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README

GNU Astronomy Utilities
=======================

Copyright (C) 2015-2021, Free Software Foundation, Inc.
See the end of the file for license conditions.

GNU Astronomy Utilities (Gnuastro) is an official GNU package of programs
and a library functions for astronomical data manipulation and
analysis. The programs are run directory on the operating system's
command-line enabling easy and efficient operation combined with other
installed programs in shell scripts or Makefiles. The libraries are also
usable in C and C++ programs. The full package comes with a comprehensive
book or documentation in various formats (plain text, info, PDF and HTML):

http://www.gnu.org/software/gnuastro/manual/

The Gnuastro book explains all the mathematical, physical and even
historical concepts (when necessary) for effective usage of all the
programs and libraries along with short examples for each program and full
descriptions of all their options (in the "Invoking ProgramName'
sections). There is also a separate chapter devoted to tutorials for
effectively use Gnuastro combined with other software already available on
your Unix-like operating system (see Chapter 2).

To install Gnuastro, follow the instructions in the "Install Gnuastro"
section below. If you have already installed gnuastro, you can read the
full book by running the following command. You can go through the whole
book by pressing the 'SPACE' key, and leave the Info environment at any
time by pressing 'q' key. See the "Getting help" section below (in this
file) or in the book for more.

info gnuastro

Gnuastro's programs are listed below followed by their executable name in
parenthesis and a short description. This list is ordered
alphabetically. In the book, they are grouped and ordered by context under
categories/chapters.

- Arithmetic (astarithmetic): For arithmetic operations on multiple
(theoretically unlimited) number of datasets (images). It has a large
and growing set of arithmetic, mathematical, and even statistical
operators (for example +, -, *, /, sqrt, log, min, average, median).

- BuildProgram (astbuildprog): Compile, link and run programs that depend
on the Gnuastro library. BuildProgram will automatically link with the
libraries that Gnuastro depends on, so there is no need to explicily
mention them every time you are compiling a Gnuastro library dependent
program.

- ConvertType (astconvertt): Convert astronomical data files (FITS or
IMH) to and from several other standard image and data formats, for
example TXT, JPEG, EPS or PDF.

- Convolve (astconvolve): Convolve (blur or smooth) data with a given
kernel in spatial and frequency domain on multiple threads. Convolve
can also do de-convolution to find the appropriate kernel to PSF-match
two images.

- CosmicCalculator (astconvolve): Do cosmological calculations, for
example the luminosity distance, distance modulus, comoving volume and
many more.

- Crop (astcrop): Crop region(s) from an image and stitch several images
if necessary. Inputs can be in pixel coordinates or world coordinates.

- Header (astheader): Print and manipulate the header data of a FITS file.

- Match (astmatch): Given two input catalogs, find the rows that match
with each other within a given aperture (may be an ellipse).

- MakeCatalog (astmkcatalog): Make catalog of labeled image (output of
NoiseChisel). The catalogs are highly customizable and adding new
calculations/columns is very streightforward.

- MakeNoise (astmknoise): Make (add) noise to an image, with a large set
of random number generators and any seed.

- MakeProfiles (astmkprof): Make mock 2D profiles in an image. The
central regions of radial profiles are made with a configurable 2D
Monte Carlo integration. It can also build the profiles on an
over-sampled image.

- NoiseChisel (astnoisechisel): Detect and signal in noise. It uses a
technique to detect very faint and diffuse, irregularly shaped signal
in noise (galaxies in the sky), using thresholds that are below the Sky
value (see arXiv:1505.01664).

- Query (astquery): High-level interface to query pre-defined remote, or
external, databases and directly download the required sub-tables on the
command-line.

- Segment (astsegment): Segment a detection based on the structure of
signal within it.

- Statistics (aststatistics): Get pixel statistics and save histogram and
cumulative frequency plots.

- Table (asttable): convert FITS binary and ASCII tables into other such
tables, or print them on the command-line, or save them in a plain text
file. Output columns can also be determined by number or regular
expression matching of column names.

- Warp (astwarp): Warp image to new pixel grid. Any projective
transformation or Homography can be applied to the input images.

The programs listed above are designed to be highly modular and
generic. For higher-level operations (combining multiple programs, or
running a program in a special way), Gnuastro also installs Bash scripts
(all prefixed with 'astscript-'). They can be run like a program and behave
very similarly (with minor differences, as explained in the book).

- astscript-ds9-region: Given a table (either as a file or from
standard input), create an SAO DS9 region file from the requested
positional columns (WCS or image coordinates).

- astscript-radial-profile: Calculate the radial profile of an object
within an image. The object can be at any location in the image, using
various measures (median, sigma-clipped mean and etc), and the radial
distance can also be measured on any general ellipse.

- astscript-sort-by-night: Given a list of FITS files, and a HDU and
keyword name for a date, this script separates the files in the same
night (possibly over two calendar days).

All the programs share the same basic command-line user interface and a set
of common options for the comfort of both the users and
developers. Gnuastro is written to comply fully with the GNU coding
standards so it integrates finely with the GNU/Linux operating system and
Unix-like operating systems in general. This also enables astronomers to
expect a fully familiar experience in the source code, building, installing
and command line user interaction that they have seen in all the other GNU
software that they use.

Behind the scenes, Gnuastro comes with a very robust infra-structure
enabling easy addition of new programs and new features to existing
programs and a full chapter devoted to explaining how to develop most
effectively (see the "Developing" chapter). Please join us in developing
this comprehensive and low level set of tools for astronomical data
manipulation and analysis. The copyright owner of Gnuastro is the Free
Software Foundation to guarantee its freedom in the future, and not any
particular astronomer or astronomical project, or astronomical institution,
so please join us and feel free to use it in your research.



Installing Gnuastro
-------------------

The mandatory dependencies which are required to install Gnuastro from the
tarball are listed below.

- GNU Scientific Library (GSL): https://www.gnu.org/software/gsl/
- CFITSIO: http://heasarc.gsfc.nasa.gov/fitsio/
- WCSLIB: http://www.atnf.csiro.au/people/mcalabre/WCS/

The optional dependencies are:

- GNU Libtool: https://www.gnu.org/software/libtool/
- Git library (libgit2): https://libgit2.github.com/
- JPEG library (libjpeg): http://ijg.org/
- TIFF library (libtiff): http://simplesystems.org/libtiff/
- Ghostscript: https://www.ghostscript.com/

See the "Dependencies" section of the book for their detailed installation
guides and optional dependencies to enable extra features. Prior to
installation, you can find it in the 'doc/gnuastro.texi' file (source of
the book), or on the web:

https://www.gnu.org/software/gnuastro/manual/html_node/Dependencies.html

If you have just cloned Gnuastro and want to install from the version
controlled source, please read the 'README-hacking' file (not available in
the tarball) or the "Bootstrapping dependencies" subsection of the manual
before continuing.

The most recent stable Gnuastro release can be downloaded from the
following link. Please see the "Downloading the source" section of the
Gnuastro book for a more complete discussion of your download options.

http://ftp.gnu.org/gnu/gnuastro/gnuastro-latest.tar.gz

Unpacking, configuring, building, checking and installing Gnuastro follows
the standard GNU Build system as shown below. After the './configure'
command, Gnuastro will print messages upon the successful completion of
each step, giving further information and suggestions for the next steps.

tar xf gnuastro-latest.tar.lz # Also works for 'tar.gz' files
cd gnuastro-X.X
./configure
make
make check
sudo make install

See the "Build and install" section of the book for more information. Also,
see the 'INSTALL' file which is distributed with this file for a standard
(very comprehensive and general) review of the GNU build and install
methods. The 'INSTALL' file is shared in many software packages, so reading
it once in any package is enough to help you greatly customize your build
of a very large collection of Free and Open Source (FOSS) software.



Getting help
------------

To access the appropriate section of the Gnuastro book/documentation from
your command-line (in the middle of your work, without distracting your
self by having to move your hand off the keyboard), please run any of the
following two commands. Note that you can leave the Info environment by
pressing the key 'q'.

info ProgramName # For example 'info NoiseChisel'
info astprogname # For example 'info astnoisechisel'

The Info environment is great for easily reading of the complete
documentation of many software packages, not just Gnuastro. It can greatly
enhance your life/work in the Unix-like operating systems. If you are not
familiar with it, please run the following command and read through it (it
is short and only takes about an hour, so we strongly recommend it):

info info

To immediately get a short list of each programs's options and a short
explanation of each, please run:

astprogname --help # For example 'astnoisechisel --help'

Ultimately you can send a mail to 'help-gnuastro@gnu.org' to get help in
installing or using Gnuastro. Some Gnuastro developers and active users are
subscribed to this list and are ready to help you in using these programs.



Reporting bugs
--------------

The most effective way to report bugs is explained in the "Report a bug"
section of the documentation, after installation, you can read it by
running (leave the Info environment by pressing the 'q' key afterwards):

info bug-gnuastro

In short, you can send a mail to 'bug-gnuastro@gnu.org', or submit a report
in the link below (the latter is recommended):

https://savannah.gnu.org/support/?func=additem&group=gnuastro

In any case, please be very descriptive and give the exact command that
produced the bug, we will be able to solve it faster and more effectively
if we can reproduce it after your first report. The list of previous bugs
along with their status can be seen here

https://savannah.gnu.org/bugs/?group=gnuastro

Have a look in the link above to see if your problem has already been
addressed. Click on "Display Criteria" and choose the "Category" of your
bug for a shorter and more relevant list to look into.





Copyright information
---------------------
Copyright (C) 2015-2021, Free Software Foundation, Inc.

Permission is granted to copy, distribute and/or modify this document under
the terms of the GNU Free Documentation License, Version 1.3 or any later
version published by the Free Software Foundation; with no Invariant
Sections, with no Front-Cover Texts, and with no Back-Cover Texts.