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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>Binning and Filtering FITS Event Files - DS9 </title>
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<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 ds9help @ 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 &
</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]" &
</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 < (less than) or > (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>
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