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diff --git a/ds9/doc/user/rgb/thread.xml b/ds9/doc/user/rgb/thread.xml new file mode 100644 index 0000000..51e3503 --- /dev/null +++ b/ds9/doc/user/rgb/thread.xml @@ -0,0 +1,412 @@ +<?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 & +</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 → + 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 → 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> + </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 → 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 + → 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 → + 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> + </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> + + + |