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Gnuastro 0.13.50 released

From: Mohammad Akhlaghi
Subject: Gnuastro 0.13.50 released
Date: Thu, 12 Nov 2020 20:09:06 +0000
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.12.0

Dear all,

I am happy to say that Gnuastro 0.13.50 (50 Git commits after version
0.13) is now available in preparation for the release of version 0.14
in a week or two. It would be great if you can try building and using
this version to inform us if there is any compilation warning or
crash, or unexpected behavior. In this way, we can have a smooth 0.14
release for everyone.

The full list of noteworthy features added/changed and bugs fixed
since version 0.13 is available in [1] below. The most prominent
feature may be the new 'astquery' program to enable direct access to
online data centers from the command-line with a unified high-level
interface. For example with the command below you can get the ID, RA,
Dec and measured parallax of all Gaia DR2 stars that are within

  astquery --database=gaia --dataset=dr2 --overlapwith=image.fits \

You can also give coordinates instead of an actual image, see the
newly added Section in the book for more (the 'info gnuastro query'
command, the webpage will be updated with the release of version
0.14). For now we have started with ESA's Gaia, but adding any other
online dataset that has a command-line interface (for example with
'curl' or 'wget') is trivial and we will be adding many commonly used
databases shortly. If you need any database in particular, please feel
free to contact us, with the relevant links that describe their
interface and example commands. Many other useful features have been
added, so don't forget to look through the descriptions in [1] for

Here is the compressed source and the GPG detached signature for this
release. To uncompress Lzip tarballs, see [2]. To check the validity
of the tarballs using the GPG detached signature (*.sig) see [3]: [3.5MB] [833 B]

Here are the MD5 and SHA1 checksums (other ways to check if the
tarball you download is what we distributed):

c40de4a5ee8f4422157086e4ecb38bd1  gnuastro-0.13.50-4605.tar.lz
2c8124eaad0b9f72d830e249b6fbedfb4579b4e0  gnuastro-0.13.50-4605.tar.lz

I am very grateful to Pedram Ashofteh Ardakani, Raul Infante-Sainz,
Zahra Sharbaf, Sachin Kumar Singh and Samane Raji for directly
contributing to the source of Gnuastro. In particular I am very happy
that with this version we have 2 women committing directly to the
source. I am also very grateful to Martin Kuemmel, Sebastian Luna
Valero, Samane Raji, Joanna Sakowska, Zahra Sharbaf, Sachin Kumar
Singh, Ignacio Trujillo for their very useful comments, suggestions
and bug fixes that have now been implemented in Gnuastro.

If any of Gnuastro's programs or libraries are useful in your work,
please cite _and_ acknowledge them. For citation and acknowledgment
guidelines, run the relevant programs with a `--cite' option (it can
be different for different programs, so run it for all the programs
you use). Citations _and_ acknowledgments are vital for the continued
work on Gnuastro, so please don't forget to support us by doing so.

This tarball was bootstrapped (created) with the tools below. Note
that you don't need these to build Gnuastro from the tarball, these
are the tools that were used to make the tarball itself. They are only
mentioned here to be able to reproduce/recreate this tarball later.
  Texinfo 6.7
  Autoconf 2.69
  Automake 1.16.2
  Help2man 1.47.16
  ImageMagick 7.0.10-37
  Gnulib v0.1-3999-ge2739ba63
  Autoconf archives v2019.01.06-97-gfd1d25c

The dependencies to build Gnuastro from this tarball on your system
are described here:

Best wishes,

Postdoctoral research fellow,
Instituto de Astrofísica de Canarias (IAC),
Calle Vía Láctea, s/n, E38205,
San Cristóbal de La Laguna, Tenerife, Spain.

[1] Noteworthy changes since release 0.13

** New features

   - Tutorial on "Detecting large extended targets" improved with better
     NoiseChisel configuration, and more clear description.
   - New sub-section on "Memory management" in the "Common program
     behavior" chapter. It fully describes how to optimally deal with large
     datasets that may exceed your system's RAM.
   - Examples and better description added to many operators in the
     "Arithmetic operators" subsection of the Arithmetic program's section.

  New program:
   - Query ('astquery') is a new program to allow easy submission of
     queries to external datasets and retrieve the result as a FITS file,
     directly on the command-line. You can either directly write the
     database's query statement yourself, or use Query's high-level
     interface to avoid having to learn it.

  All programs:
   - Plain text table inputs can have floating point columns that are in
     sexagesimal format of '_h_m_s' or '_d_m_s' (where '_' is a
     number). These are the classical format to respectively represent
     Right Ascension (RA) and Declination (Dec). They will be directly read
     as a single floating point number (in units of degrees) into
     memory. Therefore the same column of a plain-text table, can be
     degrees in some rows and sexagesimal in others. Besides large tables,
     with this feature, conversion to sexagesimal coordinates to degrees
     becomes very easy, for example:
         echo "7h34m35.5498 31d53m14.352s" | asttable
     Recall that the inverse can also be done with the more general column
         echo "113.64812416667 31.88732" \
              | asttable -c'arith $1 degree-to-ra $2 degree-to-dec'

   - New operators:
     - 'interpolate-maxofregion': interpolate connected blank regions with
       the maximum value that is immediately touching it. This can be used
       to fill the blank centers of saturated stars for example.
     - 'interpolate-minofregion': similar to 'interpolate-maxofregion', but
       for the minimum.
     - 'makenew': new operator to create an empty (zero-valued) new dataset
       with given dimension and size (given as operands).

   - New '--skycoverage' option will report the area of the input image in
     RA/Dec, both in units of center/width, and box minimum/maximum
     format. This is paritcularly useful in combination with the new
     'astquery' option, to easily search the contents of external databases
     within the image.

   --maximum: maximum value of labeled regions pixels (clump/object).
   --areaarcsec2: area of labeled region (clump/object) in arcsec^2.
   --surfacebrightness: the surface brightness of the labeled region.
   --fwhmobs: observed FWHM in pixels, along the major axis.
--halfmaxarea: number of pixels with a value larger than half the maximum.
   --halfmaxsum: sum of pixels with a value larger than half the maximum.
   --halfmaxsb: surf. brightness within half of the maximum.
   --fracmax: fractions to use in '--fracmaxarea1' or '--fracmaxarea2'.
   --fracmaxsum1: sum of pixels brighter than first given fraction of max.
   --fracmaxsum2: sum of pixels brighter than second given fraction of max.
--fracmaxarea1: number of pixels brighter than first given fraction of max. --fracmaxarea2: number of pixels brighter than second given fraction of max.
   --fracmaxradius1: radius derived from '--fracmaxarea1'.
   --fracmaxradius2: radius derived from '--fracmaxarea2'.
   --halfsumsb: Surface brightness within area reported by '--halfsumarea'.
--halfsumarea: area containing half of the summed object or clump values. --halfradiusobs: radius derived from '--halfsumarea', underestimates r_e.
   --areaminv: the number of pixels that are equal to the minimum value.
   --areamaxv: the number of pixels that are equal to the maximum value.
   - New columns to return the position of pixel with minimum or maximum
     value: '--minvx', '--maxvx', '--minvy', '--maxvy', '--minvz',

   --bgisbrightness: new option to say that the value of '--background'
     (used to simulate Poisson noise) should be interpreted as brightness,
     not magnitude.

   - It is now possible to make any custom radial profile with the 'custom'
     profile (with code '8'). A table should be given to the new
     '--customtable' option which will define each radial interval and the
     value to use for that radial interval. See the description of
     '--customtable' for more.

   - New '--noblank' option will remove all rows in output table that have
     at least one blank value in the specified columns. For example if
     'table.fits' has blank values (NaN in floating point types) in the
     'magnitude' and 'sn' columns, with '--noblank=magnitude,sn', you can
     be sure that all rows with blank values in these columns have been

   - GAL_ARITHMETIC_OP_MAKENEW: new 'makenew' operator.
   - gal_blank_flag_remove: Remove all flagged elements in a dataset.
   - gal_blank_remove_rows: remove all rows that have at least one blank.
   - gal_wcs_coverage: Return the sky coverage of given image HDU.
   - gal_wcs_dimension_name: return the name of the requested WCS dim.

** Removed features

   - No features have been removed since version 0.13 until now.

** Changed features

  All programs:
   - Memory management: Until now, an internal array was only
     allocated in the RAM when its size was smaller (in bytes) than
     the value given to the '--minmapsize' option. But this was
     annoying/buggy when the system has enough RAM to keep large
     files. From this version, all Gnuastro programs will first
     attempt to write the array in RAM if there is space, only when
     there is no space left in the RAM, will they use a memory-mapped
     file (which can dramatically slow down the program). Please see
     the newly added "Memory management" section of the book for a
     complete explanation of Gnuastro's new memory management

   - The '--pixelscale' option also prints the pixel area (for 2D inputs,
     or 2D slices of 3D inputs) and the voxel volume (for 3D inputs). Until
     now, it would only print the pixel scale along each dimension.

   - Column arithmetic operators 'degree-to-ra' and 'degree-to-dec' will
     return the sexagesimal format of '_h_m_s' and '_d_m_s'
     respectively. Until this version, they would both use colons as
     delimiters ('_:_:_').

   - gal_units_degree_to_ra: new 'usecolon' argument to optionally format
     output string with colons as delimiters ('_:_:_'). When this option is
     zero, the string will be in the '_h_m_s' format.
   - gal_units_degree_to_dec: similar to 'gal_units_degree_to_ra', but when
     'usecolon' is zero, the string will be in the '_d_m_s' format.

** Bugs fixed
bug #59017: Segment's object IDs are not thread-safe (i.e., reproducible).
  bug #59105: Column arithmetic operator degree-to-ra, returning to dec.
  bug #59136: Makeprofiles with --replace is not thread-safe.
  bug #59155: Match cannot find the proper row when coordinates have NaN.
bug #59371: MakeCatalog crash with clumps on non-contiguous object labels.

[2] Lzip has better compression ratio and archival features compared
to the `.gz' or `.xz' formats. Therefore Gnuastro's alpha/test
releases are only in this format, but for historical reasons we also
include `.gz' tarballs in the official releases. If you don't have
Lzip (you can check with `lzip --version' command), download and
install it from its webpage:

If Lzip is present and you use GNU Tar, then the single command below
should uncompress and un-pack the tarball:

  $ tar xf gnuastro-0.13.50-4605.tar.lz

If the command above doesn't work, you have to un-compress and un-pack
it with two separate commands (or use a pipe to feed the output of the
first into the second: `lzip -cd gnuastro-0.13.50-4605.tar.lz | tar -xf -'):

  $ lzip -d gnuastro-0.13.50-4605.tar.lz
  $ tar xf gnuastro-0.13.50-4605.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-0.13.50-4605.tar.lz.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 71E899012D174B66

and rerun the 'gpg --verify' command.

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