All the programs in Gnuastro are designed such that specifying an output file or directory (based on the program context) is optional. The outputs of most programs are automatically found based on the input and what the program does. For example when you are converting a FITS image named FITSimage.fits to a JPEG image, the JPEG image will be saved in FITSimage.jpg.
Another very important part of the automatic output generation is that all the directory information of the input file name is stripped off of it. This feature can be disabled with the --keepinputdir option, see Common options. It is the default because astronomical data are usually very large and organized specially with special file names. In some cases, the user might not have write permissions in those directories. In fact, even if the data is stored on your own computer, it is advised to only grant write permissions to the super user or root. This way, you won’t accidentally delete or modify your valuable data!
Let’s assume that we are working on a report and want to process the
FITS images from two projects (ABC and DEF), which are stored in the
sub-directories named ABCproject/ and DEFproject/ of our
top data directory (/mnt/data). The following shell commands
show how one image from the former is first converted to a JPEG image
through ConvertType and then the objects from an image in the latter
project are detected using NoiseChisel. The text after the
sign are comments (not typed!).
$ pwd # Current location /home/usrname/research/report $ ls # List directory contents ABC01.jpg $ ls /mnt/data/ABCproject # Archive 1 ABC01.fits ABC02.fits ABC03.fits $ ls /mnt/data/DEFproject # Archive 2 DEF01.fits DEF02.fits DEF03.fits $ astconvertt /mnt/data/ABCproject/ABC02.fits --output=jpg # Prog 1 $ ls ABC01.jpg ABC02.jpg $ astnoisechisel /mnt/data/DEFproject/DEF01.fits # Prog 2 $ ls ABC01.jpg ABC02.jpg DEF01_labeled.fits