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author: William Joye <wjoye@cfa.harvard.edu> 2016-10-27 19:01:15 (GMT)
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Binning and Filtering FITS Event Files - DS9 </title>
+</head> 
+<!--THIS FILE IS CREATED AUTOMATICALLY - DO NOT EDIT MANUALLY--> 
+<body><div class="mainbar">
+<a name="maintext"></a><div align="center"><h1>Binning and Filtering FITS Event Files</h1></div>
+<p>
+      Return to the <a href="../index.html">DS9 Users Manual</a></p>
+<hr size="5" noshade>
+<div>
+<h2>Synopsis</h2>
+        <p>
+	  When an x-ray event file is loaded, ds9 makes a virtual
+	  image for display by binning on one or more axes.
+	  This threads describes how to adjust the binning and buffer
+	  sizes.  Interactive data filtering is described, as well
+	  as binning in three dimensions.
+	</p>
+
+	<p>
+	  Note that the terms "binning" and "blocking" are used
+	  interchangeably in this thread.  They both refer to
+	  combining pixels in an image.  
+	</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#start">Getting Started</a></strong></li>
+<li><strong><a href="index.html#buffer">Buffer Size</a></strong></li>
+<li>
+<strong><a href="index.html#basics">Binning Basics</a></strong><ul>
+<li><a href="index.html#basics.block">Changing the binning factor</a></li>
+<li><a href="index.html#basics.cols">Binning different columns</a></li>
+</ul>
+</li>
+<li><strong><a href="index.html#cube">Data Cubes: Binning in three dimensions</a></strong></li>
+<li><strong><a href="index.html#filtering">Filtering Data</a></strong></li>
+<li><strong><a href="index.html#history">History</a></strong></li>
+<li>
+<strong>Images</strong><ul>
+<li><a href="#defaults">Figure 1: Data loaded with default buffer and bin size</a></li>
+<li><a href="#binmenu">Figure 2: The Bin menu</a></li>
+<li><a href="#smallbuffer">Figure 3: Buffer size set to 128x128</a></li>
+<li><a href="#largebuffer">Figure 4: Buffer size set to 4096x4096</a></li>
+<li><a href="#block4">Figure 5: Data binned by a factor of 4</a></li>
+<li><a href="#binpar">Figure 6: The Binning Parameter dialog</a></li>
+<li><a href="#detimage">Figure 7: Image binned in detector coordinates</a></li>
+<li><a href="#binpar2">Figure 8: Binning Parameter dialog for a data cube</a></li>
+<li><a href="#cubebox">Figure 9: Data Cube dialog box</a></li>
+<li><a href="#cubeimg">Figure 10: Viewing a data cube</a></li>
+<li><a href="#filterimg">Figure 11: Filtering data</a></li>
+</ul>
+</li>
+</ul>
+<hr>
+<div class="sectionlist">
+<div class="section">
+<h2><a name="start">Getting Started</a></h2>
+        
+
+	<p>
+	  This thread begins with Chandra data from an observation of
+	  the Antennae Galaxies (NGC 4038/NGC 4039, ObsID 315).  Open
+	  the file in ds9: 
+	</p>
+
+<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding:  0.5em; overflow: auto; border: thin solid black;">
+unix% ds9 acisf00315N002_evt2.fits &amp;
+</pre></div>
+
+        <p>
+	  A small section of the data is visible when the file is
+	  loaded, as shown in <a href="#defaults">Figure 1</a>.  The target of
+	  the observation is partially visible in the display frame.
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="defaults">Figure 1: Data loaded with default buffer and bin size</a></h3></div>
+<div><img alt="[The target sources of the observation are partially visible at the bottom of the frame.]" src="defaults.png"></div>
+</div>
+
+        <p>
+	  By default, the buffer size is set to 1024x1024 and the
+	  binning factor is set to 1.  These values will be adjusted
+	  in the following sections to illustrate how to make more of
+	  the data visible.
+	</p>
+
+	<p>
+	  The "Bin" menu, shown in <a href="#binmenu">Figure 2</a>, will be used to
+	  change the setting in the following examples.  From top to
+	  bottom, this menu contains the bin function setting,
+	  blocking factor, buffer size options, and access to the
+	  binning parameters dialog box.  
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="binmenu">Figure 2: The Bin menu</a></h3></div>
+<div><img alt="[The blocking factor is set to 1, the buffer size is 1024x1024, and the function is sum.]" src="binmenu.png"></div>
+</div>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="buffer">Buffer Size</a></h2>
+        
+
+	<p>
+	  The buffer size determines the size of the image generated
+	  by ds9.  By default, a full-resolution 1024x1024 image of
+	  the data is created.  If your input data file has larger
+	  dimensions, it is clipped to 1024x1024 in ds9.  The buffer
+	  settings range from 128x128 to 8192x1892.
+	</p>
+
+	<p>
+	  Setting the buffer to the smallest size, 128x128,
+	  illustrates how it works.  The data was centered on the
+	  sources in ds9 before the buffer size was changed, creating
+	  <a href="#smallbuffer">Figure 3</a>.
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="smallbuffer">Figure 3: Buffer size set to 128x128</a></h3></div>
+<div><img alt="[A small central portion of the data is visible.]" src="smallbuffer.png"></div>
+</div>
+
+	<p>
+	  Setting the buffer to a large size, e.g. 4096x4096, produces
+	  <a href="#largebuffer">Figure 4</a>.  The display frame is filled by
+	  the data, and the panner in the upper right indicates
+	  that more of the image is available.  Clicking and dragging
+	  the viewing bounding box in the panner will display a
+	  different portion of the image.
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="largebuffer">Figure 4: Buffer size set to 4096x4096</a></h3></div>
+<div><img alt="[The frame is filled by the data, and the panner indicates more of the image is outside the field of view.]" src="largebuffer.png"></div>
+</div>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="basics">Binning Basics</a></h2>
+        
+
+	<div class="subsectionlist">
+<div class="subsection">
+<h3><a name="basics.block">Changing the binning factor</a></h3>
+	    
+
+	    <p>
+	      While increasing the buffer size loads more of the file
+	      into ds9, binning the data makes more of it visible in
+	      the frame. Binning combines the specified number of
+	      pixels into one new pixel; the new pixel has a value
+	      equal to the sum of the original pixels.  (Note that if
+	      the bin method is changed to "average", the pixel values
+	      are averaged instead of summed.)
+	    </p>
+
+	    <p>
+	      The binning can changed from the "Bin" menu or from the
+	      "Bin" item in the button bar.  It's also possible to
+	      step through different binning values with the -/+
+	      buttons or the "Block In"/"Block Out" menu items.
+	    </p>
+
+	    <p>
+	      In <a href="#block4">Figure 5</a>, the buffer size is set to
+	      1024x1024, but the block factor has been set to 4.  A
+	      larger section of the data is visible in the frame.
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="block4">Figure 5: Data binned by a factor of 4</a></h3></div>
+<div><img alt="[Five of the CCDs are visible in the binned data.]" src="block4.png"></div>
+</div>
+	  <hr width="80%" align="center">
+</div>
+<div class="subsection">
+<h3><a name="basics.cols">Binning different columns</a></h3>
+	    
+
+	    <p>
+	      ds9 has the ability to display any of the other columns 
+	      stored in the event file, although it is generally only
+	      meaningful to use the spatial vector columns.   Begin by
+	      opening the "Bin → Binning Parameters" dialog box,
+	      shown in <a href="#binpar">Figure 6</a>.
+	    </p>
+
+	    <p>
+	      The "Bin Columns" menus are used to select the columns
+	      to be binned.  To create an image in detector
+	      coordinates, set the first to "detx" and the second to
+	      "dety"; the block is set to "2" for both.
+	      The "or center of data" box is checked so that the
+	      center of the data is recalculated for the new columns.
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="binpar">Figure 6: The Binning Parameter dialog</a></h3></div>
+<div><img alt="[The parameters are set to bin in detector coordinates about the center of the data.]" src="binpar.png"></div>
+</div>
+
+	    <p>
+	      Click "Apply" and the ds9 frame is updated, as shown in
+	      <a href="#detimage">Figure 7</a>.
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="detimage">Figure 7: Image binned in detector coordinates</a></h3></div>
+<div><img alt="[Some bad columns are visible in black in the detector image.]" src="detimage.png"></div>
+</div>
+
+	    <p>
+	      Alternatively, one can display an event file in specific 
+	      coordinates when starting ds9 from the command line:
+	    </p>
+
+<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding:  0.5em; overflow: auto; border: thin solid black;">
+unix% ds9 "acisf00315N002_evt2.fits[bin=detx,dety]" &amp;
+</pre></div>
+
+	  </div>
+</div>
+      <hr>
+</div>
+<div class="section">
+<h2><a name="cube">Data Cubes: Binning in three dimensions</a></h2>
+        
+
+	<p>
+	  It is possible to add a third column to the binning,
+	  creating a 3-dimensional image also known as a "data cube". 
+	  In this example, an (x,y,time) data cube is created of a
+	  Chandra observation of Jupiter (ObsID 1463).  A cube may be
+	  created from any three columns that make sense in the
+	  analysis.  For instance, you may want to create a PHA or
+	  energy axis to see how the spectral characteristics of a
+	  source change over time.  
+	</p>
+
+	<p>
+	  The data file is loaded into a new frame in ds9 and the "Bin →
+	  Binning Parameters" dialog box is opened again.  The "time"
+	  column of the file is selected from the "Bin 3rd Column"
+	  menu.  The limits of the data in that column are filled in
+	  automatically.  The "depth" field determines how many
+	  intervals the column is divided into; a depth of 25 is used.
+	  The completed parameter box is shown in
+	  <a href="#binpar2">Figure 8</a>.  
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="binpar2">Figure 8: Binning Parameter dialog for a data cube</a></h3></div>
+<div><img alt='[The third binning column is set to "time" with a depth of "25".]' src="binpar2.png"></div>
+</div>
+
+	<p>
+	  After clicking "Apply", two things
+	  happen: <a href="#cubebox">the "Data Cube" dialog
+	  box (Figure 9)</a> is launched and <a href="#cubeimg">the
+	  frame is updated to show only the (x,y) image of the first
+	  time slice (Figure 10)</a>.  (If the data cube dialog box doesn't
+	  launch, open it from the "Frame" menu.) 
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="cubebox">Figure 9: Data Cube dialog box</a></h3></div>
+<div><img alt="[The dialog box has controls to step through each slice of the data cube.]" src="cubebox.png"></div>
+</div>
+
+	<p>
+	  When "Play" is chosen, ds9 cycles through the bins of the
+	  time axis, essentially creating a movie of the (x,y)
+	  position of the object over time.  The speed of the frame
+	  changes is controlled from the "Interval" menu of the dialog
+	  box.   Any of the 25 intervals may be selected with the
+	  slider bar.
+	</p>
+	
+	<div class="figure">
+<div class="caption"><h3><a name="cubeimg">Figure 10: Viewing a data cube</a></h3></div>
+<div><img alt="[One interval of the data cube is visible at a time when displayed in ds9.]" src="cubeimg.png"></div>
+</div>
+
+	<p>
+	  The data cube can be saved as an MPEG movie from the "File →
+	  Save Image..." menu.  Select "MPEG-1 (Movie)" and click
+	  "OK"; after setting the filename, choose an MPEG Quality
+	  Factor.  The Jupiter data was saved at a quality factor of
+	  15: <a href="jupiter.mpg">jupiter.mpg</a>. 
+	</p>
+      <hr>
+</div>
+<div class="section">
+<h2><a name="filtering">Filtering Data</a></h2>
+        
+
+	<p>
+	  The "Bin Filter" field in the "Binning Parameters" dialog
+	  box is used to apply filters to the data.  A filter can be
+	  applied to any of the columns present in the input file. A
+	  colon is used to indicate a range of values.  Filters can
+	  also use &lt; (less than) or &gt; (greater than). 
+	</p>
+
+	<p>
+	  For instance, to include only the hard-band photons
+	  (2500-8000 eV): 
+	</p>
+
+<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding:  0.5em; overflow: auto; border: thin solid black;">energy=2500:8000</pre></div>
+
+	<p>
+	  Clicking "Apply" updates the ds9 display and keeps the
+	  dialog open for adjusting the filters.	 
+	</p>
+
+	<p>
+	  Multiple filters may be specified, separated by commas:
+	</p>
+
+<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding:  0.5em; overflow: auto; border: thin solid black;">energy=2500:8000, ccd_id=7</pre></div>
+
+        <p>
+	  The resulting image is shown in <a href="#filterimg">Figure 11</a>.
+	</p>
+	
+	<div class="figure">
+<div class="caption"><h3><a name="filterimg">Figure 11: Filtering data</a></h3></div>
+<div><img alt="[Only the hard-band photos on CCD 7 are displayed.]" src="filterimg.png"></div>
+</div>
+
+	<p>
+	  The filtered dataset can be saved as a FITS file for use in
+	  data analysis from the "File → Save Frame as Fits..."
+	  menu.   
+	</p>
+
+      </div>
+</div>
+<hr size="5" noshade>
+<h2><a name="history">History</a></h2>
+<table class="history">
+      <tr>
+<td class="historydate">26 Jun 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>
diff --git a/ds9/doc/user/binning/jupiter.mpg b/ds9/doc/user/binning/jupiter.mpg
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diff --git a/ds9/doc/user/binning/thread.xml b/ds9/doc/user/binning/thread.xml
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@@ -0,0 +1,358 @@
+<?xml version="1.0" encoding="us-ascii" ?>
+<!DOCTYPE thread>
+
+<thread>
+
+  <info>
+
+    <name>binning</name>
+    <version>June 2009</version>
+    <title>
+      <long>Binning and Filtering FITS Event Files</long>
+    </title>
+    <history>
+      <entry day="26" month="June" year="9" who="liz">
+	Original version
+     </entry>
+     </history>
+  </info>
+
+  <text>
+    <overview>
+
+      <synopsis>
+        <p>
+	  When an x-ray event file is loaded, ds9 makes a virtual
+	  image for display by binning on one or more axes.
+	  This threads describes how to adjust the binning and buffer
+	  sizes.  Interactive data filtering is described, as well
+	  as binning in three dimensions.
+	</p>
+
+	<p>
+	  Note that the terms "binning" and "blocking" are used
+	  interchangeably in this thread.  They both refer to
+	  combining pixels in an image.  
+	</p>
+      </synopsis>
+    </overview>
+
+    <sectionlist>
+      <section id="start">
+        <title>Getting Started</title>
+
+	<p>
+	  This thread begins with Chandra data from an observation of
+	  the Antennae Galaxies (NGC 4038/NGC 4039, ObsID 315).  Open
+	  the file in ds9: 
+	</p>
+
+<screen>
+unix% ds9 acisf00315N002_evt2.fits &amp;
+</screen>
+
+        <p>
+	  A small section of the data is visible when the file is
+	  loaded, as shown in <figlink id="defaults"/>.  The target of
+	  the observation is partially visible in the display frame.
+	</p>
+
+	<figure id="defaults">
+	  <title>Data loaded with default buffer and bin size</title>
+	  <description>The target sources of the observation are
+	  partially visible at the bottom of the frame.</description>
+	  <bitmap format="png">defaults.png</bitmap>
+	</figure>
+
+        <p>
+	  By default, the buffer size is set to 1024x1024 and the
+	  binning factor is set to 1.  These values will be adjusted
+	  in the following sections to illustrate how to make more of
+	  the data visible.
+	</p>
+
+	<p>
+	  The "Bin" menu, shown in <figlink id="binmenu"/>, will be used to
+	  change the setting in the following examples.  From top to
+	  bottom, this menu contains the bin function setting,
+	  blocking factor, buffer size options, and access to the
+	  binning parameters dialog box.  
+	</p>
+
+	<figure id="binmenu">
+	  <title>The Bin menu</title>
+	  <description>The blocking factor is set to 1, the buffer
+	  size is 1024x1024, and the function is sum.</description>
+	  <bitmap format="png">binmenu.png</bitmap>
+	</figure>
+
+      </section>
+
+
+      <section id="buffer">
+        <title>Buffer Size</title>
+
+	<p>
+	  The buffer size determines the size of the image generated
+	  by ds9.  By default, a full-resolution 1024x1024 image of
+	  the data is created.  If your input data file has larger
+	  dimensions, it is clipped to 1024x1024 in ds9.  The buffer
+	  settings range from 128x128 to 8192x1892.
+	</p>
+
+	<p>
+	  Setting the buffer to the smallest size, 128x128,
+	  illustrates how it works.  The data was centered on the
+	  sources in ds9 before the buffer size was changed, creating
+	  <figlink id="smallbuffer"/>.
+	</p>
+
+	<figure id="smallbuffer">
+	  <title>Buffer size set to 128x128</title>
+	  <description>A small central portion of the data is visible.</description>
+	  <bitmap format="png">smallbuffer.png</bitmap>
+	</figure>
+
+	<p>
+	  Setting the buffer to a large size, e.g. 4096x4096, produces
+	  <figlink id="largebuffer"/>.  The display frame is filled by
+	  the data, and the panner in the upper right indicates
+	  that more of the image is available.  Clicking and dragging
+	  the viewing bounding box in the panner will display a
+	  different portion of the image.
+	</p>
+
+	<figure id="largebuffer">
+	  <title>Buffer size set to 4096x4096</title>
+	  <description>The frame is filled by the data, and
+	  the panner indicates more of the image is outside the field
+	  of view.</description>
+	  <bitmap format="png">largebuffer.png</bitmap>
+	</figure>
+
+      </section>
+
+      <section id="basics">
+        <title>Binning Basics</title>
+
+	<subsectionlist>
+	  <subsection id="basics.block">
+	    <title>Changing the binning factor</title>
+
+	    <p>
+	      While increasing the buffer size loads more of the file
+	      into ds9, binning the data makes more of it visible in
+	      the frame. Binning combines the specified number of
+	      pixels into one new pixel; the new pixel has a value
+	      equal to the sum of the original pixels.  (Note that if
+	      the bin method is changed to "average", the pixel values
+	      are averaged instead of summed.)
+	    </p>
+
+	    <p>
+	      The binning can changed from the "Bin" menu or from the
+	      "Bin" item in the button bar.  It's also possible to
+	      step through different binning values with the -/+
+	      buttons or the "Block In"/"Block Out" menu items.
+	    </p>
+
+	    <p>
+	      In <figlink id="block4"/>, the buffer size is set to
+	      1024x1024, but the block factor has been set to 4.  A
+	      larger section of the data is visible in the frame.
+	    </p>
+
+	    <figure id="block4">
+	      <title>Data binned by a factor of 4</title>
+	      <description>Five of the CCDs are visible in the binned data.</description>
+	      <bitmap format="png">block4.png</bitmap>
+	    </figure>
+	  </subsection>
+
+	  <subsection id="basics.cols">
+	    <title>Binning different columns</title>
+
+	    <p>
+	      ds9 has the ability to display any of the other columns 
+	      stored in the event file, although it is generally only
+	      meaningful to use the spatial vector columns.   Begin by
+	      opening the "Bin &#8594; Binning Parameters" dialog box,
+	      shown in <figlink id="binpar"/>.
+	    </p>
+
+	    <p>
+	      The "Bin Columns" menus are used to select the columns
+	      to be binned.  To create an image in detector
+	      coordinates, set the first to "detx" and the second to
+	      "dety"; the block is set to "2" for both.
+	      The "or center of data" box is checked so that the
+	      center of the data is recalculated for the new columns.
+	    </p>
+
+	    <figure id="binpar">
+	      <title>The Binning Parameter dialog</title>
+	      <description>The parameters are set to bin in detector
+	      coordinates about the center of the data.</description>
+	      <bitmap format="png">binpar.png</bitmap>
+	    </figure>
+
+	    <p>
+	      Click "Apply" and the ds9 frame is updated, as shown in
+	      <figlink id="detimage"/>.
+	    </p>
+
+	    <figure id="detimage">
+	      <title>Image binned in detector coordinates</title>
+	      <description>Some bad columns are visible in black in the
+	      detector image.</description>
+	      <bitmap format="png">detimage.png</bitmap>
+	    </figure>
+
+	    <p>
+	      Alternatively, one can display an event file in specific 
+	      coordinates when starting ds9 from the command line:
+	    </p>
+
+<screen>
+unix% ds9 "acisf00315N002_evt2.fits[bin=detx,dety]" &amp;
+</screen>
+
+	  </subsection>
+	</subsectionlist>
+      </section>
+
+
+      <section id="cube">
+        <title>Data Cubes: Binning in three dimensions</title>
+
+	<p>
+	  It is possible to add a third column to the binning,
+	  creating a 3-dimensional image also known as a "data cube". 
+	  In this example, an (x,y,time) data cube is created of a
+	  Chandra observation of Jupiter (ObsID 1463).  A cube may be
+	  created from any three columns that make sense in the
+	  analysis.  For instance, you may want to create a PHA or
+	  energy axis to see how the spectral characteristics of a
+	  source change over time.  
+	</p>
+
+	<p>
+	  The data file is loaded into a new frame in ds9 and the "Bin &#8594;
+	  Binning Parameters" dialog box is opened again.  The "time"
+	  column of the file is selected from the "Bin 3rd Column"
+	  menu.  The limits of the data in that column are filled in
+	  automatically.  The "depth" field determines how many
+	  intervals the column is divided into; a depth of 25 is used.
+	  The completed parameter box is shown in
+	  <figlink id="binpar2"/>.  
+	</p>
+
+	<figure id="binpar2">
+	  <title>Binning Parameter dialog for a data cube</title>
+	  <description>The third binning column is set to "time" with a depth of "25".</description>
+	  <bitmap format="png">binpar2.png</bitmap>
+	</figure>
+
+	<p>
+	  After clicking "Apply", two things
+	  happen: <figlink id="cubebox">the "Data Cube" dialog
+	  box</figlink> is launched and <figlink id="cubeimg">the
+	  frame is updated to show only the (x,y) image of the first
+	  time slice</figlink>.  (If the data cube dialog box doesn't
+	  launch, open it from the "Frame" menu.) 
+	</p>
+
+	<figure id="cubebox">
+         <title>Data Cube dialog box</title>
+         <description>The dialog box has controls to step through each
+	   slice of the data cube.</description>
+         <bitmap format="png">cubebox.png</bitmap>
+       </figure>
+
+	<p>
+	  When "Play" is chosen, ds9 cycles through the bins of the
+	  time axis, essentially creating a movie of the (x,y)
+	  position of the object over time.  The speed of the frame
+	  changes is controlled from the "Interval" menu of the dialog
+	  box.   Any of the 25 intervals may be selected with the
+	  slider bar.
+	</p>
+	
+	<figure id="cubeimg">
+          <title>Viewing a data cube</title>
+          <description>One interval of the data cube is visible at a
+            time when displayed in ds9.</description>
+          <bitmap format="png">cubeimg.png</bitmap>
+	</figure>
+
+	<p>
+	  The data cube can be saved as an MPEG movie from the "File &#8594;
+	  Save Image..." menu.  Select "MPEG-1 (Movie)" and click
+	  "OK"; after setting the filename, choose an MPEG Quality
+	  Factor.  The Jupiter data was saved at a quality factor of
+	  15: <a href="jupiter.mpg">jupiter.mpg</a>. 
+	</p>
+      </section>
+
+
+      <section id="filtering">
+        <title>Filtering Data</title>
+
+	<p>
+	  The "Bin Filter" field in the "Binning Parameters" dialog
+	  box is used to apply filters to the data.  A filter can be
+	  applied to any of the columns present in the input file. A
+	  colon is used to indicate a range of values.  Filters can
+	  also use &lt; (less than) or &gt; (greater than). 
+	</p>
+
+	<p>
+	  For instance, to include only the hard-band photons
+	  (2500-8000 eV): 
+	</p>
+
+<screen>energy=2500:8000</screen>
+
+	<p>
+	  Clicking "Apply" updates the ds9 display and keeps the
+	  dialog open for adjusting the filters.	 
+	</p>
+
+	<p>
+	  Multiple filters may be specified, separated by commas:
+	</p>
+
+<screen>energy=2500:8000, ccd_id=7</screen>
+
+        <p>
+	  The resulting image is shown in <figlink id="filterimg"/>.
+	</p>
+	
+	<figure id="filterimg">
+          <title>Filtering data</title>
+          <description>Only the hard-band photos on CCD 7 are displayed.</description>
+          <bitmap format="png">filterimg.png</bitmap>
+	</figure>
+
+	<p>
+	  The filtered dataset can be saved as a FITS file for use in
+	  data analysis from the "File &#8594; Save Frame as Fits..."
+	  menu.   
+	</p>
+
+      </section>
+
+    </sectionlist>
+  </text>
+<!--
+	<figure id="">
+	  <title></title>
+	  <description></description>
+	  <bitmap format="png">.png</bitmap>
+	</figure>
+-->
+
+</thread>
+
+
+
diff --git a/ds9/doc/user/catalogs/2masscat.png b/ds9/doc/user/catalogs/2masscat.png
new file mode 100644
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new file mode 100644
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new file mode 100644
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@@ -0,0 +1,414 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Catalogs - DS9 </title>
+</head> 
+<!--THIS FILE IS CREATED AUTOMATICALLY - DO NOT EDIT MANUALLY--> 
+<body><div class="mainbar">
+<a name="maintext"></a><div align="center"><h1>Catalogs</h1></div>
+<p>
+      Return to the <a href="../index.html">DS9 Users Manual</a></p>
+<hr size="5" noshade>
+<div>
+<h2>Synopsis</h2>
+        <p>
+	  DS9 provides full support for loading, displaying,
+	  filtering, and saving catalogs. DS9 allows you to overlay
+	  symbols from multiple catalogs on the current image and to
+	  create expressions to style the source symbols based on
+	  catalog properties.  
+	</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#display">Displaying a Catalog</a></strong></li>
+<li><strong><a href="index.html#select">Selecting Sources with the Cursor</a></strong></li>
+<li><strong><a href="index.html#display2">Displaying Multiple Catalogs</a></strong></li>
+<li><strong><a href="index.html#clear">Clearing Catalog Sources</a></strong></li>
+<li><strong><a href="index.html#filter">Sorting and Filtering</a></strong></li>
+<li><strong><a href="index.html#symbol">Specifying Symbols with Conditional Expressions</a></strong></li>
+<li><strong><a href="index.html#save">Saving the Sources: Catalog Files and Region Files</a></strong></li>
+<li><strong><a href="index.html#cite">Citing a Catalog in Publication</a></strong></li>
+<li><strong><a href="index.html#history">History</a></strong></li>
+<li>
+<strong>Images</strong><ul>
+<li><a href="#2masssrc">Figure 1: 2MASS Sources for the Antennae Galaxies</a></li>
+<li><a href="#2masscat">Figure 2: Catalog Tool of 2MASS Sources</a></li>
+<li><a href="#cscsrc">Figure 3: CSC and 2MASS Sources for the Antennae Galaxies</a></li>
+<li><a href="#2masssort">Figure 4: 2MASS Sources Sorted by Decreasing Jmag</a></li>
+<li><a href="#jmag14">Figure 5: Filtering 2MASS Sources: Jmag&lt;14</a></li>
+<li><a href="#jmagrange">Figure 6: Filtering 2MASS Sources: Jmag&lt;14 or Jmag&gt;16.5</a></li>
+<li><a href="#editjmag14">Figure 7: Symbol Editing: Jmag&lt;14 Rule</a></li>
+<li><a href="#editjmag14ds9">Figure 8: Symbol Editing: Jmag&lt;14 Sources Displayed</a></li>
+<li><a href="#editjmagrange">Figure 9: Symbol Editing: Jmag&gt;16.5 Sources Added</a></li>
+<li><a href="#addlabels">Figure 10: Symbol Editing: Rule to Add a Label</a></li>
+<li><a href="#addlabelsds9">Figure 11: Symbol Editing: Jmag Labels Displayed</a></li>
+</ul>
+</li>
+</ul>
+<hr>
+<div class="sectionlist">
+<div class="section">
+<h2><a name="display">Displaying a Catalog</a></h2>
+        
+
+	<p>
+	  This thread uses an optical image of the Antennae Galaxies
+	  (NGC 4038/NGC 4039) from the Digital Sky Survey (DSS).   It
+	  was retrieved via the "Analysis → Image Servers" menu
+	  in ds9. 
+	</p>
+
+	<p>
+	  A number of the most popular catalogs are listed by
+	  wavelength in the "Analysis → Catalogs" menu.  More
+	  options can be accessed via the "Search for Catalogs" option
+	  in that menu.   
+	</p>
+
+	<p>
+	  First we overlay sources from 2MASS by choosing
+	  "Analysis → Catalogs → Infrared → 2MASS
+	  point sources".   The source matches are displayed on the
+	  ds9 display (<a href="#2masssrc">Figure 1</a>) and listed in a
+	  "Catalog Tool" window (<a href="#2masscat">Figure 2</a>). 
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="2masssrc">Figure 1: 2MASS Sources for the Antennae Galaxies</a></h3></div>
+<div><img alt="[The sources are displayed in green on the optical image.]" src="2masssrc.png"></div>
+</div> 
+
+	<p>
+	  A set area centered on the field of view is used for the
+	  first catalog search.  The center and size of the search
+	  area may be adjusted in the Catalog Tool by setting the
+	  RA, Dec, height, and width fields.  The "Coordinate" and
+	  "Size" menus may be used to set the units for those values
+	  (degrees/sexagesimal and degrees/arcmin/arcsec,
+	  respectively).  After changing the values, click the
+	  "Retrieve" button to update the Catalog Tool.
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="2masscat">Figure 2: Catalog Tool of 2MASS Sources</a></h3></div>
+<div><img alt="[199 sources were returned for this field.]" src="2masscat.png"></div>
+</div> 
+
+	<p>
+	  Note that ds9 attempts to select the correct (RA,Dec)
+	  columns from the catalog data file in order to display the
+	  sources.  In some cases, the user will have to explicitly
+	  set the column names by using the drop-down menus in the
+	  Catalog Tool.  In this example, ds9 correctly chose "_RAJ2000" and
+	  "_DEJ2000".
+	</p>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="select">Selecting Sources with the Cursor</a></h2>
+        
+	
+	<p>
+	  From the "Edit" menu in ds9, choose the "Catalog" cursor
+	  type.  Clicking on a source in the ds9 display highlights
+	  the corresponding row in the Catalog Tool.   Multiple sources may be
+	  selected by holding down the SHIFT key while clicking them.
+	</p>
+
+	<p> 
+	  Similarly, highlighting a row in the Catalog Tool will blink the
+	  source region in ds9.  If the "Pan to" option in the Catalog Tool
+	  "Preferences" menu is checked, the ds9 display also centers
+	  on the chosen source.  Mutiple rows may be selected by
+	  holding down the SHIFT or CTRL key while selecting them.
+	</p>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="display2">Displaying Multiple Catalogs</a></h2>
+        
+
+	<p>
+	  More than one catalog can be displayed in the same frame.	 
+	  By default, the sources are displayed as green circle
+	  points.  The color and shape can be changed in the "Symbol"
+	  menu of the Catalog Tool to distinguish between the different catalogs.    
+	</p>
+
+	<p>
+	  In <a href="#cscsrc">Figure 3</a>, the Chandra Source Catalog has been
+	  added to the display (Analysis → Catalogs → High
+	  Energy → Chandra Source).  The symbols for the CSC
+	  sources are set to red diamonds.
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="cscsrc">Figure 3: CSC and 2MASS Sources for the Antennae Galaxies</a></h3></div>
+<div><img alt="[The 2MASS sources are displayed as green circles and the CSC sources are displayed as red diamonds on the optical image.]" src="cscsrc.png"></div>
+</div> 
+
+	<p>
+	  To toggle the display of each catalog, use the "Show
+	  Regions" option in the Catalog Tool "Preferences" menu.
+	</p>
+      <hr>
+</div>
+<div class="section">
+<h2><a name="clear">Clearing Catalog Sources</a></h2>
+        
+
+	<p>
+	  Simply closing the Catalog Tool will not remove the sources from the
+	  display.  It is necessary to choose "Clear" from the
+	  corresponding Catalog Tool.
+	</p>
+
+	<p>
+	  To remove <em>all</em> the sources from the display, use
+	  "Analysis → Catalogs → Clear All". 
+	</p>
+
+	<p>
+	  For the rest of this thread, only the 2MASS sources will be
+	  used.   
+	</p>
+      <hr>
+</div>
+<div class="section">
+<h2><a name="filter">Sorting and Filtering</a></h2>
+        
+
+	<p>
+	  The source listing is sorted on position by default.  A
+	  different column for sorting may be selected from the "Sort"
+	  menu in the Catalog Tool.  Related checkboxes determine whether the
+	  results are listed in increasing or decreasing order.
+	  The Catalog Tool in <a href="#2masssort">Figure 4</a> is sorted on the
+	  "Jmag" column in decreasing order.
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="2masssort">Figure 4: 2MASS Sources Sorted by Decreasing Jmag</a></h3></div>
+<div><img alt="[The sources are sorted on the Jmag column in decreasing order.]" src="2masssort.png"></div>
+</div> 
+
+	<p>
+	  The "Filter" field in the Catalog Tool is used to filter out
+	  specific rows from the source matches.  A filter is
+	  conditional expression that is evaluated for each row of the
+	  catalog.  The column name must be referenced with a dollar
+	  sign in the expression, e.g. "$_RAJ2000".
+	</p>
+
+	<p>
+	  To select the sources with low Jmag values, the filter
+	  "$Jmag&lt;14" is used.  Click the "Filter" button to update
+	  the Catalog Tool and the ds9 display.  The results are shown in
+	  <a href="#jmag14">Figure 5</a>.
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="jmag14">Figure 5: Filtering 2MASS Sources: Jmag&lt;14</a></h3></div>
+<div><img alt="[33 sources are included in the filter.]" src="jmag14.png"></div>
+</div>
+
+	<p>
+	  TCL expression syntax can be used to construct more complex
+	  filters.  The filter "$Jmag&lt;14 || $Jmag&gt;16.5" uses the
+	  logical "OR" syntax ("||") to select any source with Jmag
+	  less than 14 or greater than 16.5, as shown in
+	  <a href="#jmagrange">Figure 6</a>. 
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="jmagrange">Figure 6: Filtering 2MASS Sources: Jmag&lt;14 or Jmag&gt;16.5</a></h3></div>
+<div><img alt="[70 sources are included in the filter.]" src="jmagrange.png"></div>
+</div> 
+
+	<p>
+	  The uniformity of the symbols doesn't distinguish between
+	  the low-Jmag sources and the high-Jmag sources.  The
+	  advanced symbol editing in the next section improves on this
+	  display.
+	</p>
+
+	<p>
+	  Before continuing the thread, clear the filter in the
+	  Catalog Tool so that all the sources are displayed.
+	</p>
+      <hr>
+</div>
+<div class="section">
+<h2><a name="symbol">Specifying Symbols with Conditional Expressions</a></h2>
+        
+
+	<p>
+	  The advanced symbol editing in the Catalog Tool allows you to
+	  specify the shape, size, color, and text of each symbol
+	  based on catalog column values. 
+	</p>
+
+	<p>
+	  Open the "Symbol Editor" from the "Symbol →
+	  Advanced..." menu in the Catalog Tool.   A conditional statement,
+	  written in the TCL expression syntax, is entered in the "If"
+	  field.  The styles that should be applied are set by the
+	  other fields (shape, color, text, etc.).  
+	</p>
+
+	<p>
+	  First, define a rule that sets the sources with
+	  Jmag&lt;14 to be red boxcircle points.  The completed form
+	  is shown in <a href="#editjmag14">Figure 7</a>.  After clicking the
+	  "Apply" button, the ds9 display is updated (<a href="#editjmag14ds9">Figure 8</a>).
+	</p>
+
+
+	<div class="figure">
+<div class="caption"><h3><a name="editjmag14">Figure 7: Symbol Editing: Jmag&lt;14 Rule</a></h3></div>
+<div><img alt="[The fields are set to display sources with Jmag&lt;14 as red boxpoints.]" src="editjmag14.png"></div>
+</div> 
+
+	<div class="figure">
+<div class="caption"><h3><a name="editjmag14ds9">Figure 8: Symbol Editing: Jmag&lt;14 Sources Displayed</a></h3></div>
+<div><img alt="[The sources with Jmag&lt;14 are displayed as red boxpoints.]" src="editjmag14ds9.png"></div>
+</div>
+
+	<p>
+	  The "Add" button in the Symbol Editor is used to create a
+	  new, empty form.  The second rule is defined such that
+	  sources with Jmag&gt;16.5 will be cyan diamonds.  
+	  After clicking the "Apply" button again, the ds9 display is
+	  as shown in <a href="#editjmagrange">Figure 9</a>. 
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="editjmagrange">Figure 9: Symbol Editing: Jmag&gt;16.5 Sources Added</a></h3></div>
+<div><img alt="[The sources with Jmag&gt;16.5 are displayed as cyan diamonds.]" src="editjmagrange.png"></div>
+</div>
+
+	<p>
+	  To edit an existing rule, highlight the rule in the Symbol
+	  Editor and adjust the parameters.  In
+	  <a href="#addlabels">Figure 10</a>, both rules have been updated
+	  so that the Text field is set to "$Jmag".  This
+	  <a href="#addlabelsds9">displays the Jmag column value
+	  next to the symbol (Figure 11)</a>. 
+	</p>
+
+
+	<div class="figure">
+<div class="caption"><h3><a name="addlabels">Figure 10: Symbol Editing: Rule to Add a Label</a></h3></div>
+<div><img alt="[The fields are set to label each source with its Jmag column value.]" src="addlabels.png"></div>
+</div> 
+
+	<div class="figure">
+<div class="caption"><h3><a name="addlabelsds9">Figure 11: Symbol Editing: Jmag Labels Displayed</a></h3></div>
+<div><img alt="[Each source is labeled with its Jmag column value.]" src="addlabelsds9.png"></div>
+</div>
+
+	<p>
+	  The ds9 Reference Manual
+	  has <a href="../../ref/catalog.html">further examples of
+	  symbol expressions</a>.
+	</p>
+
+	<p>
+	  The set of rules may be saved from the "File" menu in the
+	  Symbol Editor.  The output for these rules looks like:
+	</p>
+
+<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding:  0.5em; overflow: auto; border: thin solid black;">
+condition       shape   color   text    size    size2   units   angle
+---------       -----   -----   ----    ----    -----   -----   -----
+$Jmag&lt;14        boxcircle point red     $Jmag                   physical
+$Jmag&gt;16.5      diamond point   cyan    $Jmag                   physical
+</pre></div>
+
+	<p>
+	  The file can be loaded into a later ds9 session by opening
+	  the Symbol Editor and using the "File → Load" menu
+	  item.  Note that the column names in the symbol rules may
+	  have to be updated in order to use them with a different
+	  catalog.
+	</p>
+      <hr>
+</div>
+<div class="section">
+<h2><a name="save">Saving the Sources: Catalog Files and Region Files</a></h2>
+        
+
+
+	<p><strong>Saving a Catalog File</strong></p>
+	<p>
+	  The contents of the Catalog Tool may be saved from the "File →
+	  Save" menu.  If any filters are applied, the filtered output
+	  is saved in the catalog file.
+	</p>
+	
+	<p>
+	  ds9 supports three catalog formats: VOTable, Starbase, and
+	  tab-separated file.   If the catalog file will be loaded
+	  back into ds9 in the future, any of the three formats may be
+	  chosen.  
+	</p>	
+
+	<p><strong>Saving the Sources in a Region File</strong></p>
+	<p>
+	  The sources may also be converted to a ds9 region file for
+	  use in data analysis, e.g. spectra extraction or calculating
+	  sources counts.
+	</p>
+
+	<p>
+	  Select "Copy to Regions" from the Catalog Tool "File" menu.   Once
+	  the sources are converted to regions, individual ones may be
+	  selected and edited or deleted, if desired.  Save the
+	  regions from the "Region → Save Regions..." menu. 
+	</p>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="cite">Citing a Catalog in Publication</a></h2>
+        
+
+	<p>
+	  If you wish to use the source information in a publication,
+	  refer to the "Acknowledgment" item under the "File" menu in
+	  the Catalog Tool.  For instance, the 2MASS acknowledgment reads:
+	</p>
+
+<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding:  0.5em; overflow: auto; border: thin solid black;">
+Acknowledgments for CDS
+
+This research has made use of the VizieR catalogue access tool, CDS,
+Strasbourg, France. VizieR is a joint effort of CDS (Centre de Données 
+astronomiques de Strasbourg) and ESA-ESRIN (Information Systems Division).
+</pre></div>
+
+      </div>
+</div>
+<hr size="5" noshade>
+<h2><a name="history">History</a></h2>
+<table class="history">
+      <tr>
+<td class="historydate">08 Jan 2010</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>
diff --git a/ds9/doc/user/catalogs/jmag14.png b/ds9/doc/user/catalogs/jmag14.png
new file mode 100644
index 0000000..b521b93
--- /dev/null
+++ b/ds9/doc/user/catalogs/jmag14.png
diff --git a/ds9/doc/user/catalogs/jmagrange.png b/ds9/doc/user/catalogs/jmagrange.png
new file mode 100644
index 0000000..a063a13
--- /dev/null
+++ b/ds9/doc/user/catalogs/jmagrange.png
diff --git a/ds9/doc/user/contour/a2142.reg b/ds9/doc/user/contour/a2142.reg
new file mode 100644
index 0000000..7b279a7
--- /dev/null
+++ b/ds9/doc/user/contour/a2142.reg
@@ -0,0 +1,544 @@
+# Region file format: DS9 version 4.1
+# Filename: acisf05005N002_evt2.fits[EVENTS]
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+
diff --git a/ds9/doc/user/contour/dsscontour.png b/ds9/doc/user/contour/dsscontour.png
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--- /dev/null
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diff --git a/ds9/doc/user/contour/dssdialog.png b/ds9/doc/user/contour/dssdialog.png
new file mode 100644
index 0000000..88d425a
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diff --git a/ds9/doc/user/contour/index.html b/ds9/doc/user/contour/index.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Contours - DS9 </title>
+</head> 
+<!--THIS FILE IS CREATED AUTOMATICALLY - DO NOT EDIT MANUALLY--> 
+<body><div class="mainbar">
+<a name="maintext"></a><div align="center"><h1>Contours</h1></div>
+<p>
+      Return to the <a href="../index.html">DS9 Users Manual</a></p>
+<hr size="5" noshade>
+<div>
+<h2>Synopsis</h2>
+        <p>
+	  Contours are curves along which the pixels have a constant
+	  value.  ds9 can create and display contours as an overlay on
+	  a data image.  The contours can be copied between frames in
+	  the current session or saved to file for future use with ds9. 
+	</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#create">Creating Contours on a Dataset</a></strong></li>
+<li><strong><a href="index.html#copy">Copying the Contours to Another Frame</a></strong></li>
+<li><strong><a href="index.html#save">Saving the Contours</a></strong></li>
+<li><strong><a href="index.html#convert">Converting to Polygons and Saving</a></strong></li>
+<li><strong><a href="index.html#history">History</a></strong></li>
+<li>
+<strong>Images</strong><ul>
+<li><a href="#dialog">Figure 1: Contour Parameters dialog box</a></li>
+<li><a href="#xraycontour">Figure 2: X-ray data with contours</a></li>
+<li><a href="#dssdialog">Figure 3: SAO-DSS Server dialog box</a></li>
+<li><a href="#dsscontour">Figure 4: X-ray and optical data with contours</a></li>
+</ul>
+</li>
+</ul>
+<hr>
+<div class="sectionlist">
+<div class="section">
+<h2><a name="create">Creating Contours on a Dataset</a></h2>
+        
+
+	<p>
+	  This thread uses Chandra data from an observation of the
+	  galaxy cluster Abell 2142 (ObsID 5005).
+	</p>
+
+        <p>
+	  After loading the data into ds9 and setting the desired
+	  scale, click on the "Contours" item in the "Analysis" menu
+	  to turn on contour display.  Open the "Contour Parameters"
+	  window from "Analysis → Contours Parameters".  There
+	  are two sliding scales which are used to set the number and
+	  smoothness of the contours and fields for setting the range
+	  of values to use. 
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="dialog">Figure 1: Contour Parameters dialog box</a></h3></div>
+<div><img alt='[The "Contour Parameters" dialog box has sliding scales to set the number and smoothness of the contours and fields for setting the range of values.]' src="dialog.png"></div>
+</div> 
+
+	<p>
+	  Typically, you will want to generate between 1 and 10
+	  contours; larger numbers will take longer to generate and
+	  display.  A smoothness level of 1 will evaluate the contour
+	  at each image pixel, while a level of 2 will evaluate the
+	  contour at every other pixel, and so on.  A larger smoothing
+	  will generate contours more quickly, but less detail will be
+	  available. 
+	</p>
+	 
+	<p>
+	  By default, the range of the data scale is filled in as the
+	  limits.  Under the "Method" menu, there are two choices:
+	</p>
+
+	<ol type="1">
+	  <li>
+	    block (the default) - blocks down the image by the
+	    smoothness factor before contours are calculated.  The
+	    larger the smoothness, the faster the result.  
+	  </li>
+
+	  <li>
+	    smooth - smooths the image before calculating contours.
+	    The larger the smoothness, the slower the result. 
+	  </li>
+	</ol>	
+
+	<p>
+	  In this example, the number of levels is set to 6 and the
+	  smoothing is set to 5.  The contours will be generated over
+	  the limit 1 to 100.  The default method (block) is used.
+	</p>
+
+	<p>
+	  After clicking the "Generate" button, the list of contours
+	  is calculated and displayed in the "Levels" portion of the window.
+	   Click "Apply" and the ds9 display is updated with the new
+	   contour levels, as shown in <a href="#xraycontour">Figure 2</a>.
+	 </p>
+
+	 <div class="figure">
+<div class="caption"><h3><a name="xraycontour">Figure 2: 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="xraycontour.png"></div>
+</div> 
+
+	 <p>
+	   The contour parameters can be adjusted until the desired
+	   result is achieved.  Be sure to click "Generate" whenever
+	   an adjustment is made so that the levels are recalculated.
+	 </p>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="copy">Copying the Contours to Another Frame</a></h2>
+        
+
+	<p>
+	  In this section, we take the X-ray contours just generated
+	  and display them on an optional image from the Digital Sky Survey (DSS).
+	</p>
+	 
+	<p>
+	  From the "Analysis → Image Servers" menu, select one
+	  of the DSS server options (e.g. "SAO-DSS").  The server
+	  dialog box allows you to retrieve an optical image of the
+	  field of your observation and load it into a new frame.  The
+	  default retrieval image size and (RA,Dec) is equal to the
+	  size and center of the field currently displayed.  Here the
+	  width and height have been set to 40, but the (RA,Dec)
+	  determined by ds9 are used.
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="dssdialog">Figure 3: SAO-DSS Server dialog box</a></h3></div>
+<div><img alt="[The fields for Ra, Dec, width, and height are populated with values determined from the x-ray data image.]" src="dssdialog.png"></div>
+</div> 
+
+	<p>
+	  Click on "Retrieve" and the data is loaded into a new ds9
+	  frame.  
+	</p>
+
+	<p>
+	  To copy the x-ray contours:
+	</p>
+
+	<ol type="1">
+	  <li><p>
+	    Select the frame with the X-ray data in it.
+	  </p></li>
+	  <li><p>
+	    Use "Frame → Match Frames → WCS" to align the
+	    two images.
+	  </p></li>	
+	  <li><p>
+	    To copy the contours, open the "Contour Parameters"
+	    dialog again and select "Copy Contours" from the
+	    "File" menu. Leave the window open, as it is needed in
+	    a future step. 
+          </p></li>
+	  <li><p>
+	    Select the frame with the optical data in it.
+	  </p></li>
+	  <li><p>
+	    Using the "File" menu of the "Contour Parameters"
+	    dialog, select "Paste Contours".
+	  </p></li>
+	  <li><p>
+	    Adjust the parameters (if desired) in the small dialog box
+	    that is displayed, then click "OK".
+	  </p></li>
+	</ol>
+
+	<p>
+	  The optical image now has the x-ray contours overlaid.
+	  Since the WCS is the same, correlation between x-ray
+	  and optical features may be seen.
+	</p>
+
+        <div class="figure">
+<div class="caption"><h3><a name="dsscontour">Figure 4: 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="dsscontour.png"></div>
+</div> 
+
+	<p>
+	  To delete contours which have been pasted into a
+	  frame, select "Clear" from the "File" menu of the "Contour
+	  Parameters" dialog.
+	</p>
+	
+      <hr>
+</div>
+<div class="section">
+<h2><a name="save">Saving the Contours</a></h2>
+        
+
+	<p>
+	  To save the contours to a text file, choose "Save Contours"
+	  from the "File" menu of the "Contour Parameters" dialog.
+	  The contours are saved in a text file which can be loaded
+	  back into ds9 with the "Load Contours" menu item. 
+	</p>
+
+	<p>
+	  The contours generated in this thread have been saved as <a href="ds9.con">ds9.con</a>.
+	</p>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="convert">Converting to Polygons and Saving</a></h2>
+        
+
+	<p>
+	  The contours can be converted to ds9 polygon regions for use
+	  in filtering data.  Converting to polygons also allows you
+	  to select and/or delete specific contours.
+	</p>
+
+	<p>
+	  <strong>Note that the contours cannot be <a href="index.html#save">saved
+	  in ds9 format</a> after converting.</strong>  If you wish to
+	  save the contours, do so before continuing.
+	</p>
+
+	<p>
+	  To convert the contours, select "Convert to Polygons" from
+	  the "File" menu of the "Contour Parameters" dialog.  The
+	  contours are now defined as ds9 polygons, e.g.  
+	</p>
+
+<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding:  0.5em; overflow: auto; border: thin solid black;">
+polygon(3535.2112,4184.5,3540.5,4179.1154,3548.5,4176.8219,3555.9012,4184.5,3548.5,4191.9558,3540.5,4190.3926)
+</pre></div>
+
+
+	<p>
+	  The polygon-shaped contours can be saved as a ds9 region
+	  file from the "Region Save → Regions" menu. The region
+	  file for these contours has been saved as <a href="a2142.reg">a2142.reg</a>. 
+	</p>
+	
+      </div>
+</div>
+<hr size="5" noshade>
+<h2><a name="history">History</a></h2>
+<table class="history">
+      <tr>
+<td class="historydate">24 Jun 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>
diff --git a/ds9/doc/user/contour/thread.xml b/ds9/doc/user/contour/thread.xml
new file mode 100644
index 0000000..48d4d32
--- /dev/null
+++ b/ds9/doc/user/contour/thread.xml
@@ -0,0 +1,258 @@
+<?xml version="1.0" encoding="us-ascii" ?>
+<!DOCTYPE thread>
+
+<thread>
+
+  <info>
+    
+    <version>June 2009</version>
+    <title>
+      <long>Contours</long>
+    </title>
+    <history>
+      <entry day="24" month="June" year="9" who="liz">
+	Original version
+	<!-- copied in part from CIAO ds9 thread //-->
+     </entry>
+     </history>
+  </info>
+
+  <text>
+    <overview>
+
+      <synopsis>
+        <p>
+	  Contours are shapes which are drawn on the data at a
+	  specified pixel value.  ds9 can create and display contours
+	  as an overlay on an image.  
+	</p>
+      </synopsis>
+    </overview>
+
+    <sectionlist>
+
+      <section id="create">
+        <title>Creating Contours on a Dataset</title>
+
+	<p>
+	  This thread uses Chandra data from an observation of the
+	  galaxy cluster Abell 2142 (ObsID 5005).
+	</p>
+
+        <p>
+	  After loading the data into ds9 and setting the desired
+	  scale, click on the "Contours" item in the "Analysis" menu
+	  to turn on contour display.  Open the "Contour Parameters"
+	  window from "Analysis &#8594; Contours Parameters".  There
+	  are two sliding scales which are used to set the number and
+	  smoothness of the contours and fields for setting the range
+	  of values to use. 
+	</p>
+
+	<figure id="dialog">
+	  <title>Contour Parameters dialog box</title>
+	  <description>The "Contour Parameters" dialog box has sliding
+	  scales to set the number and smoothness of the contours and
+	  fields for setting the range of values.</description>  
+	  <bitmap format="png">dialog.png</bitmap>
+	</figure> 
+
+	<p>
+	  Typically, you will want to generate between 1 and 10
+	  contours; larger numbers will take longer to generate and
+	  display.  A smoothness level of 1 will evaluate the contour
+	  at each image pixel, while a level of 2 will evaluate the
+	  contour at every other pixel, and so on.  A larger smoothing
+	  will generate contours more quickly, but less detail will be
+	  available. 
+	</p>
+	 
+	<p>
+	  By default, the range of the data scale is filled in as the
+	  limits.  Under the "Method" menu, there are two choices:
+	</p>
+
+	<list type="1">
+	  <li>
+	    block (the default) - blocks down the image by the
+	    smoothness factor before contours are calculated.  The
+	    larger the smoothness, the faster the result.  
+	  </li>
+
+	  <li>
+	    smooth - smooths the image before calculating contours.
+	    The larger the smoothness, the slower the result. 
+	  </li>
+	</list>	
+
+	<p>
+	  In this example, the number of levels is set to 6 and the
+	  smoothing is set to 5.  The contours will be generated over
+	  the limit 1 to 100.  The default method (block) is used.
+	</p>
+
+	<p>
+	  After clicking the "Generate" button, the list of contours
+	  is calculated and displayed in the "Levels" portion of the window.
+	   Click "Apply" and the ds9 display is updated with the new
+	   contour levels, as shown in <figlink id="xraycontour"/>.
+	 </p>
+
+	 <figure id="xraycontour">
+	   <title>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">xraycontour.png</bitmap>
+	 </figure> 
+
+	 <p>
+	   The contour parameters can be adjusted until the desired
+	   result is achieved.  Be sure to click "Generate" whenever
+	   an adjustment is made so that the levels are recalculated.
+	 </p>
+
+      </section>
+
+      <section id="copy">
+        <title>Copying the Contours to Another Frame</title>
+
+	<p>
+	  In this section, we take the X-ray contours just generated
+	  and display them on an optional image from the Digital Sky Survey (DSS).
+	</p>
+	 
+	<p>
+	  From the "Analysis &#8594; Image Servers" menu, select one
+	  of the DSS server options (e.g. "SAO-DSS").  The server
+	  dialog box allows you to retrieve an optical image of the
+	  field of your observation and load it into a new frame.  The
+	  default retrieval image size and (RA,Dec) is equal to the
+	  size and center of the field currently displayed.  Here the
+	  width and height have been set to 40, but the (RA,Dec)
+	  determined by ds9 are used.
+	</p>
+
+	<figure id="dssdialog">
+	  <title>SAO-DSS Server dialog box</title>
+	  <description>The fields for Ra, Dec, width, and height are
+	  populated with values determined from the x-ray data image.</description>  
+	  <bitmap format="png">dssdialog.png</bitmap>
+	</figure> 
+
+	<p>
+	  Click on "Retrieve" and the data is loaded into a new ds9
+	  frame.  
+	</p>
+
+	<p>
+	  To copy the x-ray contours:
+	</p>
+
+	<list type="1">
+	  <li><p>
+	    Select the frame with the X-ray data in it.
+	  </p></li>
+	  <li><p>
+	    Use "Frame &#8594; Match Frames &#8594; WCS" to align the
+	    two images.
+	  </p></li>	
+	  <li><p>
+	    To copy the contours, open the "Contour Parameters"
+	    dialog again and select "Copy Contours" from the
+	    "File" menu. Leave the window open, as it is needed in
+	    a future step. 
+          </p></li>
+	  <li><p>
+	    Select the frame with the optical data in it.
+	  </p></li>
+	  <li><p>
+	    Using the "File" menu of the "Contour Parameters"
+	    dialog, select "Paste Contours".
+	  </p></li>
+	  <li><p>
+	    Adjust the parameters (if desired) in the small dialog box
+	    that is displayed, then click "OK".
+	  </p></li>
+	</list>
+
+	<p>
+	  The optical image now has the x-ray contours overlaid.
+	  Since the WCS is the same, correlation between x-ray
+	  and optical features may be seen.
+	</p>
+
+        <figure id="dsscontour">
+	  <title>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">dsscontour.png</bitmap>
+	</figure> 
+
+	<p>
+	  To delete contours which have been pasted into a
+	  frame, select "Clear" from the "File" menu of the "Contour
+	  Parameters" dialog.
+	</p>
+	
+      </section>
+
+      <section id="save">
+        <title>Saving the Contours</title>
+
+	<p>
+	  To save the contours to a text file, choose "Save Contours"
+	  from the "File" menu of the "Contour Parameters" dialog.
+	  The contours are saved in a text file which can be loaded
+	  back into ds9 with the "Load Contours" menu item. 
+	</p>
+
+	<p>
+	  The contours generated in this thread have been saved as <a href="ds9.con">ds9.con</a>.
+	</p>
+
+      </section>
+
+      <section id="convert">
+        <title>Converting to Polygons and Saving</title>
+
+	<p>
+	  The contours can be converted to ds9 polygon regions for use
+	  in filtering data.  Converting to polygons also allows you
+	  to select and/or delete specific contours.
+	</p>
+
+	<p>
+	  <strong>Note that the contours cannot be <threadlink id="save">saved
+	  in ds9 format</threadlink> after converting.</strong>  If you wish to
+	  save the contours, do so before continuing.
+	</p>
+
+	<p>
+	  To convert the contours, select "Convert to Polygons" from
+	  the "File" menu of the "Contour Parameters" dialog.  The
+	  contours are now defined as ds9 polygons, e.g.  
+	</p>
+
+<screen>
+polygon(3535.2112,4184.5,3540.5,4179.1154,3548.5,4176.8219,3555.9012,4184.5,3548.5,4191.9558,3540.5,4190.3926)
+</screen>
+
+
+	<p>
+	  The polygon-shaped contours can be saved as a ds9 region
+	  file from the "Region Save &#8594; Regions" menu. The region
+	  file for these contours has been saved as <a href="a2142.reg">a2142.reg</a>. 
+	</p>
+	
+      </section>
+
+
+    </sectionlist>
+  </text>
+
+</thread>
+
+
+
diff --git a/ds9/doc/user/contour/xraycontour.png b/ds9/doc/user/contour/xraycontour.png
new file mode 100644
index 0000000..c426f91
--- /dev/null
+++ b/ds9/doc/user/contour/xraycontour.png
diff --git a/ds9/doc/user/gui/button.png b/ds9/doc/user/gui/button.png
new file mode 100644
index 0000000..9ebfdaf
--- /dev/null
+++ b/ds9/doc/user/gui/button.png
diff --git a/ds9/doc/user/gui/color.png b/ds9/doc/user/gui/color.png
new file mode 100644
index 0000000..b59dd4b
--- /dev/null
+++ b/ds9/doc/user/gui/color.png
diff --git a/ds9/doc/user/gui/components.png b/ds9/doc/user/gui/components.png
new file mode 100644
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+++ b/ds9/doc/user/gui/components.png
diff --git a/ds9/doc/user/gui/frame.png b/ds9/doc/user/gui/frame.png
new file mode 100644
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diff --git a/ds9/doc/user/gui/index.html b/ds9/doc/user/gui/index.html
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@@ -0,0 +1,351 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Introduction to the ds9 Interface - DS9 </title>
+</head> 
+<!--THIS FILE IS CREATED AUTOMATICALLY - DO NOT EDIT MANUALLY--> 
+<body><div class="mainbar">
+<a name="maintext"></a><div align="center"><h1>Introduction to the ds9 Interface</h1></div>
+<p>
+      Return to the <a href="../index.html">DS9 Users Manual</a></p>
+<hr size="5" noshade>
+<div>
+<h2>Synopsis</h2>
+        <p>
+	  This thread provides an overview of the key components of
+	  the ds9 graphical user interface (GUI).
+	</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#gui">The ds9 Interface</a></strong><ol type="1">
+<li><a href="index.html#gui.menu">Menu bar</a></li>
+<li><a href="index.html#gui.info">Information panel</a></li>
+<li><a href="index.html#gui.pan">Panner</a></li>
+<li><a href="index.html#gui.mag">Magnifier</a></li>
+<li><a href="index.html#gui.buttons">Buttons</a></li>
+<li><a href="index.html#gui.frame">Display frame</a></li>
+<li><a href="index.html#gui.color">Colorbar</a></li>
+</ol>
+</li>
+<li><strong><a href="index.html#preferences">Setting and Saving View Preferences</a></strong></li>
+<li><strong><a href="index.html#history">History</a></strong></li>
+<li>
+<strong>Images</strong><ul>
+<li><a href="#components">Figure 1: The ds9 GUI</a></li>
+<li><a href="#vertical">Figure 2: The ds9 GUI, vertical layout</a></li>
+<li><a href="#menu">Figure 3: Menu bar</a></li>
+<li><a href="#menutear">Figure 4: Tearing off a Menu</a></li>
+<li><a href="#info">Figure 5: Information panel</a></li>
+<li><a href="#panner">Figure 6: Panner</a></li>
+<li><a href="#mag">Figure 7: Magnifier</a></li>
+<li><a href="#button">Figure 8: Buttons</a></li>
+<li><a href="#frame">Figure 9: Tiled frame display</a></li>
+<li><a href="#color">Figure 10: Colorbar</a></li>
+<li><a href="#prefs">Figure 11: Preferences dialog box</a></li>
+</ul>
+</li>
+</ul>
+<hr>
+<div class="sectionlist">
+<div class="section">
+<h2><a name="gui">The ds9 Interface</a></h2>
+        
+
+	<p>
+	  This thread uses Chandra data from an observation of the
+	  Trapezium Cluster (ObsID 1522).  The default ds9 GUI is
+	  shown in <a href="#components">Figure 1</a>.  The main components
+	  are numbered:
+	</p>
+
+	<ol type="1">
+	  <li>Menu bar</li>
+	  <li>Information panel</li>
+	  <li>Panner</li>
+	  <li>Magnifier</li>
+	  <li>Buttons</li>
+	  <li>Display frame</li>
+	  <li>Colorbar</li>
+	</ol>
+	 
+	<div class="figure">
+<div class="caption"><h3><a name="components">Figure 1: The ds9 GUI</a></h3></div>
+<div><img alt="[The default ds9 display includes the information panel, panner, magnifier, and colorbar.]" src="components.png"></div>
+</div>
+
+	<p>
+	  The default setup is a "horizontal layout", with the
+	  information panel, panner, magnifier, and buttons displayed
+	  horizontally across the window.  This may be changed to
+	  "vertical layout" in the View menu (<a href="#vertical">Figure 2</a>).
+	</p>
+	 
+	<div class="figure">
+<div class="caption"><h3><a name="vertical">Figure 2: The ds9 GUI, vertical layout</a></h3></div>
+<div><img alt="[In the vertical layout, the information panel, panner, magnifier, and buttons are displayed vertically at the left of the data frame.]" src="vertical.png"></div>
+</div>
+
+	<p>
+	  Note that the colorbar remained horizontal at the bottom of
+	  the display frame.  This may be changed with the "vertical
+	  colorbar" option in the "View" menu.
+	</p>
+
+	<div class="subsectionlist">
+<div class="subsection">
+<h3><a name="gui.menu">1. Menu bar</a></h3>
+	    
+
+	    <p>
+	      The menu bar provides access to all of ds9's 
+	      capabilities.  For a complete description of each menu,
+	      refer to the <a href="../../ref/gui.html">Menu bar
+	      section of the Reference Manual</a>. 
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="menu">Figure 3: Menu bar</a></h3></div>
+<div><img alt="[The menu bar of the ds9 GUI.]" src="menu.png"></div>
+</div>
+
+	    <p>
+	      All ds9 menus can be "torn off" to be a separate window
+	      from the main GUI.  To tear off a menu, select the
+	      dashed line, which is the first item of each menu (shown
+	      in <a href="#menutear">Figure 4</a>).  The menu will become its 
+	      own window.  
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="menutear">Figure 4: Tearing off a Menu</a></h3></div>
+<div><img alt='[The dashed line at the top of the "View" menu is highlighted.]' src="menutear.png"></div>
+</div>
+	  <hr width="80%" align="center">
+</div>
+<div class="subsection">
+<h3><a name="gui.info">2. Information panel</a></h3>
+	    
+
+	    <p>
+	      The information panel displays information about the
+	      data file and the values at the cursor position.  In
+	      <a href="#info">Figure 5</a>, the object name has been
+	      loaded from the header of the data file.    The image
+	      value and position (in WCS, physical, and image
+	      coordinates) are updated in real time as the cursor is
+	      moved.  
+	    </p>
+
+	    <p>
+	      The fields of the information panel can be customized
+	      from the "View" menu.  Any of the default entries can be
+	      removed, and additional fields can be added
+	      (e.g. detector coordinates, min/max data values).
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="info">Figure 5: Information panel</a></h3></div>
+<div><img alt="[The information panel of the ds9 GUI.]" src="info.png"></div>
+</div>
+	  <hr width="80%" align="center">
+</div>
+<div class="subsection">
+<h3><a name="gui.pan">3. Panner</a></h3>
+	    
+
+	    <p>
+	      The panner allows the user to view areas of the frame
+	      which are outside of the current field of view.
+	      Although the display frame is filled by the data, the
+	      panner indicates that more of the image is
+	      available. Clicking and dragging the viewing bounding
+	      box in the panner - shown in blue in
+	      <a href="#panner">Figure 6</a> - will display a different
+	      portion of the image.   
+	    </p>
+
+	    <p>
+	      The panner also contains axes to indicate the directions
+	      of North and East and the directions of the physical
+	      (x,y) data axes. 
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="panner">Figure 6: Panner</a></h3></div>
+<div><img alt="[The panner of the ds9 GUI.]" src="panner.png"></div>
+</div>
+ 	  <hr width="80%" align="center">
+</div>
+<div class="subsection">
+<h3><a name="gui.mag">4. Magnifier</a></h3>
+	    
+ 
+	    <p>
+	      The magnifier displays a magnified view of the current
+	      cursor location. The magnifier cursor - the small square
+	      in the center of <a href="#mag">Figure 7</a> - outlines 
+	      the size and orientation of one pixel, taking into
+	      account the current frame zoom and orientation. 
+	    </p>
+  
+	    <div class="figure">
+<div class="caption"><h3><a name="mag">Figure 7: Magnifier</a></h3></div>
+<div><img alt="[The magnifier of the ds9 GUI.]" src="mag.png"></div>
+</div>
+	  <hr width="80%" align="center">
+</div>
+<div class="subsection">
+<h3><a name="gui.buttons">5. Buttons</a></h3>
+	    
+
+	    <p>
+	      The button bar duplicates many of the options available
+	      from the menu bar.  The buttons provide quick access to
+	      change the most frequently-used ds9 actions
+	      (e.g. changing the scale and color bar, blinking and
+	      tiling frames).  
+	    </p>
+
+	    <p>
+	      When a category is chosen from the top row, the options
+	      within that category are displayed in the bottom row of
+	      buttons.  In <a href="#button">Figure 8</a>, the color category is
+	      chosen and the bottom row shows the ten most-used
+	      colormap options (additional colormaps are available
+	      from the "Color" menu).   
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="button">Figure 8: Buttons</a></h3></div>
+<div><img alt="[The buttons of the ds9 GUI.]" src="button.png"></div>
+</div>
+	  <hr width="80%" align="center">
+</div>
+<div class="subsection">
+<h3><a name="gui.frame">6. Display frame</a></h3>
+	    
+
+	    <p>
+	      The display frame is the area of ds9 where the FITS
+	      image is shown.  In <a href="#components">Figure 1</a>, a single
+	      frame is shown.
+	    </p>
+
+	    <p>
+	      Multiple frames can be opened in ds9 at the same time.
+	      In <a href="#frame">Figure 9</a>, nine frames have been
+	      opened and set to "tile" display from the "frame"
+	      button.  The current frame is indicated by a blue
+	      outline around it (second row, center frame).  How the
+	      frames are tiled is set in the "Frame → Frame
+	      Parameters → Tile" menu; the default is to tile
+	      the frames in a grid. 
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="frame">Figure 9: Tiled frame display</a></h3></div>
+<div><img alt="[Nine frames in the ds9 GUI.]" src="frame.png"></div>
+</div>
+
+	    <p>
+	      If the display is set back to "single", then the current
+	      frame fills the display area.  The other frames can be
+	      accessed via the "previous" and "next" options in the
+	      buttons bar (or from the "Frame" menu).  
+	    </p>
+
+	    <p>
+	      The "blink" option may also be used with multiple
+	      frames.  When blink is turned on, ds9 cycles through all
+	      the available frames.  The blink interval is set in the
+	      "Frame → Frame Parameters → Blink Interval" menu.
+	    </p>
+	    
+	  <hr width="80%" align="center">
+</div>
+<div class="subsection">
+<h3><a name="gui.color">7. Colorbar</a></h3>
+	    
+
+	    <p>
+	      The colorbar displays the colormap, bias, and contrast
+	      settings. The colormap correlates the colors used in the
+	      image with the pixel values in the data.
+	    </p>
+
+	    <p>
+	      To change the colormap, use the "Color" menu or button.
+	      The contrast and bias can be adjusted by right-clicking
+	      and dragging on the ds9 display.  The "Color →
+	      Colormap Parameters" dialog box can also be used to
+	      change contrast and bias.
+	    </p>
+
+	    <div class="figure">
+<div class="caption"><h3><a name="color">Figure 10: Colorbar</a></h3></div>
+<div><img alt="[The colorbar of the ds9 GUI.]" src="color.png"></div>
+</div>
+	  </div>
+</div>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="preferences">Setting and Saving View Preferences</a></h2>
+        
+	
+	<p>
+	  All of the view options described in this thread can be set
+	  and saved as a preference.  Open the "Preferences" dialog box 
+	  from the "Edit" menu and select the "View" tab, shown in 
+	  <a href="#prefs">Figure 11</a>. 
+	</p>
+
+
+	<div class="figure">
+<div class="caption"><h3><a name="prefs">Figure 11: Preferences dialog box</a></h3></div>
+<div><img alt="[The view tab is selected in the preferences dialog.]" src="prefs.png"></div>
+</div>
+
+
+	<p>
+	  The "Default" menus are used to set the defaults of the
+	  "View" menu and buttons.  For instance, uncheck the "Panner"
+	  item under "Menu" and the panner won't be displayed when ds9
+	  is launched.  (Note that some options require ds9 to be
+	  restarted before they take effect.)
+	</p>
+
+	<p>
+	  After setting the desired preferences, select "Save".  User
+	  preferences are stored in <tt>.ds9.prf</tt>.  At startup,
+	  ds9 looks for the preferences file in the following
+	  directory order: 
+	  <tt>./</tt>, <tt>$HOME</tt>, <tt>/usr/local/lib</tt>, 
+	  <tt>/opt/local/lib</tt>.   
+	</p>
+
+      </div>
+</div>
+<hr size="5" noshade>
+<h2><a name="history">History</a></h2>
+<table class="history">
+      <tr>
+<td class="historydate">06 Jul 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>
diff --git a/ds9/doc/user/gui/info.png b/ds9/doc/user/gui/info.png
new file mode 100644
index 0000000..59f4c7a
--- /dev/null
+++ b/ds9/doc/user/gui/info.png
diff --git a/ds9/doc/user/gui/mag.png b/ds9/doc/user/gui/mag.png
new file mode 100644
index 0000000..db5d82d
--- /dev/null
+++ b/ds9/doc/user/gui/mag.png
diff --git a/ds9/doc/user/gui/menu.png b/ds9/doc/user/gui/menu.png
new file mode 100644
index 0000000..457100d
--- /dev/null
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diff --git a/ds9/doc/user/gui/menutear.png b/ds9/doc/user/gui/menutear.png
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diff --git a/ds9/doc/user/gui/panner.png b/ds9/doc/user/gui/panner.png
new file mode 100644
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diff --git a/ds9/doc/user/gui/prefs.png b/ds9/doc/user/gui/prefs.png
new file mode 100644
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+++ b/ds9/doc/user/gui/prefs.png
diff --git a/ds9/doc/user/gui/thread.xml b/ds9/doc/user/gui/thread.xml
new file mode 100644
index 0000000..6b4530e
--- /dev/null
+++ b/ds9/doc/user/gui/thread.xml
@@ -0,0 +1,325 @@
+<?xml version="1.0" encoding="us-ascii" ?>
+<!DOCTYPE thread>
+
+<thread>
+
+  <info>
+    
+    <name>gui</name>
+    <version>June 2009</version>
+    <title>
+      <long>Introduction to the ds9 Interface</long>
+    </title>
+    <history>
+      <entry day="6" month="July" year="9" who="liz">
+	Original version
+     </entry>
+     </history>
+  </info>
+
+  <text>
+    <overview>
+
+      <synopsis>
+        <p>
+	  This thread provides an overview of the key components of
+	  the ds9 graphical user interface (GUI).
+	</p>
+      </synopsis>
+    </overview>
+
+    <sectionlist>
+
+      <section id="gui">
+        <title>The ds9 Interface</title>
+
+	<p>
+	  This thread uses Chandra data from an observation of the
+	  Trapezium Cluster (ObsID 1522).  The default ds9 GUI is
+	  shown in <figlink id="components"/>.  The main components
+	  are numbered:
+	</p>
+
+	<list type="1">
+	  <li>Menu bar</li>
+	  <li>Information panel</li>
+	  <li>Panner</li>
+	  <li>Magnifier</li>
+	  <li>Buttons</li>
+	  <li>Display frame</li>
+	  <li>Colorbar</li>
+	</list>
+	 
+	<figure id="components">
+	  <title>The ds9 GUI</title>
+	  <description>The default ds9 display includes the
+	  information panel, panner, magnifier, and colorbar.</description>
+	  <bitmap format="png">components.png</bitmap>
+	</figure>
+
+	<p>
+	  The default setup is a "horizontal layout", with the
+	  information panel, panner, magnifier, and buttons displayed
+	  horizontally across the window.  This may be changed to
+	  "vertical layout" in the View menu (<figlink id="vertical"/>).
+	</p>
+	 
+	<figure id="vertical">
+	  <title>The ds9 GUI, vertical layout</title>
+	  <description>In the vertical layout, the information panel,
+	  panner, magnifier, and buttons are displayed vertically at
+	  the left of the data frame.</description>
+	  <bitmap format="png">vertical.png</bitmap>
+	</figure>
+
+	<p>
+	  Note that the colorbar remained horizontal at the bottom of
+	  the display frame.  This may be changed with the "vertical
+	  colorbar" option in the "View" menu.
+	</p>
+
+	<subsectionlist type="1">
+	  <subsection id="gui.menu">
+	    <title>Menu bar</title>
+
+	    <p>
+	      The menu bar provides access to all of ds9's 
+	      capabilities.  For a complete description of each menu,
+	      refer to the <a href="../../ref/gui.html">Menu bar
+	      section of the Reference Manual</a>. 
+	    </p>
+
+	    <figure id="menu">
+	      <title>Menu bar</title>
+	      <description>The menu bar of the ds9 GUI.</description>
+	      <bitmap format="png">menu.png</bitmap>
+	    </figure>
+
+	    <p>
+	      All ds9 menus can be "torn off" to be a separate window
+	      from the main GUI.  To tear off a menu, select the
+	      dashed line, which is the first item of each menu (shown
+	      in <figlink id="menutear"/>).  The menu will become its 
+	      own window.  
+	    </p>
+
+	    <figure id="menutear">
+	      <title>Tearing off a Menu</title>
+	      <description>The dashed line at the top of the "View"
+	      menu is highlighted.</description>
+	      <bitmap format="png">menutear.png</bitmap>
+	    </figure>
+	  </subsection>
+
+	  <subsection id="gui.info">
+	    <title>Information panel</title>
+
+	    <p>
+	      The information panel displays information about the
+	      data file and the values at the cursor position.  In
+	      <figlink id="info"/>, the object name has been
+	      loaded from the header of the data file.    The image
+	      value and position (in WCS, physical, and image
+	      coordinates) are updated in real time as the cursor is
+	      moved.  
+	    </p>
+
+	    <p>
+	      The fields of the information panel can be customized
+	      from the "View" menu.  Any of the default entries can be
+	      removed, and additional fields can be added
+	      (e.g. detector coordinates, min/max data values).
+	    </p>
+
+	    <figure id="info">
+	      <title>Information panel</title>
+	      <description>The information panel of the ds9 GUI.</description>
+	      <bitmap format="png">info.png</bitmap>
+	    </figure>
+	  </subsection>
+
+	  <subsection id="gui.pan">
+	    <title>Panner</title>
+
+	    <p>
+	      The panner allows the user to view areas of the frame
+	      which are outside of the current field of view.
+	      Although the display frame is filled by the data, the
+	      panner indicates that more of the image is
+	      available. Clicking and dragging the viewing bounding
+	      box in the panner - shown in blue in
+	      <figlink id="panner"/> - will display a different
+	      portion of the image.   
+	    </p>
+
+	    <p>
+	      The panner also contains axes to indicate the directions
+	      of North and East and the directions of the physical
+	      (x,y) data axes. 
+	    </p>
+
+	    <figure id="panner">
+	      <title>Panner</title>
+	      <description>The panner of the ds9 GUI.</description>
+	      <bitmap format="png">panner.png</bitmap>
+	    </figure>
+ 	  </subsection>
+
+	  <subsection id="gui.mag">
+	    <title>Magnifier</title>
+ 
+	    <p>
+	      The magnifier displays a magnified view of the current
+	      cursor location. The magnifier cursor - the small square
+	      in the center of <figlink id="mag"/> - outlines 
+	      the size and orientation of one pixel, taking into
+	      account the current frame zoom and orientation. 
+	    </p>
+  
+	    <figure id="mag">
+	      <title>Magnifier</title>
+	      <description>The magnifier of the ds9 GUI.</description>
+              <bitmap format="png">mag.png</bitmap>
+    	    </figure>
+	  </subsection>
+
+	  <subsection id="gui.buttons">
+	    <title>Buttons</title>
+
+	    <p>
+	      The button bar duplicates many of the options available
+	      from the menu bar.  The buttons provide quick access to
+	      change the most frequently-used ds9 actions
+	      (e.g. changing the scale and color bar, blinking and
+	      tiling frames).  
+	    </p>
+
+	    <p>
+	      When a category is chosen from the top row, the options
+	      within that category are displayed in the bottom row of
+	      buttons.  In <figlink id="button"/>, the color category is
+	      chosen and the bottom row shows the ten most-used
+	      colormap options (additional colormaps are available
+	      from the "Color" menu).   
+	    </p>
+
+	    <figure id="button">
+	      <title>Buttons</title>
+	      <description>The buttons of the ds9 GUI.</description>
+	      <bitmap format="png">button.png</bitmap>
+	    </figure>
+	  </subsection>
+
+	  <subsection id="gui.frame">
+	    <title>Display frame</title>
+
+	    <p>
+	      The display frame is the area of ds9 where the FITS
+	      image is shown.  In <figlink id="components"/>, a single
+	      frame is shown.
+	    </p>
+
+	    <p>
+	      Multiple frames can be opened in ds9 at the same time.
+	      In <figlink id="frame"/>, nine frames have been
+	      opened and set to "tile" display from the "frame"
+	      button.  The current frame is indicated by a blue
+	      outline around it (second row, center frame).  How the
+	      frames are tiled is set in the "Frame &#8594; Frame
+	      Parameters &#8594; Tile" menu; the default is to tile
+	      the frames in a grid. 
+	    </p>
+
+	    <figure id="frame">
+	      <title>Tiled frame display</title>
+	      <description>Nine frames in the ds9 GUI.</description>
+	      <bitmap format="png">frame.png</bitmap>
+	    </figure>
+
+	    <p>
+	      If the display is set back to "single", then the current
+	      frame fills the display area.  The other frames can be
+	      accessed via the "previous" and "next" options in the
+	      buttons bar (or from the "Frame" menu).  
+	    </p>
+
+	    <p>
+	      The "blink" option may also be used with multiple
+	      frames.  When blink is turned on, ds9 cycles through all
+	      the available frames.  The blink interval is set in the
+	      "Frame &#8594; Frame Parameters &#8594; Blink Interval" menu.
+	    </p>
+	    
+	  </subsection>
+
+	  <subsection id="gui.color">
+	    <title>Colorbar</title>
+
+	    <p>
+	      The colorbar displays the colormap, bias, and contrast
+	      settings. The colormap correlates the colors used in the
+	      image with the pixel values in the data.
+	    </p>
+
+	    <p>
+	      To change the colormap, use the "Color" menu or button.
+	      The contrast and bias can be adjusted by right-clicking
+	      and dragging on the ds9 display.  The "Color &#8594;
+	      Colormap Parameters" dialog box can also be used to
+	      change contrast and bias.
+	    </p>
+
+	    <figure id="color">
+    	      <title>Colorbar</title>
+	      <description>The colorbar of the ds9 GUI.</description>
+	      <bitmap format="png">color.png</bitmap>
+	    </figure>
+	  </subsection>
+	</subsectionlist>
+
+      </section>
+
+
+      <section id="preferences">
+        <title>Setting and Saving View Preferences</title>
+	
+	<p>
+	  All of the view options described in this thread can be set
+	  and saved as a preference.  Open the "Preferences" dialog box 
+	  from the "Edit" menu and select the "View" tab, shown in 
+	  <figlink id="prefs"/>. 
+	</p>
+
+
+	<figure id="prefs">
+    	  <title>Preferences dialog box</title>
+	  <description>The view tab is selected in the preferences dialog.</description>
+	  <bitmap format="png">prefs.png</bitmap>
+	</figure>
+
+
+	<p>
+	  The "Default" menus are used to set the defaults of the
+	  "View" menu and buttons.  For instance, uncheck the "Panner"
+	  item under "Menu" and the panner won't be displayed when ds9
+	  is launched.  (Note that some options require ds9 to be
+	  restarted before they take effect.)
+	</p>
+
+	<p>
+	  After setting the desired preferences, select "Save".  User
+	  preferences are stored in <tt>.ds9.prf</tt>.  At startup,
+	  ds9 looks for the preferences file in the following
+	  directory order: 
+	  <tt>./</tt>, <tt>$HOME</tt>, <tt>/usr/local/lib</tt>, 
+	  <tt>/opt/local/lib</tt>.   
+	</p>
+
+      </section>
+    </sectionlist>
+  </text>
+
+</thread>
+
+
+
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+<!DOCTYPE doctype PUBLIC "-//w3c//dtd html 4.0 transitional//en">
+<html>
+<head>
+  <meta http-equiv="Content-Type"
+ content="text/html; charset=iso-8859-1">
+  <meta name="GENERATOR"
+ content="Mozilla/4.78 [en] (X11; U; Linux 2.4.7-10 i686) [Netscape]">
+  <title>DS9 Users Manual</title>
+</head>
+<body alink="#ff0000" bgcolor="#ffffff" link="#0000ee" text="#000000" vlink="#551a8b">
+
+  <h2><img alt="" src="../sun.gif" align="middle" height="98" width="100">SAOImage DS9 Users Manual</h2>
+
+  <p>
+    The DS9 Users Manual leads the user step-by-step through many
+    features of ds9, such as data binning and contours.  For an
+    in-depth description of all of ds9's capabilities, refer to the
+    <a href="../ref/index.html">Reference
+    Manual</a> 
+  </p>
+
+
+  <ul type="none">
+    <li>
+      <p>
+      <strong><a href="gui/index.html">Introduction to the ds9 Interface</a></strong>
+      </p>
+    </li>
+
+    <li>
+      <p>
+      <strong><a href="binning/index.html">Binning and Filtering FITS Event Files</a></strong>
+      </p>
+    </li>
+
+    <li>
+      <p>
+      <strong><a href="contour/index.html">Contours</a></strong>
+      </p>
+    </li>
+
+    <li>
+      <p>
+      <strong><a href="rgb/index.html">Create a True Color Image in an
+      RGB frame</a></strong>
+      </p>
+    </li>
+
+    <li>
+      <p>
+      <strong><a href="scripts/index.html">Scripting ds9</a></strong>
+      </p>
+    </li>
+
+    <li>
+      <p>
+      <strong><a href="catalogs/index.html">Catalogs</a></strong>
+      </p>
+    </li>
+  </ul>
+
+
+  <p>
+    If there are topics that you would like to see covered in the
+    Users Manual, please email: saord @ cfa.harvard.edu.
+  </p>
+</body>
+</html>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Create a True Color Image in an RGB frame - DS9 </title>
+</head> 
+<!--THIS FILE IS CREATED AUTOMATICALLY - DO NOT EDIT MANUALLY--> 
+<body><div class="mainbar">
+<a name="maintext"></a><div align="center"><h1>Create a True Color Image in an RGB frame</h1></div>
+<p>
+      Return to the <a href="../index.html">DS9 Users Manual</a></p>
+<hr size="5" noshade>
+<div>
+<h2>Synopsis</h2>
+        <p>
+	  Most astronomical images map color to intensity level,
+	  e.g. lighter tones may correspond to a brighter intensity
+	  level in a greyscale image.  An alternative way of
+	  presenting data is via an image that correllates color and
+	  energy. 
+	</p>
+	
+	<p>
+	  ds9 has the capability to create an RGB image and
+          interactively adjust many of its parameters to achieve
+          optimal display results. 
+	</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#frame">Creating an RGB Frame</a></strong><ol type="A">
+<li><a href="index.html#frame.cmdline">From the command line</a></li>
+<li><a href="index.html#frame.gui">From the ds9 GUI</a></li>
+</ol>
+</li>
+<li><strong><a href="index.html#energy">Apply Energy Filters</a></strong></li>
+<li><strong><a href="index.html#smooth">Smoothing the Data (optional)</a></strong></li>
+<li><strong><a href="index.html#scale">Adjusting the Scale Parameters</a></strong></li>
+<li><strong><a href="index.html#coordgrid">Adding a Coordinate Grid</a></strong></li>
+<li><strong><a href="index.html#output">Saving the Output</a></strong></li>
+<li><strong><a href="index.html#history">History</a></strong></li>
+<li>
+<strong>Images</strong><ul>
+<li><a href="#rgb">Figure 1: RGB window</a></li>
+<li><a href="#lock">Figure 2: Lock menu in the RGB window</a></li>
+<li><a href="#ds9">Figure 3: RGB frame with three files loaded</a></li>
+<li><a href="#efilt">Figure 4: Energy-filtered RGB data</a></li>
+<li><a href="#smooth">Figure 5: Data smoothed with a Gaussian of radius three</a></li>
+<li><a href="#scale">Figure 6: The adjusted pixel distribution for scaling</a></li>
+<li><a href="#grid">Figure 7: Coordinate Grid parameters dialog box</a></li>
+<li><a href="#color">Figure 8: Final three-color image with coordinate grid overlaid</a></li>
+</ul>
+</li>
+</ul>
+<hr>
+<div class="sectionlist">
+<div class="section">
+<h2><a name="frame">Creating an RGB Frame</a></h2>
+        
+
+	<p>
+	  To use the three-color capabilities of ds9, the data must be
+	  loaded into a special RGB frame.  This frame will contain
+	  all three files, stacked together in separate layers. 
+	</p>
+
+	<p>
+	  This thread uses Chandra data from an observation of Cas A
+	  (ObsID 198); the level=2 event file is named 
+	  "casa.fits".  The same file is loaded into each layer of the
+	  RGB frame; different energy filters will be applied to the
+	  layers in a later step.   
+	</p>
+
+	<p>
+	  There are two options for creating the RGB frame:
+	</p>
+
+        <div class="subsectionlist">
+<div class="subsection">
+<h3><a name="frame.cmdline">A. From the command line</a></h3>
+            
+
+	    <p>
+	      The command-line syntax can be used to create the
+	      RGB frame and load the three files into the red, green,
+	      and blue layers:
+	    </p>
+
+<div class="screen"><pre style="background: #cccccc; white-space: pre; border: none; padding:  0.5em; overflow: auto; border: thin solid black;">
+unix% ds9 -rgb -red casa.fits \
+               -green casa.fits \
+	       -blue casa.fits &amp;
+</pre></div>
+
+	    <p>
+	      ds9 will open with the three files in one frame.
+	      The <a href="#rgb">RGB window (Figure 1)</a> should open
+	      as well.  If it doesn't, open it from the "Frame →
+	      RGB..." menu.  
+	    </p>
+
+	  <hr width="80%" align="center">
+</div>
+<div class="subsection">
+<h3><a name="frame.gui">B. From the ds9 GUI</a></h3>
+            
+
+	    <p>
+	      To load the files from the ds9 GUI:
+	    </p>
+
+	    <ol type="1">
+	      <li>
+	        <p>
+		  Launch ds9
+		</p>
+	      </li>
+
+	      <li>
+	        <p>
+		  Choose "New Frame RGB" from the "Frame" menu.
+		</p>
+
+		<p>
+		  When the new frame is created, the 
+		  <a href="#rgb">RGB window (Figure 1)</a> should open as well.
+		  If it doesn't, open it from the "Frame → RGB..."
+		  menu. 
+		</p>
+	      </li>
+
+	      <li>
+	        <p>
+		  Make sure the "Red" band is selected in the
+		  "Current" column of the RGB window, then choose
+		  "File → Open..." in the main ds9 window and
+		  select the red file.   
+		</p>
+	      </li>
+
+	      <li>
+	        <p>
+		  Change the current band to "Green" in the RGB
+		  window and open the green file.
+		</p>
+	      </li>
+
+	      <li>
+	        <p>
+		  Change the current band to "Blue" in the RGB
+		  window and open the blue file.
+		</p>
+	      </li>
+	      </ol>
+
+	  </div>
+</div>
+
+            <div class="figure">
+<div class="caption"><h3><a name="rgb">Figure 1: RGB window</a></h3></div>
+<div><img alt="[The RGB window indicates that all three layers are visible and Blue is selected as the current one.]" src="rgb.png"></div>
+</div>
+
+	    <p>
+	      Each frame of the RGB image may have different binning,
+	      scaling, smoothing, and colorbars applied to it.  You
+	      can "lock" the frames together, so that the setting
+	      is applied to all three frames at once.  This is done
+	      with the <a href="#lock">Lock menu in the RGB
+	      window (Figure 2)</a>; all four options are checked in this
+	      thread. 
+	    </p>
+
+    	    <div class="figure">
+<div class="caption"><h3><a name="lock">Figure 2: Lock menu in the RGB window</a></h3></div>
+<div><img alt="[The lock menu is expanded and all four options are checked.]" src="lock.png"></div>
+</div>
+
+	    <p>
+	      Use the binning and zoom options in ds9 to adjust the
+	      image so that the full region of interest is visible.
+	      <a href="#ds9">Figure 3</a> uses binning=2 and zoom=1.
+	      The "Scale" is set to "log: minmax"
+	    </p>
+            
+            <div class="figure">
+<div class="caption"><h3><a name="ds9">Figure 3: RGB frame with three files loaded</a></h3></div>
+<div><img alt="[The data is loaded into one ds9 frame; the RGB window indicates the current layer is Blue.]" src="ds9.png"></div>
+</div>
+     <hr>
+</div>
+<div class="section">
+<h2><a name="energy">Apply Energy Filters</a></h2>
+        
+
+	<p>	 
+	  The following energy bands are used for the RGB layers:
+	</p>
+
+	<ul>
+	  <li>red (soft band): 200-1500 eV</li>
+	  <li>green (medium band): 1500-2500 eV</li>
+	  <li>blue (hard band): 2500-8000 eV</li>
+	</ul>
+
+	<p>
+          The values are just guidelines and may need to be adjusted for your analysis.
+	</p>
+
+	<p>
+	  To filter the data, first select the Red frame from the RGB
+	  window.  Open the <tt>Bin  → Binning Parameters</tt>
+	  dialog box and type "<tt>energy=200:1500</tt>" in the Bin
+	  Filter field.  Choose "Apply" and the ds9 display will be
+	  updated to reflect the energy filter.
+	</p>
+
+	<p>
+	  Without closing the Binning Parameters box, select the Green
+	  frame.  Type "<tt>energy=1500:2500</tt>" in the Bin
+	  Filter field and choose "Apply" again.  Repeat these two
+	  steps for the Blue layer, using the filter 
+	  "<tt>energy=2500:8000</tt>".
+	</p>
+            
+	<p>
+	  The colors in the image, as seen in <a href="#efilt">Figure 4</a>,
+	  are correlated to the energy of the data.
+	</p>
+
+            <div class="figure">
+<div class="caption"><h3><a name="efilt">Figure 4: Energy-filtered RGB data</a></h3></div>
+<div><img alt="[Each layer of data has a different energy filtered applied, correlating color and energy in the image.]" src="filtered.png"></div>
+</div>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="smooth">Smoothing the Data (optional)</a></h2>
+        
+	
+	<p>	 
+	  Smoothing can help bring out finer features in the data by
+	  removing statistical noise.  It is an optional step;
+	  experiment with smoothing to see if it improves the
+	  appearance of your data. 
+	</p>
+
+	<p>
+	  The smoothing capability in ds9 lets you interactively
+	  smooth the data.  Note that for quantitative data analysis,
+	  smoothing should be done with the appropriate data analysis
+	  software; ds9 does a nice job for publication purposes.	   
+	</p>
+
+	<p>
+	  Choose "Smooth" from the "Analysis" menu and the ds9 display
+	  is updated with the results of smoothing. The "Smooth"
+	  option can be toggled on and off during your ds9 session.  
+	</p>
+
+	<p>
+	  Open the "Smoothing Parameters..." dialog box from the same
+	  menu to adjust the function and kernel radius of the
+	  smoothing.  This data were smoothed with a Gaussian function
+	  with radius of two.  The results are shown in
+	  <a href="#smooth">Figure 5</a>. 
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="smooth">Figure 5: Data smoothed with a Gaussian of radius three</a></h3></div>
+<div><img alt="[The smoothed data are displayed in ds9.]" src="smooth.png"></div>
+</div>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="scale">Adjusting the Scale Parameters</a></h2>
+        
+
+	<p>
+	  This data is being displayed with a "log: minmax" scale.
+	  That means that ds9 stretches the scale to encompass
+	  the range of pixel values in the file.  Adjusting the
+	  minimum and maximum scale values sets a threshold for the
+	  background data and brings out features. 
+	</p>
+
+	<p>
+	  To change the minimum and maximum values, open the "Scale
+	  → Scale Parameters" dialog box.  The pixel distribution
+	  shown is for the band selected as "Current" in the RGB
+	  window; when the a different band is selected, the histogram
+	  of pixel values is updated to match. 
+	</p>
+
+	<p>
+	  To adjust the values, use the cursor to grab the red
+	  (minimum) or green (maximum) vertical lines on the plot and
+	  drag them to the desired location.  You can type a value in
+	  to the "Low" or "High" field and hit "Apply" to set the
+	  limits. 
+	</p>
+
+	<p>
+	  A basic guideline for setting the low value is to minimize
+	  the contribution of the background.  That is, adjust the
+	  minimum of each band until the background of the image is
+	  flat (i.e. solid black).  For the maximum value, bringing it
+	  in to the last data point in the pixel distribution is
+	  usually sufficient.  
+	</p>
+
+	<p>
+	  For ObsID 198 with the smoothing applied, the following
+	  limits were chosen (listed as "low:high" pairs): 
+	</p>
+
+	<ul>
+	  <li>Red - 0.4 : 20</li>
+	  <li>Green - 0.3 : 35</li>
+	  <li>Blue - 0.1 : 10</li>
+	</ul>
+
+	<p>
+	  <a href="#scale">Figure 6</a> shows the image with
+	  the new pixel value limits set. 
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="scale">Figure 6: The adjusted pixel distribution for scaling</a></h3></div>
+<div><img alt="[The background of the image is almost completely flat (black) after changing the scaling values.]" src="scale.png"></div>
+</div>
+
+      <hr>
+</div>
+<div class="section">
+<h2><a name="coordgrid">Adding a Coordinate Grid</a></h2>
+        
+
+	<p>
+	  To add a coordinate grid to the image, choose the
+	  "Coordinate Grid" option from the "Analysis"
+	  menu.  Then choose "Coordinate Grid Parameters" from the
+	  same menu to open <a href="#grid">the preferences
+	  dialog (Figure 7)</a>.  
+	</p>
+
+    	<div class="figure">
+<div class="caption"><h3><a name="grid">Figure 7: Coordinate Grid parameters dialog box</a></h3></div>
+<div><img alt="[The parameter box contains fields to set the plot title and axis labels and to change the axis spacing and numbering.]" src="grid.png"></div>
+</div>
+
+	<p>
+	  From the preferences box, you can change the color,
+	  font, line style (solid or dash), and line thickness for
+	  all elements of the grid.  The font style, size, and
+	  color can be edited, and you can add titles.  It is also
+	  possible to turn off the display of individual items via
+	  the "View" menu.  
+	</p>
+
+	<p>
+	  In <a href="#color">Figure 8</a>, we have turned
+	  off the grid lines and border.  The axes have been
+	  changed to "Exterior Axes" (from the "Type" menu).
+	</p>
+
+	<div class="figure">
+<div class="caption"><h3><a name="color">Figure 8: Final three-color image with coordinate grid overlaid</a></h3></div>
+<div><img alt="[The three-color image is displayed in ds9.]" src="color.png"></div>
+</div>
+      <hr>
+</div>
+<div class="section">
+<h2><a name="output">Saving the Output</a></h2>
+        
+
+	<p>
+	  Once you are happy with your true color image, there are a
+	  number of output options in ds9. 
+	</p>
+
+	<ul>
+	  <li>
+	    <p>
+	      <strong>Image formats:</strong> from the "File →
+	      Save Image As..." menu, you can choose JPG, PNG, or TIFF
+	      file formats. 
+	    </p>
+	  </li>
+
+	  <li>
+	    <p>
+	      <strong>Postscript:</strong>  to create a postscript
+	      file, go to "File → Print..." and select "Print To:
+	      File". 
+	    </p>
+	  </li>
+	</ul>
+
+	<p>
+	  Currently it is not possible to save the state of the ds9
+	  imager, meaning that you cannot save the composite RGB
+	  frame and reopen later for further analysis.  
+	</p>
+
+      </div>
+</div>
+<hr size="5" noshade>
+<h2><a name="history">History</a></h2>
+<table class="history">
+      <tr>
+<td class="historydate">04 Jun 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>
diff --git a/ds9/doc/user/rgb/lock.png b/ds9/doc/user/rgb/lock.png
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diff --git a/ds9/doc/user/rgb/thread.xml b/ds9/doc/user/rgb/thread.xml
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+<?xml version="1.0" encoding="us-ascii" ?>
+<!DOCTYPE thread>
+
+<thread>
+
+  <info>
+    
+    <version>June 2009</version>
+    <title>
+      <long>Create a True Color Image in an RGB frame</long>
+    </title>
+    <history>
+      <entry day="4" month="June" year="9" who="liz">
+	Original version
+	<!--// built from CIAO true_color_ds9 thread //-->
+     </entry>
+     </history>
+  </info>
+
+  <text>
+    <overview>
+
+      <synopsis>
+        <p>
+	  Most astronomical images map color to intensity level,
+	  e.g. lighter tones may correspond to a brighter intensity
+	  level in a greyscale image.  An alternative way of
+	  presenting data is via an image that correllates color and
+	  energy. 
+	</p>
+	
+	<p>
+	  ds9 has the capability to create an RGB image and
+          interactively adjust many of its parameters to achieve
+          optimal display results. 
+	</p>
+      </synopsis>
+    </overview>
+
+    <sectionlist>
+
+      <section id="frame">
+        <title>Creating an RGB Frame</title>
+
+	<p>
+	  To use the three-color capabilities of ds9, the data must be
+	  loaded into a special RGB frame.  This frame will contain
+	  all three files, stacked together in separate layers. 
+	</p>
+
+	<p>
+	  This thread uses Chandra data from an observation of Cas A
+	  (ObsID 198); the level=2 event file is named 
+	  "casa.fits".  The same file is loaded into each layer of the
+	  RGB frame; different energy filters will be applied to the
+	  layers in a later step.   
+	</p>
+
+	<p>
+	  There are two options for creating the RGB frame:
+	</p>
+
+        <subsectionlist type="A">
+          <subsection id="frame.cmdline">
+            <title>From the command line</title>
+
+	    <p>
+	      The command-line syntax can be used to create the
+	      RGB frame and load the three files into the red, green,
+	      and blue layers:
+	    </p>
+
+<screen>
+unix% ds9 -rgb -red casa.fits \
+               -green casa.fits \
+	       -blue casa.fits &amp;
+</screen>
+
+	    <p>
+	      ds9 will open with the three files in one frame.
+	      The <figlink id="rgb">RGB window</figlink> should open
+	      as well.  If it doesn't, open it from the "Frame &#8594;
+	      RGB..." menu.  
+	    </p>
+
+	  </subsection>
+
+          <subsection id="frame.gui">
+            <title>From the ds9 GUI</title>
+
+	    <p>
+	      To load the files from the ds9 GUI:
+	    </p>
+
+	    <list type="1">
+	      <li>
+	        <p>
+		  Launch ds9
+		</p>
+	      </li>
+
+	      <li>
+	        <p>
+		  Choose "New Frame RGB" from the "Frame" menu.
+		</p>
+
+		<p>
+		  When the new frame is created, the 
+		  <figlink id="rgb">RGB window</figlink> should open as well.
+		  If it doesn't, open it from the "Frame &#8594; RGB..."
+		  menu. 
+		</p>
+	      </li>
+
+	      <li>
+	        <p>
+		  Make sure the "Red" band is selected in the
+		  "Current" column of the RGB window, then choose
+		  "File &#8594; Open..." in the main ds9 window and
+		  select the red file.   
+		</p>
+	      </li>
+
+	      <li>
+	        <p>
+		  Change the current band to "Green" in the RGB
+		  window and open the green file.
+		</p>
+	      </li>
+
+	      <li>
+	        <p>
+		  Change the current band to "Blue" in the RGB
+		  window and open the blue file.
+		</p>
+	      </li>
+	      </list>
+
+	  </subsection>
+	  </subsectionlist>
+
+            <figure id="rgb">
+              <title>RGB window</title>
+              <description>The RGB window indicates that all three
+              layers are visible and Blue is selected as the current
+              one.</description> 
+              <bitmap format="png">rgb.png</bitmap>
+            </figure>
+
+	    <p>
+	      Each frame of the RGB image may have different binning,
+	      scaling, smoothing, and colorbars applied to it.  You
+	      can "lock" the frames together, so that the setting
+	      is applied to all three frames at once.  This is done
+	      with the <figlink id="lock">Lock menu in the RGB
+	      window</figlink>; all four options are checked in this
+	      thread. 
+	    </p>
+
+    	    <figure id="lock">
+    	      <title>Lock menu in the RGB window</title>
+    	      <description>The lock menu is expanded and all four
+    	      options are checked.</description>
+    	      <bitmap format="png">lock.png</bitmap>
+    	    </figure>
+
+	    <p>
+	      Use the binning and zoom options in ds9 to adjust the
+	      image so that the full region of interest is visible.
+	      <figlink id="ds9"/> uses binning=2 and zoom=1.
+	      The "Scale" is set to "log: minmax"
+	    </p>
+            
+            <figure id="ds9">
+              <title>RGB frame with three files loaded</title>
+              <description>The data is loaded into one ds9 frame; the RGB
+              window indicates the current layer is Blue.</description>
+              <bitmap format="png">ds9.png</bitmap>
+            </figure>
+     </section>
+
+      <section id="energy">
+        <title>Apply Energy Filters</title>
+
+	<p>	 
+	  The following energy bands are used for the RGB layers:
+	</p>
+
+	<list>
+	  <li>red (soft band): 200-1500 eV</li>
+	  <li>green (medium band): 1500-2500 eV</li>
+	  <li>blue (hard band): 2500-8000 eV</li>
+	</list>
+
+	<p>
+          The values are just guidelines and may need to be adjusted for your analysis.
+	</p>
+
+	<p>
+	  To filter the data, first select the Red frame from the RGB
+	  window.  Open the <tt>Bin  &#8594; Binning Parameters</tt>
+	  dialog box and type "<tt>energy=200:1500</tt>" in the Bin
+	  Filter field.  Choose "Apply" and the ds9 display will be
+	  updated to reflect the energy filter.
+	</p>
+
+	<p>
+	  Without closing the Binning Parameters box, select the Green
+	  frame.  Type "<tt>energy=1500:2500</tt>" in the Bin
+	  Filter field and choose "Apply" again.  Repeat these two
+	  steps for the Blue layer, using the filter 
+	  "<tt>energy=2500:8000</tt>".
+	</p>
+            
+	<p>
+	  The colors in the image, as seen in <figlink id="efilt"/>,
+	  are correlated to the energy of the data.
+	</p>
+
+            <figure id="efilt">
+              <title>Energy-filtered RGB data</title>
+              <description>Each layer of data has a different energy
+              filtered applied, correlating color and energy in the
+              image.</description> 
+              <bitmap format="png">filtered.png</bitmap>
+            </figure>
+
+      </section>
+
+      <section id="smooth">
+        <title>Smoothing the Data (optional)</title>
+	
+	<p>	 
+	  Smoothing can help bring out finer features in the data by
+	  removing statistical noise.  It is an optional step;
+	  experiment with smoothing to see if it improves the
+	  appearance of your data. 
+	</p>
+
+	<p>
+	  The smoothing capability in ds9 lets you interactively
+	  smooth the data.  Note that for quantitative data analysis,
+	  smoothing should be done with the appropriate data analysis
+	  software; ds9 does a nice job for publication purposes.	   
+	</p>
+
+	<p>
+	  Choose "Smooth" from the "Analysis" menu and the ds9 display
+	  is updated with the results of smoothing. The "Smooth"
+	  option can be toggled on and off during your ds9 session.  
+	</p>
+
+	<p>
+	  Open the "Smoothing Parameters..." dialog box from the same
+	  menu to adjust the function and kernel radius of the
+	  smoothing.  This data were smoothed with a Gaussian function
+	  with radius of two.  The results are shown in
+	  <figlink id="smooth"/>. 
+	</p>
+
+	<figure id="smooth">
+	  <title>Data smoothed with a Gaussian of radius three</title>
+	  <description>The smoothed data are displayed in ds9.</description>
+	  <bitmap format="png">smooth.png</bitmap>
+	</figure>
+
+      </section>
+
+      <section id="scale">
+        <title>Adjusting the Scale Parameters</title>
+
+	<p>
+	  This data is being displayed with a "log: minmax" scale.
+	  That means that ds9 stretches the scale to encompass
+	  the range of pixel values in the file.  Adjusting the
+	  minimum and maximum scale values sets a threshold for the
+	  background data and brings out features. 
+	</p>
+
+	<p>
+	  To change the minimum and maximum values, open the "Scale
+	  &#8594; Scale Parameters" dialog box.  The pixel distribution
+	  shown is for the band selected as "Current" in the RGB
+	  window; when the a different band is selected, the histogram
+	  of pixel values is updated to match. 
+	</p>
+
+	<p>
+	  To adjust the values, use the cursor to grab the red
+	  (minimum) or green (maximum) vertical lines on the plot and
+	  drag them to the desired location.  You can type a value in
+	  to the "Low" or "High" field and hit "Apply" to set the
+	  limits. 
+	</p>
+
+	<p>
+	  A basic guideline for setting the low value is to minimize
+	  the contribution of the background.  That is, adjust the
+	  minimum of each band until the background of the image is
+	  flat (i.e. solid black).  For the maximum value, bringing it
+	  in to the last data point in the pixel distribution is
+	  usually sufficient.  
+	</p>
+
+	<p>
+	  For ObsID 198 with the smoothing applied, the following
+	  limits were chosen (listed as "low:high" pairs): 
+	</p>
+
+	<list>
+	  <li>Red - 0.4 : 20</li>
+	  <li>Green - 0.3 : 35</li>
+	  <li>Blue - 0.1 : 10</li>
+	</list>
+
+	<p>
+	  <figlink id="scale"/> shows the image with
+	  the new pixel value limits set. 
+	</p>
+
+	<figure id="scale">
+	  <title>The adjusted pixel distribution for scaling</title>
+	  <description>The background of the image is almost
+	  completely flat (black) after changing the scaling
+	  values.</description> 
+	  <bitmap format="png">scale.png</bitmap>	  
+	</figure>
+
+      </section>
+
+      <section id="coordgrid">
+        <title>Adding a Coordinate Grid</title>
+
+	<p>
+	  To add a coordinate grid to the image, choose the
+	  "Coordinate Grid" option from the "Analysis"
+	  menu.  Then choose "Coordinate Grid Parameters" from the
+	  same menu to open <figlink id="grid">the preferences
+	  dialog</figlink>.  
+	</p>
+
+    	<figure id="grid">
+    	  <title>Coordinate Grid parameters dialog box</title>
+    	  <description>The parameter box contains fields to set
+    	    the plot title and axis labels and to change the
+    	    axis spacing and numbering.</description> 
+    	  <bitmap format="png">grid.png</bitmap>
+    	</figure>
+
+	<p>
+	  From the preferences box, you can change the color,
+	  font, line style (solid or dash), and line thickness for
+	  all elements of the grid.  The font style, size, and
+	  color can be edited, and you can add titles.  It is also
+	  possible to turn off the display of individual items via
+	  the "View" menu.  
+	</p>
+
+	<p>
+	  In <figlink id="color"/>, we have turned
+	  off the grid lines and border.  The axes have been
+	  changed to "Exterior Axes" (from the "Type" menu).
+	</p>
+
+	<figure id="color">
+	  <title>Final three-color image with coordinate grid overlaid</title>
+	  <description>The three-color image is displayed in ds9.</description>
+	  <bitmap format="png">color.png</bitmap>
+	</figure>
+      </section>
+
+      <section id="output">
+        <title>Saving the Output</title>
+
+	<p>
+	  Once you are happy with your true color image, there are a
+	  number of output options in ds9. 
+	</p>
+
+	<list>
+	  <li>
+	    <p>
+	      <strong>Image formats:</strong> from the "File &#8594;
+	      Save Image As..." menu, you can choose JPG, PNG, or TIFF
+	      file formats. 
+	    </p>
+	  </li>
+
+	  <li>
+	    <p>
+	      <strong>Postscript:</strong>  to create a postscript
+	      file, go to "File &#8594; Print..." and select "Print To:
+	      File". 
+	    </p>
+	  </li>
+	</list>
+
+	<p>
+	  Currently it is not possible to save the state of the ds9
+	  imager, meaning that you cannot save the composite RGB
+	  frame and reopen later for further analysis.  
+	</p>
+
+      </section>
+
+    </sectionlist>
+  </text>
+
+</thread>
+
+
+
diff --git a/ds9/doc/user/scripts/contour.png b/ds9/doc/user/scripts/contour.png
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+++ b/ds9/doc/user/scripts/contour.png
diff --git a/ds9/doc/user/scripts/contourdss.png b/ds9/doc/user/scripts/contourdss.png
new file mode 100644
index 0000000..c80f8fe
--- /dev/null
+++ b/ds9/doc/user/scripts/contourdss.png
diff --git a/ds9/doc/user/scripts/index.html b/ds9/doc/user/scripts/index.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Scripting ds9 - DS9 </title>
+</head> 
+<!--THIS FILE IS CREATED AUTOMATICALLY - DO NOT EDIT MANUALLY--> 
+<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 &amp;
+</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 &amp;
+</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 &amp;
+</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>
diff --git a/ds9/doc/user/scripts/thread.xml b/ds9/doc/user/scripts/thread.xml
new file mode 100644
index 0000000..e9da6af
--- /dev/null
+++ b/ds9/doc/user/scripts/thread.xml
@@ -0,0 +1,330 @@
+<?xml version="1.0" encoding="us-ascii" ?>
+<!DOCTYPE thread>
+
+<thread>
+
+  <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>
+
+
+
author	William Joye <wjoye@cfa.harvard.edu>	2016-10-27 19:01:15 (GMT)
committer	William Joye <wjoye@cfa.harvard.edu>	2016-10-27 19:01:15 (GMT)
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