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[info-gnuastro] Gnuastro 0.8 released

From: Mohammad Akhlaghi
Subject: [info-gnuastro] Gnuastro 0.8 released
Date: Fri, 28 Dec 2018 02:53:13 +0000
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:60.0) Gecko/20100101 Thunderbird/60.3.3

Hi everyone,

I am happy to announce the 8th release of 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 (modeled on GNU Coreutils). For the full
list of Gnuastro's library, programs, and a comprehensive general
tutorial (recommended place to start using Gnuastro), please see the
links below respectively:

Many new features have been added in this release and many bugs have
been fixed. Some noteworthy changes are 1) improved NoiseChisel
detection over images with a gradient in the background (even better
improvements are being tested for the next release). 2) All programs
write their configuration parameters as keywords into the first
extension of their output FITS files. 3) Standard input is now also
available for programs that accept ASCII tables. 4) Single channel
FITS images can now be converted to colored JPEG or EPS/PDF images
using color maps. For a detailed list of these (and other) features,
please see the NEWS file in the tarball, also see [1] below.

Here are the compressed sources, to uncompress Lzip tarballs, see [2]:   (5.0MB)   (3.2MB)

Here are the GPG detached signatures, to check the validity of the
tarballs using the GPG detached signature see [3]. (833B) (833B)

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

1f9fe021bf153ac7291af95c95e2d716  gnuastro-0.8.tar.gz
cd341c3f6a8928602d5d4f0046e62b23  gnuastro-0.8.tar.lz
56d04dab2910876a75967df3d8d43384c7b06c2b  gnuastro-0.8.tar.gz
d67043de9a459daf7261bb919dda3c09fea5b237  gnuastro-0.8.tar.lz

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). Citations _and_ acknowledgments
are vital for the continued work on Gnuastro, so please don't forget
to support us by doing so.

I am very grateful to Andreas Stieger for contributing to the source
of this release and (in alphabetical order) to Fernando Buitrago,
Pierre-Alain Duc, Gaspar Galaz, Raúl Infante Sainz, Johan Knapen,
Mamta Pommier, Michael Stein, Ignacio Trujillo and David Valls-Gabaud
for the great suggestions and bug reports.

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 6.5
  Autoconf 2.69
  Automake 1.16.1
  Help2man 1.47.8
  ImageMagick 7.0.8-20
  Gnulib v0.1-2306-g8cb410df8
  Autoconf archives v2018.03.13-105-gf2fb003

The dependencies to build Gnuastro from this tarball are described

Best wishes,

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

[1] Noteworthy changes in release 0.8 (library 6.0.0) (2018-12-28) [stable]

** 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).
   - Standard input (for example from pipes) is now available to feed input
     to all programs that accept plain text input (ConvertType, Convolve,
     Match, MakeProfiles, Statistics, Table).
   - Updated acknowledgment statement (output of `--cite' option).

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

    --colormap: color map to display a single-channel dataset (for example
      FITS image) with a range of colors in formats that support color
      (like JPEG, or PDF). Until now, the only available mapping was
      grayscale. Now "Hue, Saturation, Value" (HSV) and "SLS" (from SAO
      DS9) colormaps are also supported.
    --rgbtohsv: Convert the RGB input channels to HSV (when the output is
      in FITS format).

    - Convolves 1D arrays (table columns, for example spectra)
      also. Therefore two new options have been added to it: `--column'
      (`-c', similar to other programs that read table columns), and
      `--kernelcolumn' (to specify the column of the kernel in its own

    --numhdus: prints the number of HDUs in the given FITS file.

    - 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.

    - If an input table has only one column, Statistics won't complain and
      abort when no `--column' (`-c') is given: there is only one column to
      use anyway, so it will be used. In the absence of which column to
      use, it will still complain and abort if the input has more than one
    - Sky estimation: new outlier estimation algorithm similar to
    - Input can be given using the standard input (for example a pipe).

    - 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.
- gal_txt_stdin_read: Read lines in standard input into a list of strings.

** Removed features

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

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

** Changed features

    - 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'

    - The short option for `--numchannels' is now `-n'. Until now, it was
      `-c', but that would conflict with the short option used for
      `--column' in all the other programs that also read from a table.

    --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'.

    - 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
      sensitive to outliers (signal). Therefore the old `--modmedqdiff' is
      now called `--meanmedqdiff' .

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

    - gal_array_read: list of strings (from standard input) acceptable.
    - gal_array_read_to_type: list of strings (from stin) acceptable.
    - gal_array_read_one_ch: list of strings (from stdin) acceptable.
- gal_array_read_one_ch_to_type: list of strings (from stdin) acceptable.
    - gal_data_copy_to_allocated: Also copies string metadata (e.g., name).
    - 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.
    - gal_statistics_outlier_positive: Window-size is now adjustable.
    - gal_table_info: list of strings (from stdin) acceptable.
    - gal_table_read: list of strings (from stdin) acceptable.
    - gal_txt_table_info: list of strings (from stdin) acceptable.
    - gal_txt_image_info: list of strings (from stdin) acceptable.
    - gal_txt_table_read: list of strings (from stdin) acceptable.
    - gal_txt_image_read: list of strings (from stdin) acceptable.

** 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.
  bug #54782: Segment's check image not removing sky clumps some tiles.
  bug #54810: Arithmetic crash when previously named operand renamed.
  bug #55025: MakeCatalog's `--prepforconv' option being ignored.
  bug #55079: Blank EPS or PDF page when width options not given.
  bug #55157: No sanity check on values given to Crop's --section.
  bug #55295: Crash when more than one collapse operator called.
  bug #55298: Arithmetic reading 255 on command-line as blank.

[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, 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-0.8.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-0.8.tar.lz | tar -xf -'):

  $ lzip -d gnuastro-0.8.tar.lz
  $ tar xf gnuastro-0.8.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-0.8.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 71E899012D174B66

and rerun the 'gpg --verify' command.

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