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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<title>Create a True Color Image in an RGB frame - DS9 </title>
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<!--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 &
</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>
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