	  X Public Access (XPA) is a messaging system which provides 
	  communication between Unix programs through a set of access
	  points. The two most common actions are retrieving
	  information (<tt>xpaget</tt>) and issuing commands
	  (<tt>xpaset</tt>). For more information, see the <a
	  href="http://hea-www.harvard.edu/RD/xpa/">XPA Messaging
	  System</a> page and the <a 
	  href="../../ref/xpa.html">XPA Access Points</a>
	  section of the ds9 manual.  
	</p>

	<p>
	  XPA commands may be issued one at a time from the terminal
	  or collected in a script to run in batch mode.
	  Unlike the command line syntax, there is no predetermined
	  stopping point - commands may be sent to ds9 as long as the
	  GUI is open.
	</p>

	<p>
	  First, open ds9 with the data file:
	</p>

<screen>
unix% ds9 acisf05005N002_evt2.fits &amp;
</screen>

        <p>
	  The <a
	  href="http://hea-www.harvard.edu/RD/xpa/xpans.html">xpans
	  name server</a> is used to manage the names and ports
	  of XPA access points.  Use "<tt>xpaget xpans</tt>" to see
	  the list of available access points:  
	</p>

<screen>
unix% xpaget xpans
DS9 ds9 gs /tmp/.xpa/DS9_ds9.22972 username
</screen>

	<p>
	  Now that ds9 is running and linked to an XPA server, we can
	  use xpaset to modify the display and add contours.  (Refer
	  to the <a
	  href="http://hea-www.harvard.edu/RD/xpa/programs.html#xpaset">XPA
	  documentation</a> for details on <tt>xpaset</tt> syntax.) 
	</p>

<screen>
unix% xpaset -p ds9 bin about 3800 3800 
unix% xpaset -p ds9 bin factor 2 
unix% xpaset -p ds9 scale log 
unix% xpaset -p ds9 cmap b  
unix% xpaset -p ds9 contour yes 
unix% xpaset -p ds9 contour limits 1 100 
unix% xpaset -p ds9 contour smooth 5 
unix% xpaset -p ds9 contour nlevels 6 
unix% xpaset -p ds9 contour save xpa.con
</screen>

        <p>
	  This command line produces <figlink id="xpacontour"/>.
	</p>

	 <figure id="xpacontour">
	   <title>XPA: x-ray data with contours</title>
	   <description>Diffuse emission with
	   contours overlaid; a point source is visible in the upper
	   left corner of the image.</description>  
	   <bitmap format="png">contour.png</bitmap>
	 </figure> 

        <p>
	  The options direct ds9 to:
	</p>

	<list type="1">
	  <li><tt>xpaset -p bin about 3800 3800</tt> : center the image display at (x,y)=(3800,3800)</li>
	  <li><tt>xpaset -p bin factor 2</tt> : bin the data by a factor of 2</li> 
	  <li><tt>xpaset -p scale log</tt> : set the display to log scale</li> 
	  <li><tt>xpaset -p cmap b</tt> : use the "b" colormap</li>
	  <li><tt>xpaset -p contour yes</tt> : display contours</li> 
	  <li><tt>xpaset -p contour limits 1 100</tt> : set the minimum and maximum contour limits</li>
	  <li><tt>xpaset -p contour smooth 5</tt> : set contour smoothness to "5"</li>	  
	  <li><tt>xpaset -p contour nlevels 6</tt> : create six contour levels</li> 
	  <li><tt>xpaset -p contour save xpa.com</tt> : save the contours to the file "xpa.con"</li> 
	</list>

	<p>
	  As long as the ds9 GUI remains open, we can continue to
	  modify the display.  Here we build on the previous example
	  by retrieving a DSS image and copying the contours to the
	  new frame:
	</p>

<screen>
unix% xpaset -p ds9 contour copy 
unix% xpaset -p ds9 dsssao A2142 
unix% xpaset -p ds9 cmap grey
unix% xpaset -p ds9 contour paste 
unix% xpaset -p ds9 frame first
unix% xpaset -p ds9 match frames wcs
</screen>

	<p>
	  The resulting image is shown in <figlink id="clcontourdss"/>.
	</p>

        <figure id="xpacontourdss">
	  <title>XPA: x-ray and optical data with contours</title>
	  <description>The x-ray data is in the left frame and the
	    optical data is in the right frame; both have the x-ray
	    contours displayed on the data.</description>
	  <bitmap format="png">contourdss.png</bitmap>
	</figure> 

	<p>
	  The options which have been added from the previous command
	  line are:
	</p>

	<list type="1">
	  <li><tt>xpaset -p contour copy</tt> : copy the x-ray contours</li>
	  <li><tt>xpaset -p dsssao A2142</tt> : retrieve a DSS image of A2142
	  from the DSS-SAO server (there are also a "dsseso" and
	  "dssstsci" options)</li>
	  <li><tt>xpaset -p cmap grey</tt> : use the "grey" colormap in the DSS frame</li>
	  <li><tt>xpaset -p contour paste</tt> : paste the x-ray contours onto
	  the optical data</li>
	  <li><tt>xpaset -p frame first</tt> : select the first ds9 frame</li>
	  <li><tt>xpaset -p match frames wcs</tt> : match the WCS of the DSS
	  frame to the current (x-ray) frame</li>
	</list>

	<p>
	  At this point, we can end the ds9 session, issue further XPA
	  commands, or modify the display interactively via the ds9
	  GUI.
	</p>

      </section>

      <section id="samp">
        <title>SAMP: Simple Application Messaging Protocol</title>

	<p>
	  A third method of scripting ds9 is via
	  <a href="http://www.ivoa.net/Documents/latest/SAMP.html">SAMP</a>,
	  a messaging protocol that enables astronomy software
	  tools to interoperate and communicate.  SAMP is also used by
	  such applications
	  as <a href="http://www.star.bris.ac.uk/~mbt/topcat/">TOPCAT</a>,
	  an interactive graphical viewer and editor for tabular data
	  and <a href="http://aladin.u-strasbg.fr/">Aladin</a>, an
	  interactive software sky atlas.      
	</p>

	<p>
	  Information on the ds9 SAMP implementation is available in
	  the  <a href="../../ref/samp.html">ds9 Reference Manual</a>.
	</p>    
      </section>

    </sectionlist>
  </text>

</thread>