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Re: Gnuastro 0.14.98 released [alpha]

From: Mohammad Akhlaghi
Subject: Re: Gnuastro 0.14.98 released [alpha]
Date: Thu, 15 Apr 2021 14:12:57 +0100
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.9.0

Hi Sylvain,

WoW! What a terrible typo! Thanks for reporting it :-).

I just sent out a correction.

Thanks again,

On 4/15/21 8:15 AM, Sylvain Mottet wrote:
Hi Mohammad,

it's nice to see that Gnuastro is quickly and steadily improving.

In your message, when you say "it is not possible to change between WCS coordinate systems", by reading the notes, I believe it should be "it is *now* possible to change between WCS coordinate systems".

many thanks and have a good day


On 4/15/21 3:22 AM, Mohammad Akhlaghi wrote:
Dear all,

Since the release of Gnuastro 0.14 in January, we have been actively
developing it with new features and some bug fixes. In order to
prepare for the next stable release, I am now sharing Gnuastro 0.14.98
(98 Git commits after version 0.14).

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,
wrong or degraded behavior during your normal operation. In this way,
we can have a smooth Gnuastro 0.15 release for everyone.

For the full list of noteworthy changes since version 0.14 see [1]
below. To summarize the most prominent: two new installed scripts have
been added, one to easily convert table columns into DS9 region files
and another to measure the radial profile of an object in an
image. Also, the tutorials have been improved, it is not possible to
change between WCS coordinate systems, many new features have been
added to Table for inspecting rows, and with Query you can now get the
Galactic extinction values from NED. See [1] below for the full list
and more explanation/examples.

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]:

   https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.14.98-8832.tar.lz (3.6MB)    https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.14.98-8832.tar.lz.sig (833B)

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

463db4fc43f9eef6a0817053b96dd2eb  gnuastro-0.14.98-8832.tar.lz
5d9aa7177735fa19ed6d4b73155b64177b6f27bb  gnuastro-0.14.98-8832.tar.lz

I am very grateful to Raul Infante-Sainz, Carlos Morales-Socorro,
François Ochsenbein, Samane Raji and Zahra Sharbaf for directly
contributing to the source code. Also, I should really thank Mark
Calabretta, Sepideh Eskandarlou, Raul Infante-Sainz, Alberto Madrigal,
Juan Miro, Carlos Morales Socorro, Sylvain Mottet, Francois
Ochsenbein, Samane Raji, Zahra Sharbaf, Ignacio Trujillo for their
great suggestions for improvement and reported bugs 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 2.71
   Automake 1.16.3
   Help2man 1.48.3
   ImageMagick 7.0.11-7
   Gnulib v0.1-4566-g371ab715d
   Autoconf archives v2021.02.19-1-ge68e8f6

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 Gnuastro 0.14

** New features

   New program:
    - astscript-ds9-region: 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). For example with the
      command below you can select certain rows of a given table, and show
      them over an image:
         asttable table.fits --range=MAGNITUDE,18:20 --column=RA,DEC \
             | astscript-ds9-region --column=1,2 --radius=0.5 \
                                    --command="ds9 image.fits"
    - astscript-radial-profile: Measure the radial profile of an object on
      an image. The profile can be centered anywhere in the image and any
      circular, or elliptical distance can be defined. The output is a table
      with the profile's value in one column and any requested measure in
      the other columns (any MakeCatalog measurement is possible).

   All programs:
    --wcslinearmatrix: new option in all programs that lets you select the       output WCS linear matrix format. It takes one of two values: 'pc' (for       the 'PCi_j' formalism) and 'cd' (for 'CDi_j'). Until now, the outputs
      were always stored in the 'PCi_j' formalism (which is still the
      recommended/default format).

    - New "Image surface brightness limit" section added to the third
      tutorial (on "Detecting large extended targets"). It describes the
      different ways to measure a dataset's surface brightness limit and
      upper-limit surface brightness.

    - New operators (all also available in Table's column arithmetic):
      - sin: Trigonometric sine (input in degrees).
      - cos: Trigonometric cosine (input in degrees).
      - tan: Trigonometric tangent (input in degrees).
      - asin: Inverse of trigonometric sine (output in degrees).
      - acos: Inverse of trigonometric cosine (output in degrees).
      - atab: Inverse of trigonometric tangent (output in degrees).
      - sinh: Hyperbolic sine.
      - cosh: Hyperbolic cosine.
      - tanh: Hyperbolic tangent.
      - asinh: Inverse of hyperbolic sine.
      - acosh: Inverse of hyperbolic cosine.
      - atabh: Inverse of hyperbolic tangent.
      - counts-to-mag: Convert counts to magnitudes with given zero point.       - counts-to-jy: Convert counts to Janskys through a zero point based
           on AB magnitudes.

    --globalhdu: Use a single HDU identifier for all the input files
      files. Its operation is identical to the similarly named option in
      Arithmetic. Until now it was necessary to call '--hdu' three times if
      you had three input FITS files with input in the same HDU.

    --wcscoordsys: convert the WCS coordinate system of the input into any       recognized coordinate system (currently supports: equatorial (J2000,
      B1950), ecliptic (J2000, B1950), Galactic and Supergalactic. For
      example if 'image.fits' is in galactic coordinates, you can use this
      command to convert its WCS to equatorial (J2000):
           astfits image.fits --wcscoordsys=eq-j2000
      This option only works with WCSLIB 7.5 and above (released in March
      2021), otherwise it will not work (abort with an informative warning).

    - Newly added measurement columns:
      --upperlimitsb: upper-limit surface brightness for the given label
        (object or clump). This is useful for measuring a dataset's
        realistic surface-brightness limit (not extrapolated like the
        surface brightness limit, but using the actual object footprint).

    - When given a value of '_all', the '--noblank' option (that will remove
      all rows with a blank value in the given columns) will check all
      columns of the final output table. This is handy when you want a
      "clean" (no NaN values in any column) table, but the table has many
    --rowlimit: new option to specify the positional interval of rows to
      show. Until now the '--head' or '--tail' options would just allow
      seeing the first or last few rows. You can use this to view a
      contiguous set of rows in the middle of the table.
    --rowrandom: Make a random selection of the rows. This option is useful       when you have a large dataset and just want to see a random sub-set of       the rows. It takes an integer, selects that many rows from the input
    - New column arithmetic operators:
      - 'set-AAA' operator (which allows storing the popped operand into a         named variable for easy usage in complex operations) is also usable
        in Table's column arithmetic. Until now this operator was only
        available in the Arithmetic program (for operation on images).
      - 'date-to-sec' Convert FITS date format ('YYYY-MM-DDThh:mm:ss') into         seconds from the Unix epoch (1970-01-01,00:00:00 UTC). This can be         very useful in combination with the new '--keyvalue' option of the
        Fits program to sort your FITS images based on observation time.

    --keyvalue: Print only the values of the FITS keywords given to this
      option in separate columns. This option can take multiple values and       many FITS files. Thus generating a table of keyword values (with one
      row per file). Its output can thus either be piped to the Table
      program for selecting a certain sub-set of your FITS files, or sorting
      them for example.

    - NED's Galactic extinction calculator is now available for any
      coordinate with a command like below. See the description of the
      'extinction' dataset of NED in the "Available datasets" section of the
          astquery ned --dataset=extinction --center=49.9507,41.5116

    - gal_units_counts_to_mag: Convert counts to magnitudes.
    - gal_units_counts_to_jy: Convert counts to Janskys.
    - New arithmetic operator macros (for the 'gal_arithmetic' function):
      - GAL_ARITHMETIC_OP_SIN: sine (input in deg).
      - GAL_ARITHMETIC_OP_COS: cosine (input in deg).
      - GAL_ARITHMETIC_OP_TAN: tangent (input in deg).
      - GAL_ARITHMETIC_OP_ASIN: Inverse sine (output in deg).
      - GAL_ARITHMETIC_OP_ACOS: Inverse cosine (output in deg).
      - GAL_ARITHMETIC_OP_ATAN: Inverse tangent (output in deg)
      - GAL_ARITHMETIC_OP_ATAN2: Inverse tangent (with two inputs, out deg).
      - GAL_ARITHMETIC_OP_SINH: Hyperbolic sine.
      - GAL_ARITHMETIC_OP_COSH: Hyperbolic cosine.
      - GAL_ARITHMETIC_OP_TANH: Hyperbolic tangent.
      - GAL_ARITHMETIC_OP_ASINH: Inverse hyperbolic sine.
      - GAL_ARITHMETIC_OP_ACOSH: Inverse hyperbolic cosine.
      - GAL_ARITHMETIC_OP_ATANH: Inverse hyperbolic tangent.
      - GAL_ARITHMETIC_OP_COUNTS_TO_JY: Convert counts to Janskys.
    - WCS coordinate system identifiers:
      - GAL_WCS_COORDSYS_EQB1950: 1950.0 (Besselian-year) equatorial coords.
      - GAL_WCS_COORDSYS_EQJ2000: 2000.0 (Julian-year) equatorial coords.
      - GAL_WCS_COORDSYS_ECB1950: 1950.0 (Besselian-year) ecliptic coords.
      - GAL_WCS_COORDSYS_ECJ2000: 2000.0 (Julian-year) ecliptic coords.
      - GAL_WCS_COORDSYS_GALACTIC: Galactic coordinates.
      - GAL_WCS_COORDSYS_SUPERGALACTIC: Supergalactic coordinates.
    - gal_wcs_coordsys_from_string: WCS coordinate system from string.
    - gal_wcs_coordsys_identify: Parse WCS struct to find  coordinate system.
    - gal_wcs_coordsys_convert: Convert the coordinate system of the WCS.

** Removed features
    Nothing has been removed in this release.

** Changed features

    - Thanks to the new features in the Fits and Table programs (described       above), the efficiency of this script has improved dramatically (from
      19 seconds to 0.42 seconds for about 650 FITS files used in the
    - The default end to a "night" is set to 11:00a.m. Until now it was
      9:00a.m. But in some cases, calibration images may be taken after
      that. So to be safer in general it was incremented by 2 hours.

    - Surface brightness limit calculations are now written as standard FITS
      keywords in the output catalog/table. Until now, they were simply
      stored as 'COMMENT' keywords with no name so it was hard to parse
      them. From this version, the following keywords are also written into       the output table(s), see the "MakeCatalog output" section of the book
      for more: 'SBLSTD', 'SBLNSIG', 'SBLMAGPX', 'SBLAREA', 'SBLMAG'.
    - Upper-limit settings are also written into the output tables as
      keywords (like surface brightness limit numbers above): 'UPNSIGMA',

    - gal_fits_key_write_wcsstr: also takes WCS structure as argument.
    - gal_fits_key_read_from_ptr: providing a numerical datatype for the
      desired keyword's value is no longer mandatory. When not given, the
      smallest numeric datatype that can keep the value will be found and
    - gal_wcs_read: allows specifying the linear matrix of the WCS.
    - gal_wcs_read_fitsptr: allows specifying the linear matrix of the WCS.

** Bugs fixed
   bug #60082: Arithmetic library crash for integer operators like modulo
   bug #60121: Arithmetic segfault when multi-operand output given to set-    bug #60368: CosmicCalculator fails --setdirconf when redshift isn't given

[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-0.14.98-8832.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-0.14.98-8832.tar.lz | tar -xf -'):

   $ lzip -d gnuastro-0.14.98-8832.tar.lz
   $ tar xf gnuastro-0.14.98-8832.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-0.14.98-8832.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 keys.gnupg.net --recv-keys 71E899012D174B66

and rerun the 'gpg --verify' command.

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