Gnuastro 0.3 released

[Mohammad Akhlaghi]

Hello,

I am pleased to announce the third (version 0.3) release of GNU
Astronomy Utilities (Gnuastro).

Gnuastro is a collection of programs and libraries 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.

This release is a full re-write of Gnuastro. Most importantly,
Gnuastro now has a new generic data contaihtner (`gal_data_t'). This
new container can now deal natively with all standard numeric data
types, work in RAM or HDD/SSD, keep data in any dimensions and has
enabled many other very useful features in the programs and
libraries. Some of the most prominent of the new features are
discussed in the NEWS file below [*]. It is strongly recommended to
review the respective section of the Gnuastro manual/book for a better
feeling of all the new features.

As discussed below, some program names have changed, if you have a
previous version of Gnuastro installed from source, it is recommended
to uninstall it first (with `make uninstall' using the corresponding
tarball), then install this new version. Building Gnuastro 0.3 can be
slower than previous versions, so please build in parallel with Make's
`-j8' option (to build on 8 threads for example).

Here are the compressed sources:
  http://ftp.gnu.org/gnu/gnuastro/gnuastro-0.3.tar.gz   (4.4MB)
  http://ftp.gnu.org/gnu/gnuastro/gnuastro-0.3.tar.lz   (2.9MB)

Here are the GPG detached signatures[**]:
  http://ftp.gnu.org/gnu/gnuastro/gnuastro-0.3.tar.gz.sig
  http://ftp.gnu.org/gnu/gnuastro/gnuastro-0.3.tar.lz.sig

Use a mirror for higher download bandwidth:
  http://www.gnu.org/order/ftp.html

Here are the MD5 and SHA1 checksums:

04f2cb5eae45725aeeae575080c835a0  gnuastro-0.3.tar.gz
aa787aaf80383519322727ff5ee02258  gnuastro-0.3.tar.lz
7b1e0f1cbfc81fd042eccbe617b23c78e9feaa6d  gnuastro-0.3.tar.gz
50730e84d3c43fadccbd079e3159fd7e42b9ee3d  gnuastro-0.3.tar.lz

Gnuastro 0.2 tarball was bootstrapped with the following tools:
  Texinfo 6.3
  Autoconf 2.69
  Automake 1.15
  Libtool 2.4.6
  Help2man 1.47.4
  Gnulib v0.1-1405-g6ec17baf9
  Autoconf Archives v2017.03.21-99-gcfa14e9
(These are not installation dependencies, for those, please see
https://www.gnu.org/software/gnuastro/manual/html_node/Dependencies.html )

I am most greatful to Boud Roukema and Vladimir Markelov for the
contributions to the code and to Lee Kelvin, Ole Streicher, Alan
Lefor, Mosè Giordano, Guillaume Mahler, Rosa Calvi, Nicolas Bouché,
Francesco Montanari, William Pence, David Valls-Gabaud and Christopher
Willmer for the great comments, suggestions, bug reports and helps in
testing.

Cheers,
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.










[*] NEWS file:

** New programs or library features

  Library functions that deal with datasets now use this generic data
  container for inputs and outputs, significantly simplifying their
  API. Nearly all library functions have been re-written with much more
  clear names, argument lists and individual purpose. Some example library
  functions are shown below, also see the "Library demos" section of the
  book for some complete working example:

     -- `gal_table_read' and `gal_table_write' will read and write data to
        plain text, FITS ASCII and FITS Binary formats.

     -- `gal_fits_img_read' and `gal_fits_img_write' can read a FITS image
        to memory or write a FITS image from memory.

  Gnuastro now defines a simple comment line format to keep basic
  information in a plain text table, see the "Gnuastro text table format"
  section of the book. In short for every column, a comment line like below
  can be used to give a name, units, comments, or a type to a column. This
  allows a FITS binary table for eample to be written to plain text and
  converted back to binary without loosing any information (except for very
  small floating point errors if not enough decimals are printed).

      # Column N: NAME [UNIT, TYPE, BLANK] COMMENT

  The new Fits program replaces the old Header program. But besides
  reading/checking FITS header keywords, it can now also work on FITS
  extensions/HDUs. For example with no options, it will list all the HDUs
  in a FITS file along with basic information. It can copy a whole HDU to
  another file, or delete a HDU from a FITS file. To get the previous
  behavior of listing all the keywords in a FITS HDU, you can run it with
  the `-p' option.

  All programs now write data into the second HDU of a FITS file to allow a
  clean first HDU. Note that following CFITSIO, HDU counting still starts
  from zero, so FITS images and tables written by Gnuastro in a new file
  can always be accessed with the `--hdu=1' option (which is now the
  default).

  If any program is run within a Git version controlled directory, a
  `COMMIT' header keyword will be added to the created FITS files, see the
  "Output headers" section of the book for a discussion on the usefulness
  of this new feature.

  BuildProgram: a new program to easily compile, link and run a C program
  you have written with Gnuastro's libraries without having to worry about
  which libraries (Gnuastro dependencies) your program needs. Debugging
  (`-g'), optimizations (`-O'), warnings (`-W'), include search path
  (`-I'), link search path (`-L'), and linked libraries (`-l') compiler
  options are also supported. BuildProgram will greatly facilitate the easy
  usage of Gnuastro's libraries.

** Removed programs or library features

  The following program names have been renamed:

    ImageCrop       --> Crop
    ImageWarp       --> Warp
    ImageStatistics --> Statistics
    Header          --> Fits

  SubtractSky has been removed. The Statistics program now has tools to
  estimate the Sky value and it can be subtracted with Arithmetic.

** New features

  All Gnuastro programs that read and write tables can now do so in plain
  text table format or in FITS ASCII or FITS Binary tables. Depending on
  the filename or with the new `--tableformat' common option to all
  programs.

  The option management system in all Gnuastro programs has been completely
  re-written with many new features, some of the most important ones are
  listed below. For developers, you will notice that there is no more usage
  of macros and adding new options has become much more easier.

     -- All programs will now also look for a `gnuastro.conf' configuration
        file to keep common options for all programs in every directory.

     -- The `--lastconfig' opion can be used on the command-line or in any
        configuration file to stop parsing any further configuration files.

     -- The `--config' option can now be used to identify any arbitrary
        file to be parsed as a configuration file. Any file that is given
        to this option is parsed immediately.

     -- The `--printparams' option now also prints the short documentation
        of each option (same description in `--help') after its value.

  It is now possible to choose columns in tables based on column names as
  well as column numbers. It is also possible to search for columns based
  on searching in their units or comments. When using column numbers,
  counting now starts from 1 (one), not 0 (as before). See the new
  "Selecting table columns" section for more on these new features.

  Where relevant, all programs now accept a `--type' option that you can
  use to specify the numerical datatype of the output.

  With the new common option `--minmapsize', you can specify a minimum size
  of an array (in bytes) to store data in SSD/HDD and not in RAM. This can
  be instrumental when you are dealing with large datasets, or even smaller
  ones, but when your RAM is getting full.

  Making a log file is now optional and users have to explicitly ask for it
  with the `--log' option.

  Slower building of Gnuastro: Binary operators (e.g., plus or multiply)
  are now done in the native type of the input dataset. Doing so for all
  the different combinations of types, greatly slows down the initial
  compilation of Gnuastro (after running `make'). So for every type there
  is now a `--enable-bin-op-*' configure time option. When the dataset's
  type isn't compiled (only for the binary operators), it will be converted
  to a compiled type and then converted back in the end.

  Arithmetic: all operations are done in the native data type of the
  dataset. Until now, it would convert the data internally to double
  precision floating point, do the requested operation and write the data
  back in the proper type. So this new implementation is much more
  efficient.

  Arithmetic: two new classes of operators: type conversion operators to
  all standard types and integer-only operators (all C bit-wise operators
  and the modulo operator).

  ConvertType: can also print the input dataset to the command-line
  (`stdout'). To use this feature set the output filename to `stdout'.

  Convolve now has the `--minsharpspec' option to specify the minimum
  spectrum value to use in deconvolution (matching PSFs).

  Crop: when in WCS mode it can still only work on aligned images. However,
  very small floating point errors in writing the WCS (for example 10e-13
  degrees) are now acceptable. Until now these would cause Crop to complain
  and abort.

  Crop: the name of the crop can be pre-determined based on the values in a
  given in a table column. This allows your object's IDs to be directly
  used as the crop's file name for example.

  MakeCatalog now also reports the surface brightness in
  mag/arcsec^2. Until now, MakeCatalog would only print the dataset's
  surface brightness in units of magnitudes/pixel. But that is not nicely
  comparable to other datasets. Hence, using a simple calculation (from the
  pixel projected size, fully derived in the book), it now also reports the
  surface brightness in magnitudes/arcsec^2 also.

  MakeProfiles: Profile codes now start from `1' (until now they started
  from `0').

  MakeProfiles: now accepts the radial function of profiles as
  human-readable strings instead of a code for each profile (which was very
  cryptic, although codes are also still acceptable). For example in the
  profile column you can now write `sersic' instead of the code `1'.

  NoiseChisel: the new `--cleandilated' option will remove dilated objects
  that have a low S/N (it is mainly useful on very clean or mock images).
  For non-clean noise, it will result in a decrease of completeness. With
  this new option, NoiseChisel will also print detection S/N values when
  run with the `--checkdetsn' option.

  Statistics: now reads table columns as well as images and does basic
  operations on them. It can also only work on a certain range of the data
  (instead of the whole set). Alternatively, you can define the range on
  another reference column, but use values of the main column.

  Statistics: all its single-valued measurements can now be done on a
  tessellation (tile grid) over the input dataset.

  Statistics: can now estimate the Sky value on the input dataset using the
  mode's quantile similar to what NoiseChisel does to find its initial
  threshold.

  Statistics: has several new single valued calculations: `--quantile',
  `--quantfunc' (quantile function), `--mode', `--modequant', `--modesym',
  and `--modesymvalue'.

  Warp: align the image with the celestial coordiates using the `--align'
  option.

  Warp: standard modular warpings can now be requested without an input
  matrix, using the following options: `--shear', `--flip', `--project',
  `--rotate', `--scale', `--translate'. Any number of these transformations
  (along with the `--align' option) can be called on the command-line and
  they will be applied in the same order to create one warping matrix. By
  default the WCS will also be corrected.

** Changes in behavior

  Mask image options have been removed from all programs. Instead, all
  programs can work directly on data with blank values. So when some pixels
  must be masked, the Arithmetic program's `where' operator can be used to
  select special pixels and set them to blank. In particular bit-wise
  operations are now available in Arithmetic to use bit-mask
  images. Managing all these different choices in every program would only
  confuse the user (with too many options).

  Arithmetic: the `x' letter is now used to represent the multiplication
  operator. Previously it was `*' which needed quotation and was thus very
  inconvenient.

  Convolve: the old `--frequency' and `--spatial' options have been removed
  and are replaced by `--domain' which accepts values of `frequency' and
  `spatial'.

  Convolve: the old `--viewfreqsteps' was changed to `--checkfreqsteps' to
  fit with the general style of such check images in all Gnuastro's
  programs.

  Crop: `--section' syntax is now inclusive in both bounds.

  Crop: only checks if the center of a crop is filled when the crop was
  defined by its center (for example with `--ra' and `--dec'). The verbose
  outputs of Crop are also not cryptic 0s or 1s. The are human readable
  text.

  Crop: doesn't have separate `--imgmode' and `--wcsmode' options any
  more. There is now a single `--mode' option which accepts values of `img'
  or `wcs'.

  MakeProfiles: the old `--inputascanvas' is now called `--clearcanvas'.

  MakeProfiles: until now, it would abort with an error when the input
  columns had blank values. But for masking, it might happen that you set a
  blank magnitude. So this check has now been removed when reading the
  magnitude column.

  NoiseChisel: default value of the `--minskyfrac' option (new name for the
  old `--minbfrac') is now 0.7 as opposed to 0.5. This will allow much
  better estimation of noise properties (by default). It may be slightly
  too high for a crowded field, but the users can change it on the
  command-line (or in a configuration file) for such datasets.

  NoiseChisel: when it is run with any of the `--check' options, it will
  abort after all the check images have been created. This is very useful
  for checking your parameters until each step and not be distracted (or
  have to wait) for later steps to finish.

  Statistics: will not make a histogram and cumulative frequency files, or
  calculate sigma-clipped results by default (with no options). It will
  just print some basic information.

  Table: Previously, if a column was requested, the `-i' option would be
  ignored. But it often happens that the users forget a column name after
  already typing several of their desired columns. So the opposite behavior
  is preferred. Because when more than a couple of columns are needed, you
  will probably forget the column identifiers of the last few and having to
  retype everything is very frustrating. Something like how `--help' takes
  precedence over all other options.

  Table: to select column(s) by regular expression searching, the name now
  has to be put in `/ /' (similar to AWK). If a value isn't in `/ /', the
  programs will only select a column with the exact match.

  Warp: when a 2 by 2 matrix is given, the FITS pixel positions (which
  define the center of a pixel as an integer) are automatically implemented
  internally, see "Invoking Warp" in the manual for more.

  Warp: the old `--nofitscorrect' option has been changed to
  `--centeroncorner' to be more clear. The new option is now more general
  than before and also works on warping with a matrix, not just on modular
  warpings.

  Warp: the old `--nowcscorrection' option has been given a more clear name
  of `--keepwcs'. With this option, Warp will not apply the warp the
  input's WCS structure.

  Warp: the old `--maxblankfrac' option has been changed to
  `--coveredfrac'. Until now, Warp would only look for the fraction of
  input blank/NaN pixel area over the output pixel. But this would be
  useless on the edges of the image. So the new `--coveredfrac' option
  takes the acceptable fraction of output pixel area that must be covered
  by input pixels in order to give that output pixel a value. You can use
  this to set edge pixels that are not fully covered in the new grid to
  blank and have a flat warped image.

** Bug fixes

  Using `%zu' to print `size_t' variables for clean build on 32-bit
  systems.

  Crash in Table for some operating systems due to memory is now fixed (bug
  #49347).

  Table's man-page is now created and installed (bug #49418).

  Fixes in the documentation (sr #109170, bug #49419).

  Check for malloc returning valid pointer (bug #49459).

  Segfault in mesh interpolation corrected (bug #49588).

  Corrected bad status usage in calls to wcsp2s and wcss2p (bug #49752).

  Strickter checking in Crop's polygon point list (bug #48978).

  Correction in alignment and getting pixel scale (bug #50072).

  Decomposing PCi_j and CDELTi matices in output WCS (bug #50073).

  Using image naxes[n] when checkcenter is larger (bug #50099).

  Memory leak in MakeCatalog corrected (bug #51118).

  Fix copy-paste error in MakeCatalog flag arrays (bug #51130).





[**] Use a .sig file to verify that the corresponding file (without the
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and the corresponding tarball.  Then, run a command like this:

  gpg --verify gnuastro-0.3.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 16A8A4B2AEC42AFF

and rerun the 'gpg --verify' command.