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Gnuastro 0.5 released

From: Mohammad Akhlaghi
Subject: Gnuastro 0.5 released
Date: Sat, 23 Dec 2017 16:28:23 +0100
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:52.0) Gecko/20100101 Thunderbird/52.5.0

Dear all,

As a small holiday gift, I am happy to announce the fifth release of
Gnuastro (version 0.5).

GNU Astronomy Utilities (Gnuastro) is an official GNU package
consisting of various command-line programs and library functions for
the manipulation and analysis of astronomical data. All the programs
share the same basic command-line user interface for the comfort of
both the users and developers. For the full list of Gnuastro's library
and programs along with a comprehensive general tutorial, please see
the links below, respectively:

Many new features have been added since the fourth release and almost
all bugs that were found have been fixed. For the full list of new
features, please see the NEWS file below [1]. Some of the highlights
are as follows: there is a new "Match" program to match catalogs (in
1D or 2D). NoiseChisel uses signal contiguity to grow the true
detections (before it was a blind dilation). This is much more
successful in tracing the outer low surface brightness
regions. Filtering operators are added to Arithmetic.
CosmicCalculator's functions are now available in the library for use
in your own programs, and now it can also print single requested
calculations (instead of a full list of all calculations). Gnuastro's
top webpage is now also available in French.

You will also find a new section in the "Tutorial" chapter of the book
("General program usage tutorial", link above). It contains an
extended and pedagogic tutorial to help you get started in using
Gnuastro's infra-structure effectively. With the aim of detecting
galaxies in an image and estimating their colors, it takes you through
most of the programs. Just be patient and follow through the steps to
master Gnuastro's powerful features. This tutorial was made as part of
the "Exploring the ultra-low surface brightness universe" workshop in
the International Space Science Institute (ISSI in Bern,
Switzerland). I am very grateful to the hosts and participants for the
very fruitful week.

If any of Gnuastro's program are useful in your work, please run the
relevant programs with a `--cite' option (it can be different for
different programs). Citations are vital for the continued work on
Gnuastro, so please don't forget to support us by doing so.

Boud Roukema and Vladimir Markelov contributed to the code of this
release. Lucas MacQuarrie, Thérèse Godefroy and the GNU French
Translation Team also kindly initiated and are managing the French
translation of the top Gnuastro webpage. I am finally very grateful to
(in alphabetic order) Leindert Boogaard, Nicolas Bouché, Benjamin
Clement, Madusha Gunawardhana, Takashi Ichikawa, Raúl Infante Sainz,
Aurélien Jarno, Floriane Leclercq, Alan Lefor, Bob Proulx, Alejandro
Serrano Borlaff, Lee Spitler, Ole Streicher, Alfred Szmidt, Ignacio
Trujillo and David Valls-Gabaud who provided many great comments,
suggestions and bug reports to this release.

Below, you can get the compressed sources and a GPG detached
signatures for this release. See [2] for uncompressing Lzip tarballs.      (4.6 MB)      (3.1 MB)

Use a mirror for higher download bandwidth:   (4.6 MB)   (3.1 MB)

The GPG detached signatures are also available below. See [3] for how
to verify the integrity of this tarball with the signature.  (833 B)  (833 B)

Here are the MD5 and SHA1 checksums:
  b88cbc593d6a59b0a3bd85b7e81bd4a0  gnuastro-0.5.tar.gz
  2ed4ed0357a373c19291b1c67fd8bd8f  gnuastro-0.5.tar.lz
  d920c0d0796e9e74d06f2682bebe73d79cb960de  gnuastro-0.5.tar.gz
  1dcc6f36e0c1ddf603cbc8d39445d356a39208d8  gnuastro-0.5.tar.lz

This tarball was bootstrapped (initially built) with the tools
below. Note that these are not installation dependencies.
  Texinfo 6.5
  Autoconf 2.69
  Automake 1.15.1
  Help2man 1.47.5
  Gnulib v0.1-1729-gf583f328b
  Autoconf archives v2017.09.28-14-g2445b89

For installation dependencies, please see:

I wish you happy holidays,

Postdoctoral research fellow,
Centre de Recherche Astrophysique de Lyon (CRAL),
Observatoire de Lyon. 9, Avenue Charles André,
Saint Genis Laval (69230), France.

[1] NEWS file for Gnuastro 0.5:

** New features

  Manual/Book: An extended tutorial is added showing some general
  applications of almost all the programs. This may be a good place to get
  a feeling of how Gnuastro is intended to be used and some of the

  New Program and library: Match is a new program that will match two given
  inputs (currently catalogs). Its output is the re-arranged inputs with
  the same number of rows/records such that all the rows match. The main
  work is also done with the new low-level `gal_match_catalog' library
  function which can also be used in more generic contexts.

  All programs: a value of `0' to the `--numthreads' option will use the
  number of threads available to the system at run time.

  Arithmetic: The new operators `filter-median' and `filter-mean' can be
  used to filter (smooth) the input. The size of the filter can be set as
  the other operands to these operators.

  BuildProgram: The new `--la' option allows the identification of a
  different Libtool `.la' file for Libtool linking information.

  BuildProgram: The new `--deletecompiled' option will delete the compiled
  program after running it.

  CosmicCalculator: all the various cosmological calculations can now be
  requested individually in one line with a specific option added for each
  calculation (for example `--age' or `--luminositydist' for the age of the
  universe at a given redshift or the luminosity distance). Therefore the
  old `--onlyvolume' and `--onlyabsmagconv' options are now removed. To
  effectively use these new features, please review the "Invoking
  CosmicCalculator" section of the book.

  Fits: when an extension/HDU is identified on the command-line with the
  `--hdu' option and no operation is requested, the full list of header
  keywords in that HDU will be printed (as if only `--printallkeys' was

  MakeCatalog: physical nature agnostic WCS column names. Previously the
  first WCS axis was always assumed to be RA and the second DEC. So for
  example even if you had a spectrum (with X and wavelength as the two WCS
  dimensions), you would have to ask for `--ra' and `--dec'. The new `--w1'
  and `--w2' options are now generic and don't assume any particular type
  only their order in the FITS header. MakeCatalog now also uses the CTYPE
  and CUNIT keywords to set the names and units of its output columns. The
  `--ra' and `--dec' options are now just internal aliases for `--w1' or
  `--w2' which will be determined based on the input's CTYPE keyword. Also
  the new `--geow1', `--geow2', `--clumpsw1', `--clumpsw2',
  `--clumpsgeow1', `--clumpsgeow2' options replace the old options
  `--geora', `--geodec', `--clumpsra', `--clumpsdec', `--clumpsgeora',
  `--clumpsgeodec'. No alias is currently defined for the latter group.

  MakeCatalog: the new `--uprange' option allows you to specify a range for
  the random values around each object. This is useful when the noise
  properties of the dataset vary gradually and sampling from the whole
  dataset might produce biased results.

  NoiseChisel: with the new `--convolved' and `--convolvedhdu' options,
  NoiseChisel will not convolve the input any more and use the given
  dataset instead. In many cases, as the inputs get larger, convolution is
  the most time consuming step of NoiseChisel. With this option, you can
  greatly speed up your tests (to find the best parameters by varying them,
  for a given analysis). See the book for more information and examples.

  NoiseChisel: with the new `--widekernel' option it is now possible to use
  a wider kernel to identify which tiles contain signal. The rest of the
  steps (identifying the quantile threshold on the selected tiles and etc)
  are done on the dataset convolved with `--kernel' as they were
  before. Since it is time consuming, this is an optional feature.

  NoiseChisel: with the new `--qthreshtilequant' option, it is now possible
  to discard high-valued (outlier) tiles before estimating qthresh over the
  whole image. This can be useful in detecting very large diffuse/flat
  regions that would otherwise be detected as background (and effectively

  NoiseChisel: the finally selected true detections are now grown based on
  signal contiguity, not by blind dilation. The growth process is the same
  as the growing of clumps to define objects. Only for true detections, the
  growth occurs in the noise. You can configure this growth with the
  `--detgrowquant' and `--detgrowmaxholesize'. With this new feature it is
  now possible to detect signal out to much lower surface brightness limits
  and the detections don't look boxy any more.

  Cosmology library: A new set of cosmology functions are now included in
  the library (declared in `gnuastro/cosmology.h'). These functions are
  also used in the CosmicCalculator program.

  `gal_table_read' can now return the number of columns matched with each
  input column (for example with regular expressions), a new argument has
  been added to allow this feature.

  `gal_fits_key_img_blank': returns the value that must be used in the
  BLANK keyword for the given type as defined by the FITS standard.

  `gal_txt_write' and `gal_fits_tab_write' now accept an extension name as
  argument to allow a name for the FITS extension they write.

  `gal_box_bound_ellipse_extent' will return the maximum extent of an
  ellipse along each axis from the ellipse center in floating point.

** Removed features

  Installation: The `--enable-bin-op-*' configuration options that were
  introduced in Gnuastro 0.3 have been removed. By managing the arithmetic
  functions in a better manner (a separate source file for each operator),
  compilation for all types (when done in parallel) takes about the same
  time as it took with the default (only four) types until now.

  MakeCatalog: `--zeropoint' option doesn't have a short option name any
  more. Previously it was `-z' which was confusing because `-x' and `-y'
  were used to refer to image coordinate positions.

  NoiseChisel: The `--dilate' and `--dilatengb' options have been
  removed. Growing of true detections is no longer done through dilation
  but through the `--detgrowquant' and `--detgrowmaxholesize' options (see

** Changed features

  CosmicCalculator: The redshift is no longer mandatory. When no redshift
  is given, it will only print the input parameters (cosmology) and abort.

  MakeCatalog: when the output is a FITS file, the two object and clumps
  catalogs will be stored as multiple extensions of a single file. Until
  now, two separate FITS files would be created. Plain text outputs are the
  same as before (two files will be created).

  `gal_binary_fill_holes' now accepts a `connectivity' and `maxsize'
  argument to specify the connectivity of the holes and the maximum size of
  acceptable holes to fill.

  `gal_fits_img_read' and `gal_fits_img_read_to_type' now also read the WCS
  structure of the extension/HDU in a FITS file and have two extra
  arguments: `hstartwcs' and `hendwcs'. With these options it is possible
  to limit the range of header keywords to read the WCS, similar to how
  they are used in `gal_wcs_read'.

  `gal_txt_write', `gal_table_write_log', `gal_fits_tab_write' and
  `gal_txt_write' don't have the `dontdelete' argument any more. The action
  they take if the file already exists depends on the file: for FITS, a new
  extension will be added and for text, they will abort with an error.

  `gal_tile_block_write_const_value' and `gal_tile_full_values_write' now
  accept a new `withblank' option to set all pixels that are blank in the
  tile's block to be blank in the check image.

  `gal_wcs_pixel_area_arcsec2' will return NaN (instead of aborting) when
  input is unreasonable (not two dimensions or not in units of degrees).

  `gal_wcs_world_to_img' and `gal_wcs_img_to_world': Until now, these two
  WCS conversion functions would explicitly assume RA and Dec and work
  based on input arrays (so for example it was also necessary to give the
  number of elements and etc). They now accept `gal_data_t' as input for
  the input coordinates, thus their API has been greatly simplified and
  their functionality increased.

** Bug fixes

  ConvertType crash when changing values (bug #52010).

  Arithmetic not accounting for integer blank pixels in binary operators
  (bug #52014).

  NoiseChisel segfault when memory mapping to a file (bug #52043).

  CFITSIO 3.42 and libcurl crash at Gnuastro configure time (bug #52152).

  MakeCatalog crash in upper-limit with full size label (bug #52281).

  NoiseChisel leaving unlabeled regions after clump growth (bug #52327).

  Arithmetic crash with no input tokens (bug #52422).

  Libtool checks only in non-current directory (bug #52427).

[2] Lzip has a much better compression ratio and much better archival
features than the common `.gz' or `.xz'. Therefore Gnuastro's stable
releases are made in `.gz' (for historical reasons) and `.lz'. The
alpha/test releases are only in `.lz'. If you don't have Lzip, can
download and install it from its webpage:

If you have GNU Tar, then the single command below should uncompress and
un-pack the tarball:

  $ tar xf gnuastro-0.5.tar.lz

If the command above doesn't work, you have to un-compress and un-pack it
with two separate commands:

  $ lzip -d gnuastro-0.5.tar.lz
  $ tar xf gnuastro-0.5.tar

[3] Use a .sig file to verify that the corresponding file (without the
.sig suffix) is intact.  First, be sure to download both the .sig file
and the corresponding tarball.  Then, run a command like this:

  gpg --verify gnuastro-0.5.tar.gz.sig

If that command fails because you don't have the required public key,
then run this command to import it:

  gpg --keyserver --recv-keys 1849814357EFB73A

and rerun the 'gpg --verify' command.

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