[info-gnuastro] Gnuastro 0.7.42 released [alpha]

[Mohammad Akhlaghi]

Hi everyone,

I am happy to announce the first Gnuastro alpha-release since the
version 0.7. The full list of new, removed and changed features in
this release are available in the tarball's `NEWS' file (also see [1]
below). Please try building, installing and using this version and
send us your feedback (any build warnings, crashes, or unexpected
behavior), so we can have a clean 0.8 release later.

In summary, this release includes some major improvements to
NoiseChisel: 1) To find tiles without significant signal, NoiseChisel
now uses the quantile distance between _mean_ (until now it was the
mode) and median. 2) An outlier rejection algorithm is now included
prior to interpolating over useful tiles to find the quantile
thresholds. The latter allows default parameters to detect large and
extended low surface brightness structures much more reasonably
without any tweaking. Of course, tweaking of parameters (sign of the
professional scientist) is always encouraged, and can still result in
significant improvements.

The NoiseChisel sections of the two tutorials have been updated to
reflect the new changes. Please review those parts if you commonly use
NoiseChisel. In particular, in the "Detecting large extended targets"
tutorial, you'll see how the default parameters don't give such a bad
initial result now. This tutorial now finishes the detection step by
calculating the detected outer surface brightness limit of M51: in the
single-exposure SDSS image, it is ~30 magnitudes per square
arcseconds!

Here are the compressed sources and a GPG detached signature of this
alpha-release. To uncompress Lzip tarballs, see [2] below, and to
check the validity of the tarballs using the GPG detached signature
see [3] below.
  https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.7.42-22d2.tar.lz 
[3.1Mb]
  https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.7.42-22d2.tar.lz.sig [833b]

Here are the MD5 and SHA1 checksums (other ways to check if the
tarball you download is what we distributed):
e72c123a44d8e8dd75e71d1836498877  gnuastro-0.7.42-22d2.tar.lz
bb24a8827af95377d2d6cd96aaf6cbf0353befbe  gnuastro-0.7.42-22d2.tar.lz

I am very grateful to Andreas Stieger for contributing to the source
of this release and (in alphabetical order) to Pierre-Alain Duc,
Gaspar Galaz, Mamta Pommier, Michael Stein, and Ignacio Trujillo for
providing many useful comments and finding bugs. Generally, I would
also like to thank the organizers and attendees of the "The
Bewildering Nature of Ultra-diffuse Galaxies" workshop in the Lorentz
Center (Leiden, Netherlands) for many great discussions during that
meeting that were effective in making the NoiseChisel improvements of
this release.

If any of Gnuastro's programs or libraries are useful in your work,
please cite _and_ acknowledge it. For citation and acknowledgement
guidelines, run the relevant programs with a `--cite' option (it can
be different for different programs). 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 made the tarball and only mentioned here to be able
to reproduce/recreate this tarball later.
  Texinfo 6.5
  Autoconf 2.69
  Automake 1.15.1
  Help2man 1.47.6
  ImageMagick 7.0.8-11
  Gnulib v0.1-2119-g7897cfcc1
  Autoconf archives v2018.03.13-99-g76956d7
For Gnuastro's build dependencies, please see:
https://www.gnu.org/s/gnuastro/manual/html_node/Dependencies.html

Best wishes,
Mohammad

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





[1] Noteworthy changes in release 0.7.42:

** New features

  All programs:
   - Input files and parameters written as keywords in the first extension
     of output when it is FITS. This is only relevant for some programs,
     (for example not the Fits or Table programs).

  Arithmetic:
    --onedasimage: write output as an image if it has one dimension, 
not table.

  NoiseChisel:
    - New outlier identification algorithm for quantile thresholds. This is
      very useful when there are extended and bright sources in the
      dataset: the tiles containing very faint signal that pass the general
      pixel-value distribution test due to the flatness of the extended
      profiles, can be identified and removed as outliers in comparison
      with the other passed tiles. The outlier finding algorithm
      (`gal_statistics_outlier_positive': a new library function) uses the
      distribution of distances between the sorted elements and is
      configured with these options.
       --outliersclip: Sigma-clipping parameters for the process.
       --outliersigma: Multiple of sigma to define an outlier.
    --blankasforeground: Treat blank elements as foreground (regions above
          the threshold) in the binary processing steps: initial erosion
          and opening as well as the filling holes and opening of
          pseudo-detections. From this version, by default, blank elements
          in the dataset are considered to be background, so if a
          foreground pixel is touching it, it will be eroded. This option
          is irrelevant if the datasets contains no blank elements, but can
          help remove false positives that are touching blank elements.
    --holengb: allows defining the connectivity of the holes that are
          filled when defining pseudo-detections. Until now, this was
          hard-wired into the code (=8) and not modifiable at run-time.
    --skyfracnoblank: Ignore blank pixels when estimating the fraction of
          undetected pixels for Sky estimation. NoiseChisel only measures
          the Sky over the tiles that have a sufficiently large fraction of
          undetected pixels. This is done to decrease the bias caused by
          faint un-detected wings of bright galaxies or stars, see
          description of `--minskyfrac' for more. Until now the reference
          for this fraction was the whole tile size (irrespective of how
          many blank elements it contains). With this option, it is now
          possible to ask for ignoring blank pixels when calculating the
          fraction. This is useful when blank/masked pixels are distributed
          across the image.

  Statistics:
    - Sky estimation: new outlier estimation algorithm similar to 
NoiseChisel.

  Library:
    - gal_blank_flag_apply: Set all flagged/masked elements to blank.
    - gal_fits_key_list_reverse: Reverse the given list of FITS keywords.
    - gal_fits_key_write_title_in_ptr: Write a two-line title FITS keyword.
    - gal_fits_key_write_in_ptr: New name of gal_fits_key_write.
    - gal_fits_key_write_version_in_ptr: old gal_fits_key_write_version.
    - gal_fits_key_write_config: write key list and version as config 
header.
    - gal_statistics_outlier_positive: Find the first positive outlier.

** Removed features

  NoiseChisel:
    --mirrordist: mean quantile is now used (not mode), see changes below.
    --qthreshtilequant: removed due to new outlier rejection algorithm.

  Statistics:
    --mirrordist: mean quantile is now used (not mode), see changes below.

** Changed features

  Arithmetic:
    - If the output has one dimension, it will be written as a table, not a
      FITS image/array. This can be changed with the new `--onedasimage'
      option.

  MakeProfiles:
    --mergedsize: new name for the old `--naxis' option. Since the option
          names and values are now written into the FITS header of the
          output, this option's name would get confused with the mandatory
          FITS keyword `NAXIS'.

  NoiseChisel:
    - Until now, the mode's quantile was used to identify tiles with no
      significant signal. But from this version, the mean's quantile in
      each tile is used instead. The reason is that the mean is more
      sensative to outliers (signal). Therefore the old `--modmedqdiff' is
      now called `--meanmedqdiff' .

  Statistics:
    --meanmedqdiff: new name for `--modmedqdiff'. Similar to NoiseChisel.

  Library:
    - gal_fits_key_write: filename and hdu instead of FITS pointer.
    - gal_fits_key_write_version: filename and hdu instead of FITS pointer.
    - gal_fits_key_write_filename: write at the top or end of the input 
list.

** Bugs fixed
  bug #54493: Warp crashes when type isn't set.
  bug #54526: Invalid r, q and truncation of point profiles in 
MakeProfiles.
  bug #54579: NoiseChisel pseudo-detection failure when dataset is 
negative.





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

  https://www.nongnu.org/lzip/lzip.html

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

  $ tar xf gnuastro-0.7.42-22d2.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 -d gnuastro-0.7.42-22d2.tar.lz
  $ tar xf gnuastro-0.7.42-22d2.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-0.7.42-22d2.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 keys.gnupg.net --recv-keys 1849814357EFB73A

and rerun the 'gpg --verify' command.