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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<title>Scripting ds9 - DS9 </title>
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<body><div class="mainbar">
<a name="maintext"></a><div align="center"><h1>Scripting ds9</h1></div>
<p>
Return to the <a href="../index.html">DS9 Users Manual</a></p>
<hr size="5" noshade>
<div>
<h2>Synopsis</h2>
<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>
<p>
If you encounter any problems, please email saord @ cfa.harvard.edu.
</p>
</div>
<hr size="5" noshade>
<h2><a name="toc">Contents</a></h2>
<ul>
<li><strong><a href="index.html#commandline">Command-line Scripting</a></strong></li>
<li><strong><a href="index.html#xpa">XPA Scripting</a></strong></li>
<li><strong><a href="index.html#samp">SAMP: Simple Application Messaging Protocol</a></strong></li>
<li><strong><a href="index.html#history">History</a></strong></li>
<li>
<strong>Images</strong><ul>
<li><a href="#clcontour">Figure 1: Command line: x-ray data with contours</a></li>
<li><a href="#clcontourdss">Figure 2: Command line: x-ray and optical data with contours</a></li>
<li><a href="#xpacontour">Figure 3: XPA: x-ray data with contours</a></li>
<li><a href="#xpacontourdss">Figure 4: XPA: x-ray and optical data with contours</a></li>
</ul>
</li>
</ul>
<hr>
<div class="sectionlist">
<div class="section">
<h2><a name="commandline">Command-line Scripting</a></h2>
<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>
<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding: 0.5em; overflow: auto; border: thin solid black;">
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 &
</pre></div>
<p>
This command line produces <a href="#clcontour">Figure 1</a>.
</p>
<div class="figure">
<div class="caption"><h3><a name="clcontour">Figure 1: Command line: x-ray data with contours</a></h3></div>
<div><img alt="[Diffuse emission with contours overlaid; a point source is visible in the upper left corner of the image.]" src="contour.png"></div>
</div>
<p>
The options direct ds9 to:
</p>
<ol 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>
</ol>
<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>
<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding: 0.5em; overflow: auto; border: thin solid black;">
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 &
</pre></div>
<p>
The resulting image is shown in <a href="#clcontourdss">Figure 2</a>.
</p>
<div class="figure">
<div class="caption"><h3><a name="clcontourdss">Figure 2: Command line: x-ray and optical data with contours</a></h3></div>
<div><img alt="[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.]" src="contourdss.png"></div>
</div>
<p>
The options which have been added from the previous command
line are:
</p>
<ol 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>
</ol>
<p>
At this point, we can end the ds9 session or modify the
display interactively via the ds9 GUI.
</p>
<hr>
</div>
<div class="section">
<h2><a name="xpa">XPA Scripting</a></h2>
<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>
<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding: 0.5em; overflow: auto; border: thin solid black;">
unix% ds9 acisf05005N002_evt2.fits &
</pre></div>
<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>
<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding: 0.5em; overflow: auto; border: thin solid black;">
unix% xpaget xpans
DS9 ds9 gs /tmp/.xpa/DS9_ds9.22972 username
</pre></div>
<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>
<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding: 0.5em; overflow: auto; border: thin solid black;">
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
</pre></div>
<p>
This command line produces <a href="#xpacontour">Figure 3</a>.
</p>
<div class="figure">
<div class="caption"><h3><a name="xpacontour">Figure 3: XPA: x-ray data with contours</a></h3></div>
<div><img alt="[Diffuse emission with contours overlaid; a point source is visible in the upper left corner of the image.]" src="contour.png"></div>
</div>
<p>
The options direct ds9 to:
</p>
<ol 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>
</ol>
<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>
<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding: 0.5em; overflow: auto; border: thin solid black;">
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
</pre></div>
<p>
The resulting image is shown in <a href="#clcontourdss">Figure 2</a>.
</p>
<div class="figure">
<div class="caption"><h3><a name="xpacontourdss">Figure 4: XPA: x-ray and optical data with contours</a></h3></div>
<div><img alt="[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.]" src="contourdss.png"></div>
</div>
<p>
The options which have been added from the previous command
line are:
</p>
<ol 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>
</ol>
<p>
At this point, we can end the ds9 session, issue further XPA
commands, or modify the display interactively via the ds9
GUI.
</p>
<hr>
</div>
<div class="section">
<h2><a name="samp">SAMP: Simple Application Messaging Protocol</a></h2>
<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>
</div>
</div>
<hr size="5" noshade>
<h2><a name="history">History</a></h2>
<table class="history">
<tr>
<td class="historydate">21 Sep 2009</td>
<td>
Original version
</td>
</tr>
</table>
<hr size="5" noshade>
<p>
Return to the <a href="../index.html">DS9 Users Manual</a></p>
</div></body>
</html>
|
