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[info-gnuastro] Gnuastro 0.2.206 released

From: Mohammad Akhlaghi
Subject: [info-gnuastro] Gnuastro 0.2.206 released
Date: Fri, 5 May 2017 02:10:21 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:52.0) Gecko/20100101 Thunderbird/52.1.0


I am very happy to announce the release of Gnuastro 0.2.206-ea30. This is
the final alpha release prior to the 0.3 release.

The 0.3 release will be made in a week. It would be great if you could
build and check Gnuastro (commands below) until then and inform us if you
confront any problems or warnings on your operating system. Any comments on
how the new updates have affected your work would be most welcome.

  $ ./configure
  $ make -j8              # Build on 8 threads, some new libraries will
  $ make check -j8        # take a little longer to build than before.
  $ make install

This is an almost complete re-write of Gnuastro (58801 lines replacing
44505). Most importantly, Gnuastro now has a new generic data container
(called `gal_data_t'). This new container can now deal natively with all
standard numeric data types, work in RAM or HDD/SSD (for large datasets),
keep data with any dimensionality and etc. It has enabled many other very
useful features to all Gnuastro programs and libraries. Some of the most
prominent of the new features are discussed below [1: NEWS file shown
below]. It is strongly recommended to review the respective section of the
Gnuastro manual/book for a better feeling of all the new features.

Since the changes are significant, the webpage manual won't be updated
until the 0.3 release next week. If you have LaTeX, you can build the PDF
manual with this command:

  $ make pdf

After installation, you can also access the manual on the command-line with

  $ info gnuastro

Any comments/corrections in the manual would also be highly appreciated.

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.

Here are the compressed sources:   (4.4MB)   (2.9MB)

Here are the GPG detached signatures[2]:

Use a mirror for higher download bandwidth:

Here are the MD5 and SHA1 checksums:

87bb696df90b585baee3f0ba287e1ab1  gnuastro-0.2.206-ea30.tar.gz
5e00a2b72f35d7bba5a04f949ccc04ea  gnuastro-0.2.206-ea30.tar.lz
c547b595e8565110e7256e6c70fcb1590007bac1  gnuastro-0.2.206-ea30.tar.gz
da59cea6e410f392d56fbc62a1f3219637cd569f  gnuastro-0.2.206-ea30.tar.lz

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

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] NEWS file for this release:

* Noteworthy changes in release 0.2.206 (library 1.0.0) (2017-05-05) [alpha]

** 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. Major new library
  features are:

     -- `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).


  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

  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.

  Gnuastro now has a new program called "BuildProgram" 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. For example if your C source code is called
  `myprog.c', you can compile, link and run it with this simple command and
  let GNU Libtool worry about the linking.

      $ astbuildprog myprog.c

** 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

  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.

  ImageWarp can now align the image with the celestial coordiates using the
  `--align' option.

  ImageWarp can now warp 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 at runtime and they will be applied in
  the same order to create one warping matrix. By default the FITS
  coordinates will also be corrected.

  Arithmetic now does all its operations 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 than the 0.2 version.

  Arithmetic now accepts 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).

  Arithmetic does the binary operators (e.g., plus or multiply) also 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. Only for a the binary
  operators, when the dataset's type isn't compiled, it will be converted
  to a compiled type and then converted back.

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

  MakeProfile can now accept 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'. Also
  compared to the previous versions where the codes started from `0', not
  they start from `1'.

  Crop can now read the name of the crop based on a value in a given in a
  table column. This allows your object's IDs to be directly used as the
  crop's file name.

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

  The Statistics program can now read table columns as well as images and
  do basic operations on them. It can also only work on a certain range of
  the data. Alternatively, you can define the range on another reference
  column, but use values of the main column.

  Statistics can also do all its single-valued measurements on a
  tessellation (tile grid) over the input dataset.

  Statistics now has features to estimate the Sky value on the image using
  the mode's quantile similar to what NoiseChisel does to find its initial

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

  When in WCS mode, Crop 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.

  NoiseChisel now has a new `--cleandilated' option to 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.

** Changes in behavior

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

  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.

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

  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 also available in Arithmetic which can be used with
  Arithmetic's `where' also. Managing all these different choices in every
  program would only confuse the user (with too many options).

  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

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

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

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

  Warp's 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's 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.

  Warp's 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

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

  Until now, MakeProfiles 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

  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.

  NoiseChisel's 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.

  When NoiseChisel 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.

** Bug fixes

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

  Crash in Table for some operating systems due to memory is now fixed (bug

  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).

[2] 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-0.2.206-ea30.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 16A8A4B2AEC42AFF

and rerun the 'gpg --verify' command.

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