[gnuastro-commits] master 431660bd: Book: List of programs brought in the introduction chapter

[Mohammad Akhlaghi]

branch: master
commit 431660bdc09bb355b67285c091f9ca663d209347
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    Book: List of programs brought in the introduction chapter
    
    Until now, the list of Gnuastro's programs was in the Appendix (at the end
    of the book). Therefore many new users will miss it.
    
    With this commit, that appendix "node" has been moved into the
    "Introduction" chapter. This was done after a discussion with Faezeh
    Bidjarchian and Pedram Ashofte-Ardakani.
---
 doc/gnuastro.texi | 256 ++++++++++++++++++++++++++----------------------------
 1 file changed, 124 insertions(+), 132 deletions(-)

diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index 6a84e407..ca630051 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -1000,6 +1000,130 @@ We therefore recommend to read (an run the commands in) 
the tutorials before sta
 
 
 
+@node Gnuastro programs list, Other useful software, Developing, Top
+@section Gnuastro programs list
+
+GNU Astronomy Utilities @value{VERSION}, contains the following programs.
+They are sorted in alphabetical order and a short description is provided for 
each program.
+The description starts with the executable names in @file{thisfont} followed 
by a pointer to the respective section in parenthesis.
+Throughout this book, they are ordered based on their context, please see the 
top-level contents for contextual ordering (based on what they do).
+
+@table @asis
+
+@item Arithmetic
+(@file{astarithmetic}, see @ref{Arithmetic}) 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, @command{+}, @command{-}, @command{*}, 
@command{/}, @command{sqrt}, @command{log}, @command{min}, @command{average}, 
@command{median}, see @ref{Arithmetic operators}).
+
+@item BuildProgram
+(@file{astbuildprog}, see @ref{BuildProgram}) Compile, link and run custom C 
programs that depend on the Gnuastro library (see @ref{Gnuastro library}).
+This program will automatically link with the libraries that Gnuastro depends 
on, so there is no need to explicitly mention them every time you are compiling 
a Gnuastro library dependent program.
+
+@item ConvertType
+(@file{astconvertt}, see @ref{ConvertType}) Convert astronomical data files 
(FITS or IMH) to and from several other standard image and data formats, for 
example, TXT, JPEG, EPS or PDF.
+Optionally, it is also possible to add vector graphics markers over the output 
image (for example, circles from catalogs containing RA or Dec).
+
+@item Convolve
+(@file{astconvolve}, see @ref{Convolve}) 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.
+
+@item CosmicCalculator
+(@file{astcosmiccal}, see @ref{CosmicCalculator}) Do cosmological 
calculations, for example, the luminosity distance, distance modulus, comoving 
volume and many more.
+
+@item Crop
+(@file{astcrop}, see @ref{Crop}) Crop region(s) from one or many image(s) and 
stitch several images if necessary.
+Input coordinates can be in pixel coordinates or world coordinates.
+
+@item Fits
+(@file{astfits}, see @ref{Fits}) View and manipulate FITS file extensions and 
header keywords.
+
+@item MakeCatalog
+(@file{astmkcatalog}, see @ref{MakeCatalog}) Make catalog of labeled image 
(output of NoiseChisel).
+The catalogs are highly customizable and adding new calculations/columns is 
very straightforward.
+
+@item MakeNoise
+(@file{astmknoise}, see @ref{MakeNoise}) Make (add) noise to an image, with a 
large set of random number generators and any seed.
+
+@item MakeProfiles
+(@file{astmkprof}, see @ref{MakeProfiles}) 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.
+
+@item Match
+(@file{astmatch}, see @ref{Match}) Given two input catalogs, find the rows 
that match with each other within a given aperture (may be an ellipse).
+
+@item NoiseChisel
+(@file{astnoisechisel}, see @ref{NoiseChisel}) Detect 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 @url{http://arxiv.org/abs/1505.01664, arXiv:1505.01664}.
+
+@item Query
+(@file{astquery}, see @ref{Query}) High-level interface to query pre-defined 
remote, or external databases, and directly download the required sub-tables on 
the command-line.
+
+@item Segment
+(@file{astsegment}, see @ref{Segment}) Segment detected regions based on the 
structure of signal and the input dataset's noise properties.
+
+@item Statistics
+(@file{aststatistics}, see @ref{Statistics}) Statistical calculations on the 
input dataset (column in a table, image or datacube).
+This includes man operations such as generating histogram, sigma clipping, and 
least squares fitting.
+
+@item Table
+(@file{asttable}, @ref{Table}) Convert FITS binary and ASCII tables into other 
such tables, print them on the command-line, save them in a plain text file, do 
arithmetic on the columns or get the FITS table information.
+For a full list of operations, see @ref{Operation precedence in Table}.
+
+@item Warp
+(@file{astwarp}, see @ref{Warp}) Warp image to new pixel grid.
+By default it will align the pixel and WCS coordinates, removing any 
non-linear WCS distortions.
+Any linear warp (projective transformation or Homography) can also be applied 
to the input images by explicitly calling the respective operation.
+@end table
+
+The programs listed above are designed to be highly modular and generic.
+Hence, they are naturally for lower-level operations.
+In Gnuastro, higher-level operations (combining multiple programs, or running 
a program in a special way), are done with installed Bash scripts (all prefixed 
with @code{astscript-}).
+They can be run just like a program and behave very similarly (with minor 
differences, see @ref{Installed scripts}).
+
+@table @code
+@item astscript-ds9-region
+(See @ref{SAO DS9 region files from table}) 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).
+
+@item astscript-fits-view
+(see @ref{Viewing FITS file contents with DS9 or TOPCAT}) Given any number of 
FITS files, this script will either open SAO DS9 (for images or cubes) or 
TOPCAT (for tables) to view them in a graphic user interface (GUI).
+
+@item astscript-radial-profile
+(See @ref{Generate 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, etc.), and the radial distance can also be 
measured on any general ellipse.
+
+@item astscript-sort-by-night
+(See @ref{Sort FITS files 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).
+
+@item astscript-psf-*
+The following scripts are used to estimate the extended PSF estimation and 
subtraction as described in the tutorial @ref{Building the extended PSF}:
+
+@table @code
+@item astscript-psf-select-stars
+(see @ref{Invoking astscript-psf-select-stars}) Find all the stars within an 
image that are suitable for constructing an extended PSF.
+If the image has WCS, this script can automatically query Gaia to find the 
good stars.
+
+@item astscript-psf-stamp
+(see @ref{Invoking astscript-psf-stamp}) build a crop (stamp) of a certain 
width around a star at a certain coordinate in a larger image.
+This script will do sub-pixel re-positioning to make sure the star is centered 
and can optionally mask all other background sources).
+
+@item astscript-psf-scale-factor
+(see @ref{Invoking astscript-psf-scale-factor}) Given a PSF model, and the 
central coordinates of a star in an image, find the scale factor that has to be 
multiplied by the PSF to scale it to that star.
+
+@item astscript-psf-unite
+(see @ref{Invoking astscript-psf-unite}) Unite the various components of a PSF 
into one.
+Because of saturation and non-linearity, to get a good estimate of the 
extended PSF, it is necessary to construct various parts from different 
magnitude ranges.
+
+@item astscript-psf-subtract
+(see @ref{Invoking astscript-psf-subtract}) Given the model of a PSF and the 
central coordinates of a star in the image, do sub-pixel re-positioning of the 
PSF, scale it to the star and subtract it from the image.
+@end table
+
+@end table
+
+
+
+
+
+
 
 @node Science and its tools, Your rights, Quick start, Introduction
 @section Gnuastro manifesto: Science and its tools
@@ -41263,138 +41387,6 @@ This will enable you to start your branch (work) from 
the most recent commit and
 
 
 
-
-
-
-
-
-
-@node Gnuastro programs list, Other useful software, Developing, Top
-@appendix Gnuastro programs list
-
-GNU Astronomy Utilities @value{VERSION}, contains the following programs.
-They are sorted in alphabetical order and a short description is provided for 
each program.
-The description starts with the executable names in @file{thisfont} followed 
by a pointer to the respective section in parenthesis.
-Throughout this book, they are ordered based on their context, please see the 
top-level contents for contextual ordering (based on what they do).
-
-@table @asis
-
-@item Arithmetic
-(@file{astarithmetic}, see @ref{Arithmetic}) 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, @command{+}, @command{-}, @command{*}, 
@command{/}, @command{sqrt}, @command{log}, @command{min}, @command{average}, 
@command{median}, see @ref{Arithmetic operators}).
-
-@item BuildProgram
-(@file{astbuildprog}, see @ref{BuildProgram}) Compile, link and run custom C 
programs that depend on the Gnuastro library (see @ref{Gnuastro library}).
-This program will automatically link with the libraries that Gnuastro depends 
on, so there is no need to explicitly mention them every time you are compiling 
a Gnuastro library dependent program.
-
-@item ConvertType
-(@file{astconvertt}, see @ref{ConvertType}) Convert astronomical data files 
(FITS or IMH) to and from several other standard image and data formats, for 
example, TXT, JPEG, EPS or PDF.
-Optionally, it is also possible to add vector graphics markers over the output 
image (for example, circles from catalogs containing RA or Dec).
-
-@item Convolve
-(@file{astconvolve}, see @ref{Convolve}) 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.
-
-@item CosmicCalculator
-(@file{astcosmiccal}, see @ref{CosmicCalculator}) Do cosmological 
calculations, for example, the luminosity distance, distance modulus, comoving 
volume and many more.
-
-@item Crop
-(@file{astcrop}, see @ref{Crop}) Crop region(s) from one or many image(s) and 
stitch several images if necessary.
-Input coordinates can be in pixel coordinates or world coordinates.
-
-@item Fits
-(@file{astfits}, see @ref{Fits}) View and manipulate FITS file extensions and 
header keywords.
-
-@item MakeCatalog
-(@file{astmkcatalog}, see @ref{MakeCatalog}) Make catalog of labeled image 
(output of NoiseChisel).
-The catalogs are highly customizable and adding new calculations/columns is 
very straightforward.
-
-@item MakeNoise
-(@file{astmknoise}, see @ref{MakeNoise}) Make (add) noise to an image, with a 
large set of random number generators and any seed.
-
-@item MakeProfiles
-(@file{astmkprof}, see @ref{MakeProfiles}) 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.
-
-@item Match
-(@file{astmatch}, see @ref{Match}) Given two input catalogs, find the rows 
that match with each other within a given aperture (may be an ellipse).
-
-@item NoiseChisel
-(@file{astnoisechisel}, see @ref{NoiseChisel}) Detect 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 @url{http://arxiv.org/abs/1505.01664, arXiv:1505.01664}.
-
-@item Query
-(@file{astquery}, see @ref{Query}) High-level interface to query pre-defined 
remote, or external databases, and directly download the required sub-tables on 
the command-line.
-
-@item Segment
-(@file{astsegment}, see @ref{Segment}) Segment detected regions based on the 
structure of signal and the input dataset's noise properties.
-
-@item Statistics
-(@file{aststatistics}, see @ref{Statistics}) Statistical calculations on the 
input dataset (column in a table, image or datacube).
-This includes man operations such as generating histogram, sigma clipping, and 
least squares fitting.
-
-@item Table
-(@file{asttable}, @ref{Table}) Convert FITS binary and ASCII tables into other 
such tables, print them on the command-line, save them in a plain text file, do 
arithmetic on the columns or get the FITS table information.
-For a full list of operations, see @ref{Operation precedence in Table}.
-
-@item Warp
-(@file{astwarp}, see @ref{Warp}) Warp image to new pixel grid.
-By default it will align the pixel and WCS coordinates, removing any 
non-linear WCS distortions.
-Any linear warp (projective transformation or Homography) can also be applied 
to the input images by explicitly calling the respective operation.
-@end table
-
-The programs listed above are designed to be highly modular and generic.
-Hence, they are naturally for lower-level operations.
-In Gnuastro, higher-level operations (combining multiple programs, or running 
a program in a special way), are done with installed Bash scripts (all prefixed 
with @code{astscript-}).
-They can be run just like a program and behave very similarly (with minor 
differences, see @ref{Installed scripts}).
-
-@table @code
-@item astscript-ds9-region
-(See @ref{SAO DS9 region files from table}) 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).
-
-@item astscript-fits-view
-(see @ref{Viewing FITS file contents with DS9 or TOPCAT}) Given any number of 
FITS files, this script will either open SAO DS9 (for images or cubes) or 
TOPCAT (for tables) to view them in a graphic user interface (GUI).
-
-@item astscript-radial-profile
-(See @ref{Generate 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, etc.), and the radial distance can also be 
measured on any general ellipse.
-
-@item astscript-sort-by-night
-(See @ref{Sort FITS files 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).
-
-@item astscript-psf-*
-The following scripts are used to estimate the extended PSF estimation and 
subtraction as described in the tutorial @ref{Building the extended PSF}:
-
-@table @code
-@item astscript-psf-select-stars
-(see @ref{Invoking astscript-psf-select-stars}) Find all the stars within an 
image that are suitable for constructing an extended PSF.
-If the image has WCS, this script can automatically query Gaia to find the 
good stars.
-
-@item astscript-psf-stamp
-(see @ref{Invoking astscript-psf-stamp}) build a crop (stamp) of a certain 
width around a star at a certain coordinate in a larger image.
-This script will do sub-pixel re-positioning to make sure the star is centered 
and can optionally mask all other background sources).
-
-@item astscript-psf-scale-factor
-(see @ref{Invoking astscript-psf-scale-factor}) Given a PSF model, and the 
central coordinates of a star in an image, find the scale factor that has to be 
multiplied by the PSF to scale it to that star.
-
-@item astscript-psf-unite
-(see @ref{Invoking astscript-psf-unite}) Unite the various components of a PSF 
into one.
-Because of saturation and non-linearity, to get a good estimate of the 
extended PSF, it is necessary to construct various parts from different 
magnitude ranges.
-
-@item astscript-psf-subtract
-(see @ref{Invoking astscript-psf-subtract}) Given the model of a PSF and the 
central coordinates of a star in the image, do sub-pixel re-positioning of the 
PSF, scale it to the star and subtract it from the image.
-@end table
-
-@end table
-
-
-
-
-
-
-
-
 @node Other useful software, GNU Free Doc License, Gnuastro programs list, Top
 @appendix Other useful software