Segmenting FITS imaging with DS9 and shell scripting.
- Key Files
- Supplementary Files
- Software Requirements
- Testing
- Installation
- Getting Started
- Acknowledgments
- Reference
- fits_segmenter.sh Bash shell script.
The Bash shell script automates segmentation of FITS files into smaller JPEG image segments. The script executes metaprogrammed DS9 command line functions. It supports arbitrary-resolution FITS files and screen sizes. Note, the shell script assumes a single-monitor system setup.
- differencer.cl IRAF Command Language script.
The IRAF Command Language script (differencer.cl) was used to create difference FITS files (test data) from on/off-band [O III] FITS files. The FITS segmenter doesn't need it to run, but it's included here for the purposes of reproducing testing data.
- Bash shell.
- DS9.
- IRAF (optional).
If running DS9 on the macOS, an X11 port, not Aqua port, is needed.
The FITS segmenter has been tested with the following system configurations.
| Operating System | DS9 Version |
|---|---|
| Debian GNU/Linux 13 | 8.7b2 (Debian 12 Intel) |
| Kali GNU/Linux Rolling (2025.3) | 8.7b2 (Debian 12 Intel) |
| macOS Monterey 12.7.6 | 8.6 (macOS Monterey 12 Intel, X11 port) |
| openSUSE Leap 16.0 | 8.7b2 (OpenSUSE 15 Intel) |
| Ubuntu 24.04.3 LTS | 8.7b2 (Ubuntu 24 Intel) |
The IRAF Command Language script (differencer.cl) has been tested with IRAF community distribution 2.17.1, on Ubuntu 24.04.3.
Example command-line commands for installing DS9 and the utilities supporting the FITS segmenter are given below. Users who already have DS9 or the associated utilities installed, don't need to reinstall them, and may skip the relevant steps.
The example installation instructions were valid as of Nov-2025. Users should amend package names and DS9 download file paths, as new versions become available.
Installing DS9 8.7b2 (Debian 12 Intel) and supporting utilities in Debian...
$ sudo apt-get update
$ sudo apt-get install bc
$ sudo apt-get install libx11-6
$ sudo apt-get install libxft2
$ sudo apt-get install libxml2
$ sudo apt-get install libxss1
$ sudo apt-get install wget
$ sudo apt-get install x11-xserver-utils
$ wget https://ds9.si.edu/download/debian12x86/ds9.debian12x86.8.7b2.tar.gz
$ tar -xzvf ds9.debian12x86.8.7b2.tar.gz
$ rm ds9.debian12x86.8.7b2.tar.gz
$ sudo mv ds9 /usr/local/bin/
$ sudo chmod +x /usr/local/bin/ds9
Installing DS9 8.7b2 (Debian 12 Intel) and supporting utilities in Kali Linux...
$ sudo apt-get update
$ sudo apt-get install bc
$ sudo apt-get install libxft2
$ sudo apt-get install libxml2
$ sudo apt-get install libxss1
$ sudo apt-get install x11-xserver-utils
$ wget https://ds9.si.edu/download/debian12x86/ds9.debian12x86.8.7b2.tar.gz
$ tar -xzvf ds9.debian12x86.8.7b2.tar.gz
$ rm ds9.debian12x86.8.7b2.tar.gz
$ sudo mv ds9 /usr/local/bin/
$ sudo chmod +x /usr/local/bin/ds9
Installing DS9 8.6 (Monterey 12 Intel, X11 port) and supporting utilities in macOS Monterey...
$ curl -O https://ds9.si.edu/download/darwinmontereyx86/ds9.darwinmontereyx86.8.6.tar.gz
$ tar -xvzf ds9.darwinmontereyx86.8.6.tar.gz
$ rm ds9.darwinmontereyx86.8.6.tar.gz
$ sudo mkdir -p /usr/local/bin/
$ sudo mv ds9 ds9.zip /usr/local/bin/
$ sudo chmod +x /usr/local/bin/ds9
Additionally, if XQuartz isn't already available, install XQuartz from the macOS GUI using the package available at www.xquartz.org.
Installing DS9 8.7b2 (OpenSUSE 15 Intel) and supporting utilities in openSUSE Leap 16.0...
$ sudo zypper update
$ sudo zypper install bc
$ sudo zypper install gzip
$ sudo zypper install libX11-6
$ sudo zypper install libXft2
$ sudo zypper install noto-fonts
$ sudo zypper install tar
$ sudo zypper install xrandr
$ wget https://ds9.si.edu/download/opensuse15x86/ds9.opensuse15x86.8.7b2.tar.gz
$ tar -xzvf ds9.opensuse15x86.8.7b2.tar.gz
$ rm ds9.opensuse15x86.8.7b2.tar.gz
$ sudo mv ds9 /usr/local/bin/
$ sudo chmod +x /usr/local/bin/ds9
Installing DS9 8.7b2 (Ubuntu 24 Intel) and supporting utilities in Ubuntu...
$ sudo apt-get update
$ sudo apt-get install libxft2
$ sudo apt-get install libxss1
$ sudo apt-get install x11-xserver-utils
$ wget https://ds9.si.edu/download/ubuntu24x86/ds9.ubuntu24x86.8.7b2.tar.gz
$ tar -xzvf ds9.ubuntu24x86.8.7b2.tar.gz
$ rm ds9.ubuntu24x86.8.7b2.tar.gz
$ sudo mv ds9 /usr/local/bin/
$ sudo chmod +x /usr/local/bin/ds9
Usage: ./fits_segmenter.sh [-h] [-m <mode argument>] [target FITS files list]
[-h]
Displays script help information.
[-m <mode argument>]
Ensure <mode argument> is either single or dual.
Single mode
- Assumes one FITS file per DS9 frame.
Dual mode
- Assumes two FITS files per DS9 frame.
- The first is rendered red and the second green, in an RGB frame.
- An even number of target FITS files should be specified.
[target FITS files list]
A list of FITS files to be segmented should be specified as a script parameter.
Target FITS files should be in the same directory as fits_segmenter.sh.
Omit file extensions, a '.fits' extension is assumed for each target file.
For dual mode, specify complementary FITS file pairs, e.g., narrowband and broadband filter exposures.
For dual mode, a FITS file pair should have the same (x, y) dimensions.
Example, single mode:
./fits_segmenter.sh -m single F1759-2841_diff F1759-2915_diff F1803-2807_diff
Example, dual mode:
./fits_segmenter.sh -m dual F1759-2841_O3 F1759-2841_O3_off F1759-2915_O3 F1759-2915_O3_off F1803-2807_O3 F1803-2807_O3_off
This work used public data from the US National Science Foundation's (NSF) NOIRLab Astro Data Archive. Those data were generated from observations at the NSF CTIO, NSF NOIRLab (NOIRLab Prop. ID 2008A-0549; PI: Q. Parker), which the Association of Universities for Research in Astronomy (AURA) manages under a cooperative agreement with the US NSF. Data reduction was performed via Community IRAF. SAOImageDS9, developed by the Smithsonian Astrophysical Observatory, was also used.
Stenborg, TN 2026, "DS9 FITS Segmentation with Linux and macOS Shell Script Metaprogramming", K Polsterer & S Wagner (eds), in Astronomical Data Analysis Software and Systems XXXV, Astronomical Society of the Pacific Conference Series (submitted).