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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=windows-1252">
<meta name="GENERATOR" content="Mozilla/4.78 [en] (X11; U; Linux
2.4.7-10 i686) [Netscape]">
<title>File Formats</title>
</head>
<body alink="#ff0000" bgcolor="#ffffff" link="#0000ee" text="#000000"
vlink="#551a8b">
<h3><img alt="" src="../sun.gif" align="middle" height="98"
width="100"> File Formats</h3>
<blockquote> <a href="#FITS">FITS</a><br>
<a href="#FITSImage">FITS Image</a><br>
<a href="#FITSTable">FITS Table</a><br>
<a href="#FITSBinaryEventsTable">FITS Binary Events Table</a><br>
<a href="#FITSHEALPIXTable">FITS HEALPIX Table</a><br>
<a href="#FITSDataCube">FITS Data Cube</a><br>
<a href="#FITSMultipleExtensionDataCube">FITS Multiple Extension
Data Cube</a><br>
<a href="#FITSMultipleExtensionMultipleFrames">FITS Multiple
Extension Multiple Frames</a><br>
<a href="#FITSMosaic">FITS Mosaic</a><br>
<a href="#FITSMosaicDataCube">FITS Mosaic Data Cube</a><br>
<a href="#FITSRGB">FITS RGB </a><br>
<a href="#SplitFITS">Split FITS</a><br>
<a href="#array">Array</a> <br>
<a href="file:///Users/joye/saods9/doc/ref/file.html#nrrd">NRRD</a><br>
<a href="#envi">ENVI</a><br>
<a href="#gif">GIF</a><br>
<a href="#tiff">TIFF</a><br>
<a href="#jpeg">JPEG</a><br>
<a href="#png">PNG</a><br>
<a href="#ExternalFileSupport">External Format Support</a> <br>
<a href="#ExternalAnalysisSupport">External Analysis Support</a> <br>
<a href="#RegionFiles">Region Files</a> <br>
<a href="#ColorLookupTable">Color Lookup Table</a> <br>
<a href="#WCS">WCS</a> <br>
<a href="#PreferenceFile">Preference File</a> <br>
<a href="#StartupFile">Startup File</a> <br>
<a href="#TCL">TCL</a><br>
<p><b><a name="FITS"></a>FITS</b></p>
DS9 supports FITS images and FITS binary tables. The following
algorithm is used to locate and to load the FITS image or table if
no additional information is provide:
<blockquote> <tt> Look for FITS image in primary HDU. <br>
If no image is found, examine each extension HDU<br>
If image, load <br>
If bin table, load if the following is true<br>
extension name is EVENTS or STDEVT or
RAYEVENT <br>
column names X and Y are present<br>
If DS9 traverses the entire FITS file without satisfying one
of the above, an error is generated.</tt> </blockquote>
FITS keyword inheritance is supported. All valid FITS <tt>BITPIX</tt>
values are supported, along with <tt>-16,</tt> for <tt>UNSIGNED
SHORT</tt>. The following FITS keywords are supported:
<blockquote> <tt> OBJECT<br>
BSCALE / BZERO<br>
BLANK<br>
DATASEC<br>
LTV / LTM for physical coords<br>
DTV / DTM for detector coords<br>
ATV / ATM for amplifier coords<br>
WCS keywords<br>
WCS# keywords </tt> </blockquote>
<p><b> <a name="FITSImage"></a>FITS Image</b></p>
At load time, the user may provide just a filename or a filename
along with FITS extension name/number and image section
specification. FITS extension names are case insensitive. When
specifying an extention, be sure to quote strings correctly to
pass both the shell and DS9 parser. A image section specification
is used to specify the x,y limits of an image subsection. By
default, numerics are in <tt>IMAGE</tt> coordinates, use a <tt>'p'</tt>
to indicate <tt>PHYSICAL</tt> coordinates. A <tt>'*'</tt>
indicates use the default for that axis only.<br>
<blockquote> <tt> Syntax:<br>
filename<br>
filename[<name>|#]<br>
filename[xmin:xmax,ymin:ymax[p]]<br>
filename[*,ymin:ymax[p]]<br>
filename[xmin:xmax,*[p]]<br>
filename[xdim@xcenter,ydim@ycenter[p]]<br>
filename[dim@xcenter@ycenter[p]]<br>
</tt><tt>filename[xmin:xmax,ymin:ymax,zmin:zmax]</tt><br>
<tt> filename[*,ymin:ymax,zmin:zmax]<br>
filename[xmin:xmax,*,zmin:zmax]<br>
</tt><tt>filename[xmin:xmax,ymin:ymax,*]</tt><br>
<tt> filename[xdim@xcenter,ydim@ycenter,zdim@zcenter]<br>
filename[dim@xcenter@ycenter@zcenter]</tt><tt><br>
<br>
Example:<br>
$ds9 foo.fits # default load <br>
$ds9 foo.fits[1] # load first extension<br>
$ds9 foo.fits[BCKGRD] # load extension named 'BCKGRD'<br>
$ds9 foo.fits[10:200,40:100] # image section<br>
$ds9 foo.fits[*,40:100] # only section y axis<br>
$ds9 foo.fits[256@512@512] # section box at 512,512<br>
$ds9 foo.fits[2][100:200,100:200] # second extension, image
section<br>
</tt><tt>$ds9 foo.fits[10:200,40:100,5:20] # cube section<br>
$ds9 foo.fits[*,40:100,5:20] # only section y and z axes<br>
$ds9 foo.fits[256@512@512@512] # section cube at 512,512<br>
$ds9 foo.fits[2][100:200,100:200,5:20] # second extension,
cube section</tt><br>
</blockquote>
<p><b> <a name="FITSTable"></a>FITS Table</b></p>
At load time, the user may provide just a filename or a filename
along with FITS extension name or number and file parameters. FITS
extension names and parameters are case insensitive.<br>
<blockquote> <tt> Syntax: <br>
filename <br>
filename[ext] <br>
filename[params] <br>
filename[ext][params] <br>
filename[ext,params] <br>
where ext = [<extension name> | <extension #>]</tt><br>
</blockquote>
<p><b> <a name="FITSBinaryEventsTable"></a>FITS Binary Events
Table<br>
</b></p>
DS9 will automatically convert an FITS binary events table into a
2D image for display. The users may specify a number of parameters
on how to construct the image and how to filter data. When
specifying a filter, be sure to quote strings correctly to pass
both the shell and DS9 parser. </blockquote>
<blockquote>
<blockquote> <tt>Syntax: <br>
filename[ext,params]</tt> <br>
<tt>where params:<br>
[bin=colx,coly] # bin counts <br>
[bin colx,coly] # bin counts <br>
[bin=colx,coly,colz] # bin on colz <br>
[bin colx,coly,colz] # bin on colz <br>
[bin=colz] # bin cols 'x', 'y', and colz <br>
[key=colx,coly] <br>
[binkey=colx,coly]<br>
[<filter>]<br>
</tt><br>
(see <a
href="http://hea-www.harvard.edu/saord/funtools/filters.html">Introduction
to Filtering</a>)<br>
<br>
<tt>Example: </tt><br>
<tt> $ds9 foo.fits # default load </tt><br>
<tt> $ds9 foo.fits[1] # load first extension </tt><br>
<tt> $ds9 foo.fits[BCKGRD] # load extension named 'BCKGRD' </tt><br>
<tt> $ds9 foo.fits[bin=detx,dety] # bin on detx,dety </tt><br>
<tt> $ds9 foo.fits[2][bin=rawx,rawy] # load ext 2, cols
rawx,rawy </tt><br>
<tt> $ds9 foo.fits[bg_events,bin=rawx,rawy] # load ext
bg_events, cols rawx,rawy </tt><br>
<tt> $ds9 foo.fits[bin=x,y,pha] # bin on x,y,pi </tt><br>
<tt> $ds9 foo.fits[bin=pi] # bin on x,y,pi</tt><br>
<tt> $ds9 'foo.fits[ccd_id==3&&energy>4000]' # quoted
filter</tt><br>
<tt> $ds9 '"foo.fits[ccd_id==3 && energy>4000]"' #
double quoted filter</tt><br>
<tt> $ds9 'foo.fits[events][pha>5,pi<2]' # load extension
'events' and filter</tt></blockquote>
</blockquote>
<blockquote>
<blockquote> </blockquote>
<p>The shell environment variable <tt>DS9_BINKEY </tt>may be
used to specify default bin cols for FITS bin tables. Example:</p>
<blockquote> <tt>$ export DS9_BINKEY='[bin=rawx,rawy]'</tt> <br>
<tt>$ ds9 foo.fits # load FITS bin table, bin on rawx, rawy<br>
</tt></blockquote>
<p><b> <a name="FITSHEALPIXTable"></a>FITS HEALPIX Table<br>
</b></p>
DS9 will automatically convert an FITS HEALPIX binary or ascii
table into a 2D image for display. The users may specify a number
of parameters on how to construct the image. Any table with
keyword PIXTYPE=HEALPIX or NSIDE=x will be processed as an HEALPIX
image. The following FITS keywords will be used if present and not
overwritten by a command line option: NSIDE, COORDSYS, ORDER.<br>
<blockquote>
<blockquote> </blockquote>
<tt>Syntax: <br>
filename[ext,params]</tt> <br>
<tt>where params:</tt><br>
<tt>[order=ring|nested] # default ring<br>
[layout=equatorial|north|south] # default equatorial<br>
[col=<column number>] # defaut 1<br>
[quad=<quadurant number>] # (1-4) default 1<br>
[system=equatorial|galactic|ecliptic|unknown] # default
unknown</tt><br>
<br>
<tt>Example: </tt><tt><br>
$ds9 foo.fits # default load </tt><tt><br>
$ds9 foo.fits[1] # load first extension </tt><tt><br>
$ds9
foo.fits[order=ring,layout=equatorial,col=1,quad=1,system=unknown]<br>
</tt><tt>$ds9 foo.fits[1,order=nested] # first extension, nested
order</tt><br>
</blockquote>
<blockquote> </blockquote>
<p><b><a name="FITSDataCube"></a>FITS Cube</b></p>
A FITS Cube is a FITS image which contains more than 2 axes
(NAXES>2). DS9 will automatically detect if a cube is present
and will load all additional images. In addition, individual
images can be loaded one at a time into a cube. DS9 will display
the Cube dialog box which allows the user to select which 2 image
to be displayed.
<p><b><a name="FITSMultipleExtensionDataCube"></a>FITS Multiple
Extension Cube</b></p>
A FITS Multiple Extension Data Cube file is a FITS file with one
or more extensions, that is to be displayed as a data cube. Each
image does not have to be the same size, however, only the
coordinate systems from the first extension will be used for
contours and grids. <br>
<blockquote><tt> Example:</tt><br>
<tt> $ds9 -mecube foo.fits # load multiple extension fits file
as data cube</tt></blockquote>
<p><b><a name="FITSMultipleExtensionMultipleFrames"></a>FITS
Multiple Extension Multiple Frames</b></p>
Load a multiple extension FITS file into multiple frames. Please
note that files loaded via standard-in or the xpa fits command can
not be displayed using this method. <br>
<blockquote><tt> Example:</tt><br>
<tt> $ds9 -multiframe foo.fits # load multiple extension fits
file as multiple frames</tt></blockquote>
<p><b><a name="FITSMosaic"></a>FITS Mosaic</b></p>
A FITS mosaic image may exist as a series of FITS files, or as one
FITS file with many extensions. A FITS mosaic may be loaded all a
one time, or by the segment. Once loaded, the multiple FITS images
are treated as one FITS image. <br>
<br>
DS9 supports three forms of mosaics:
<center>
<table align="center" border="1" cellpadding="2" cellspacing="2"
width="50%">
<tbody>
<tr>
<td valign="top"><tt>IRAF</tt><br>
</td>
<td valign="top"> <tt>contains the DETSEC and DETSIZE
keywords.<br>
See <a
href="http://iraf.noao.edu/projects/ccdmosaic/imagedef/imagedef.html">NOAO
IRAF
Mosaic
Data
Structures</a></tt> <br>
</td>
</tr>
<tr>
<td align="left" valign="top"> <tt>WCS</tt><br>
</td>
<td align="left" valign="top"><tt>each FITS image contains
a valid WCS.</tt><br>
</td>
</tr>
<tr>
<td align="left" valign="top"> <tt>HST WFPC2</tt><br>
</td>
<td align="left" valign="top"> <tt>valid HST WFPC2 data
cube, consisting of 4 planes, along with a fits ascii
table containing wcs information. </tt></td>
</tr>
</tbody>
</table>
</center>
<tt></tt>
<blockquote><tt>Example:</tt><br>
<tt> $ds9 -mosaicimage iraf foo.fits # load mosaic iraf from one
fits file with multiple exts</tt><br>
<tt> $ds9 -mosaic iraf foo.fits bar.fits wow.fits # load mosaic
iraf from 3 files</tt><br>
<tt> $ds9 -mosaicimage wcs foo.fits # load mosaic wcs from one
fits file with multiple exts</tt><br>
<tt> $ds9 -mosaic wcs foo.fits bar.fits wow.fits # load mosaic
wcs from 3 files</tt><br>
<tt> $ds9 -mosaicimage wfpc2 bar.fits # load wfpc2 mosaic</tt><br>
<tt> $ds9 -mosaic foo.fits bar.fits wow.fits # load mosaic (wcs)
from 3 files</tt><br>
<tt> </tt></blockquote>
<p><b><a name="FITSMosaicDataCube"></a>FITS Mosaic Data Cube</b></p>
A FITS Mosaic Data Cube is a FITS mosaic image which contains more
than 2 axes (NAXES>2). DS9 will automatically detect if a
mosaic data cube is present and will load all additional images.
At the same time, DS9 will display the DataCube dialog box which
allows the user to select which 2 image to be displayed.
<p><b><a name="FITSRGB"></a>FITS RGB</b></p>
A FITS RGB image may exist as three of FITS images, one FITS file
with three extensions, or as a FITS 3D Data cube, with three
slices, each representing the red, green, and blue channel. A FITS
RGB image may be loaded all a one time, or by the channel. Once
loaded, the multiple FITS images are treated as one FITS image.<br>
<blockquote><tt>Example:</tt><br>
<tt> $ds9 -rgbimage rgb.fits # load rgb image consisting of one
fits file with 3 image exts</tt><br>
<tt> $ds9 -rgbcube cube.fits # load rgb image consisting of one
fits data cube</tt><br>
<tt> $ds9 -rgb -red foo.fits -green bar.fits -blue wow.fits #
rgb image from 3 fits images</tt><br>
<tt> </tt></blockquote>
<p><b><a name="SplitFITS"></a>Split FITS</b></p>
A split fits is a valid fits file in which two files contain the
header and data segments.
<p><b><a name="array"></a>Array</b></p>
Raw data arrays are supported. To load an array, the user must
provide the dimensions, pixel depth, and optional header size and
architecture type.
<blockquote> <tt> Syntax: <br>
filename[options]<br>
options are:<br>
xdim=value <br>
ydim=value <br>
zdim=value # default is a depth of 1<br>
dim=value <br>
dims=value <br>
bitpix=[8|16|-16|32|64|-32|-64] <br>
skip=value # must be even, most must be factor of 4 <br>
arch|endian=[big|bigendian|little|littleendian]<br>
<br>
Example:<br>
$ds9 -array bar.arr[xdim=512,ydim=512,zdim=1,bitpix=16] # load
512x512 short<br>
$ds9 -array bar.arr[dim=256,bitpix=-32,skip=4] # load 256x256
float with 4 byte head<br>
$ds9 -array bar.arr[dim=512,bitpix=32,arch=little] # load
512x512 long, intel<br>
</tt>
<p>or alternate format:</p>
<tt>filename[array(<type><dim><:skip><endian>)]<br>
type:
<blockquote> 'b' 8 -bit unsigned char<br>
's' 16-bit short int<br>
'u' 16-bit unsigned short int<br>
'i' 32-bit int<br>
'l' 64-bit int<br>
'r' 32-bit float<br>
'f' 32-bit float<br>
'd' 64-bit float </blockquote>
dim:
<blockquote> int # x,y dim<br>
int.int # x,y dim<br>
int.int.int # x,y,z dim<br>
</blockquote>
skip:
<blockquote> int # number of bytes to
skip </blockquote>
endian:
<blockquote> 'l' little endian<br>
'b' big endian<br>
</blockquote>
Example:<br>
$ds9 -array bar.arr[array(s512)] # load 512x512
short<br>
$ds9 -array bar.arr[array(r256:4)] # load 256x256 float with 4
byte head<br>
$ds9 -array bar.arr[array(i512l)] # load 512x512 long,
intel </tt>
<p>The shell environment variable <tt>DS9_ARRAY </tt>may be
used to specify default array parameters. </p>
<tt> Example:<br>
$export DS9_ARRAY='[dim=256,bitpix=-32]'<br>
$ds9 -array foo.arr # load 256x256 float<br>
</tt></blockquote>
<p><b><a name="nrrd"></a>NRRD (Nearly Raw Raster Data)</b><br>
</p>
Images in NRRD are supported directly. Encodings supported: <tt>raw,
gzip</tt><br>
<tt>Example:</tt><br>
<tt>$ds9 -nrrd foo.nrrd<br>
$ds9 -nrrd foo.nrrd[100:200,100:200] # cropped</tt><br>
<p><b><a name="envi"></a>ENVI</b><br>
</p>
Images in ENVI are supported directly. Encodings supported: <tt>BIL,
BIP, BSQ.</tt><br>
<tt>Example:</tt><br>
<tt>$ds9 -envi foo.hdr foo.bsq<br>
$ds9 -envi foo.hdr foo.bsq[100:200,100:200] # cropped<br>
</tt>
<p><b><a name="gif"></a>GIF</b><br>
</p>
Images in GIF are supported directly. For a <tt>Frame</tt>, the
average of the luminosity is used. For <tt>Frame RGB</tt>, each
channel is loaded directly.<br>
<tt>Example:</tt><br>
<tt>$ ds9 -gif foo.gif</tt><br>
<p><b><a name="tiff"></a>TIFF</b><br>
</p>
Images in TIFF are supported directly. For a <tt>Frame</tt>, the
average of the luminosity is used. For <tt>Frame RGB</tt>, each
channel is loaded directly.<br>
<tt>Example:</tt><br>
<tt>$ ds9 -tiff foo.tiff</tt><br>
<p><b><a name="jpeg"></a>JPEG</b><br>
</p>
Images in JPEG are supported directly. For a <tt>Frame</tt>, the
average of the luminosity is used. For <tt>Frame RGB</tt>, each
channel is loaded directly.<br>
<tt>Example:</tt><br>
<tt>$ ds9 -jpeg foo.jpeg</tt><br>
<p><b><a name="png"></a>PNG</b><br>
</p>
Images in PNG are supported directly. For a <tt>Frame</tt>, the
average of the luminosity is used. For <tt>Frame RGB</tt>, each
channel is loaded directly.<br>
<tt>Example:</tt><br>
<tt>$ ds9 -png foo.png</tt><br>
<p><b> <a name="ExternalFileSupport"></a>External File Support</b></p>
DS9 supports external file formats via an ASCII description file.
When loading a file into DS9, these descriptions are referenced
for instructions for loading the file, based on the file
extension. If found, the command is executed and the result, a
FITS image or FITS Binary Table, is read into DS9 via stdin. <br>
At start-up, DS9 first searches for the ASCII file, named <tt>.ds9.fil</tt>in
the
local
directory,
then in the users home directory. <br>
The file command first is macro-expanded to fill in user-defined
arguments and then is executed externally. <br>
The ASCII file that defines the known image files consists of one
or more file descriptors, each of which has the following format:
<blockquote> <tt> Help description<br>
A space-separated list of templates<br>
A space-separated list of file types (not currently used)<br>
The command line for the loading this file type<br>
</tt> </blockquote>
Note that blank lines separate the file descriptions and should
not be used as part of a description. Also, the '#' character is a
comment character. <br>
<br>
The following macros are supported: <tt>$filename</tt><br>
<blockquote><tt> For Example: </tt><br>
<tt> # File access descriptions:</tt><br>
<tt> # help explanation</tt><br>
<tt> # file template</tt><br>
<tt> # file type</tt><br>
<tt> # access command</tt><br>
<tt> IRAF IMH files</tt><br>
<tt> *.imh</tt><br>
<tt> IMH</tt><br>
<tt> i2f -s $filename </tt></blockquote>
<p><b> <a name="ExternalAnalysisSupport"></a>External Analysis
Support</b></p>
For more information about external analysis support files, see <a
href="analysis.html">Analysis</a>.
<p><b> <a name="RegionFiles"></a>Region Files</b></p>
DS9 can read and write a number of region file formats. See <a
href="region.html">Regions</a> documentation for more
information.
<blockquote> <tt> <a href="region.html#RegionDescriptions">DS9</a><br>
<a href="region.html#FUNTools">FUNTools</a><br>
<a href="region.html#Ciao">Ciao</a><br>
<a href="region.html#SAOimage">SAOimage</a><br>
<a href="region.html#IRAFPROS">IRAF PROS</a><br>
<a href="region.html#FITSREGIONBinaryTable">FITS REGION Binary
Table</a><br>
<a href="region.html#XY">X Y</a> </tt> </blockquote>
<p><b> <a name="ColorLookupTable"></a>Color Lookup Table</b></p>
DS9 has a number of default colormaps available to the user. DS9
also supports reading and writing color lookup table formats from
the following programs:
<blockquote> <tt> <a
href="http://tdc-www.harvard.edu/software/saoimage/saoimage.color.html#cmap">SAOimage</a><br>
<a
href="http://hea-www.harvard.edu/RD/saotng/adding_cmaps.html">SAOtng</a><br>
XImtool<br>
</tt> </blockquote>
DS9 uses the file extension to determine the color table format:
<center>
<table nosave="" border="1" cellpadding="2" cellspacing="2"
width="50%">
<tbody>
<tr nosave="">
<td nosave="">
<center><tt>Ext</tt></center>
</td>
<td>
<center><tt>Format</tt></center>
</td>
</tr>
<tr>
<td><tt>.lut</tt></td>
<td><tt>XImtool, SAOtng</tt></td>
</tr>
<tr>
<td><tt>.sao</tt></td>
<td><tt>DS9, SAOimage</tt></td>
</tr>
<tr>
<td><tt>any other</tt></td>
<td><tt>DS9</tt></td>
</tr>
</tbody>
</table>
</center>
<p><b> <a name="WCS"></a>WCS</b></p>
A new WCS specification can be loaded and used by the current
image regardless of the WCS that was contained in the image file.
WCS specification can be sent to DS9 as an ASCII file via XPA. The
format of the specification is a set of valid FITS keywords that
describe a WCS.
<blockquote> <tt> Example: <br>
CRPIX1
=
257.75<br>
CRPIX2
=
258.93<br>
CRVAL1
= -201.94541667302 <br>
CRVAL2
=
-47.45444<br>
CDELT1
= -2.1277777E-4 <br>
CDELT2
= 2.1277777E-4
<br>
CTYPE1 = 'RA---TAN' <br>
CTYPE2 = 'DEC--TAN' <br>
</tt> </blockquote>
Note that the WCS definitions can contain standard FITS 80
character WCS card images, as shown above, or free-form name/value
pairs without the intervening "=" sign:
<blockquote> <tt> CRPIX1
257.75 <br>
CRPIX2 258.93 <br>
CRVAL1 -201.94541667302 <br>
CRVAL2 -47.45444 <br>
CDELT1 -2.1277777E-4 <br>
CDELT2 2.1277777E-4 <br>
CTYPE1 'RA---TAN' <br>
CTYPE2 'DEC--TAN' </tt> </blockquote>
<p><b> <a name="PreferenceFile"></a>Preference File</b></p>
A preference file is a valid tcl script generated by DS9 to save
the current preference items. See <a href="prefs.html">Preferences</a>
for more information.
<p><b> <a name="StartupFile"></a>Startup File</b></p>
If a startup file <tt>ds9.ini</tt> is available, it is sourced as
the last step in initialization. The following directories are
searched in order: <tt>./, $HOME, /usr/local/lib, /opt/local/lib</tt>.
<p><b> <a name="TCL"></a>TCL</b></p>
TCL/TK script file. Users may customize the appearance and enhance
the capabilities of DS9 by sourcing their own TCL scripts. </blockquote>
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