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diff --git a/ds9/doc/user/binning/index.html b/ds9/doc/user/binning/index.html new file mode 100644 index 0000000..281df7f --- /dev/null +++ b/ds9/doc/user/binning/index.html @@ -0,0 +1,367 @@ +<!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 & +</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> +</html> |