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Gnuastro 0.5 released

Item posted by Mohammad Akhlaghi <makhlaghi> on Sat 23 Dec 2017 04:26:14 PM UTC.

As a small holiday gift, I am happy to announce the fifth release of Gnuastro (version 0.5).

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 for the comfort of both the users and developers. For the full list of Gnuastro's library and programs along with a comprehensive general tutorial, please see the links below, respectively:

Many new features have been added since the fourth release and almost all bugs that were found have been fixed. For the full list of new features, please see the NEWS file below [1]. Some of the highlights are as follows: there is a new "Match" program to match catalogs (in 1D or 2D). NoiseChisel uses signal contiguity to grow the true detections (before it was a blind dilation). This is much more successful in tracing the outer low surface brightness regions. Filtering operators are added to Arithmetic. CosmicCalculator's functions are now available in the library for use in your own programs, and now it can also print single requested calculations (instead of a full list of all calculations). Gnuastro's top webpage is now also available in French.

You will also find a new section in the "Tutorial" chapter of the book ("General program usage tutorial", link above). It contains an extended and pedagogic tutorial to help you get started in using Gnuastro's infra-structure effectively. With the aim of detecting galaxies in an image and estimating their colors, it takes you through most of the programs. Just be patient and follow through the steps to master Gnuastro's powerful features. This tutorial was made as part of the "Exploring the ultra-low surface brightness universe" workshop in the International Space Science Institute (ISSI in Bern, Switzerland). I am very grateful to the hosts and participants for the very fruitful week.

If any of Gnuastro's program are useful in your work, please run the relevant programs with a `--cite' option (it can be different for different programs). Citations are vital for the continued work on Gnuastro, so please don't forget to support us by doing so.

Boud Roukema and Vladimir Markelov contributed to the code of this release. Lucas MacQuarrie, Thérèse Godefroy and the GNU French Translation Team also kindly initiated and are managing the French translation of the top Gnuastro webpage. I am finally very grateful to (in alphabetic order) Leindert Boogaard, Nicolas Bouché, Benjamin Clement, Madusha Gunawardhana, Takashi Ichikawa, Raúl Infante Sainz, Aurélien Jarno, Floriane Leclercq, Alan Lefor, Bob Proulx, Alejandro Serrano Borlaff, Lee Spitler, Ole Streicher, Alfred Szmidt, Ignacio Trujillo and David Valls-Gabaud who provided many great comments, suggestions and bug reports to this release.

Below, you can get the compressed sources and a GPG detached signatures for this release. See [2] for uncompressing Lzip tarballs. (4.6 MB) (3.1 MB)

Use a mirror for higher download bandwidth: (4.6 MB) (3.1 MB)

The GPG detached signatures are also available below. See [3] for how to verify the integrity of this tarball with the signature. (833 B) (833 B)

Here are the MD5 and SHA1 checksums:

This tarball was bootstrapped (initially built) with the tools
below. Note that these are not installation dependencies.

  • Texinfo 6.5
  • Autoconf 2.69
  • Automake 1.15.1
  • Help2man 1.47.5
  • Gnulib v0.1-1729-gf583f328b
  • Autoconf archives v2017.09.28-14-g2445b89

For installation dependencies, please see:

I wish you happy holidays,

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 Gnuastro 0.5

New features

  • Manual/Book: An extended tutorial is added showing some general applications of almost all the programs. This may be a good place to get a feeling of how Gnuastro is intended to be used and some of the programs.
  • New Program and library: Match is a new program that will match two given inputs (currently catalogs). Its output is the re-arranged inputs with the same number of rows/records such that all the rows match. The main work is also done with the new low-level `gal_match_catalog' library function which can also be used in more generic contexts.
  • All programs: a value of `0' to the `--numthreads' option will use the number of threads available to the system at run time.
  • Arithmetic: The new operators `filter-median' and `filter-mean' can be used to filter (smooth) the input. The size of the filter can be set as the other operands to these operators.
  • BuildProgram: The new `--la' option allows the identification of a different Libtool `.la' file for Libtool linking information.
  • BuildProgram: The new `--deletecompiled' option will delete the compiled program after running it.
  • CosmicCalculator: all the various cosmological calculations can now be requested individually in one line with a specific option added for each calculation (for example `--age' or `--luminositydist' for the age of the universe at a given redshift or the luminosity distance). Therefore the old `--onlyvolume' and `--onlyabsmagconv' options are now removed. To effectively use these new features, please review the "Invoking CosmicCalculator" section of the book.
  • Fits: when an extension/HDU is identified on the command-line with the `--hdu' option and no operation is requested, the full list of header keywords in that HDU will be printed (as if only `--printallkeys' was called).
  • MakeCatalog: physical nature agnostic WCS column names. Previously the first WCS axis was always assumed to be RA and the second DEC. So for example even if you had a spectrum (with X and wavelength as the two WCS dimensions), you would have to ask for `--ra' and `--dec'. The new `--w1' and `--w2' options are now generic and don't assume any particular type only their order in the FITS header. MakeCatalog now also uses the CTYPE and CUNIT keywords to set the names and units of its output columns. The `--ra' and `--dec' options are now just internal aliases for `--w1' or `--w2' which will be determined based on the input's CTYPE keyword. Also the new `--geow1', `--geow2', `--clumpsw1', `--clumpsw2', `--clumpsgeow1', `--clumpsgeow2' options replace the old options `--geora', `--geodec', `--clumpsra', `--clumpsdec', `--clumpsgeora', `--clumpsgeodec'. No alias is currently defined for the latter group.
  • MakeCatalog: the new `--uprange' option allows you to specify a range for the random values around each object. This is useful when the noise properties of the dataset vary gradually and sampling from the whole dataset might produce biased results.
  • NoiseChisel: with the new `--convolved' and `--convolvedhdu' options, NoiseChisel will not convolve the input any more and use the given dataset instead. In many cases, as the inputs get larger, convolution is the most time consuming step of NoiseChisel. With this option, you can greatly speed up your tests (to find the best parameters by varying them, for a given analysis). See the book for more information and examples.
  • NoiseChisel: with the new `--widekernel' option it is now possible to use a wider kernel to identify which tiles contain signal. The rest of the steps (identifying the quantile threshold on the selected tiles and etc) are done on the dataset convolved with `--kernel' as they were before. Since it is time consuming, this is an optional feature.
  • NoiseChisel: with the new `--qthreshtilequant' option, it is now possible to discard high-valued (outlier) tiles before estimating qthresh over the whole image. This can be useful in detecting very large diffuse/flat regions that would otherwise be detected as background (and effectively removed).
  • NoiseChisel: the finally selected true detections are now grown based on signal contiguity, not by blind dilation. The growth process is the same as the growing of clumps to define objects. Only for true detections, the growth occurs in the noise. You can configure this growth with the `--detgrowquant' and `--detgrowmaxholesize'. With this new feature it is now possible to detect signal out to much lower surface brightness limits and the detections don't look boxy any more.
  • Cosmology library: A new set of cosmology functions are now included in the library (declared in `gnuastro/cosmology.h'). These functions are also used in the CosmicCalculator program.
  • `gal_table_read' can now return the number of columns matched with each input column (for example with regular expressions), a new argument has been added to allow this feature.
  • `gal_fits_key_img_blank': returns the value that must be used in the BLANK keyword for the given type as defined by the FITS standard.
  • `gal_txt_write' and `gal_fits_tab_write' now accept an extension name as argument to allow a name for the FITS extension they write.
  • `gal_box_bound_ellipse_extent' will return the maximum extent of an ellipse along each axis from the ellipse center in floating point.

Removed features

  • Installation: The `--enable-bin-op-*' configuration options that were introduced in Gnuastro 0.3 have been removed. By managing the arithmetic functions in a better manner (a separate source file for each operator), compilation for all types (when done in parallel) takes about the same time as it took with the default (only four) types until now.
  • MakeCatalog: `--zeropoint' option doesn't have a short option name any more. Previously it was `-z' which was confusing because `-x' and `-y' were used to refer to image coordinate positions.
  • NoiseChisel: The `--dilate' and `--dilatengb' options have been removed. Growing of true detections is no longer done through dilation but through the `--detgrowquant' and `--detgrowmaxholesize' options (see above).

Changed features

  • CosmicCalculator: The redshift is no longer mandatory. When no redshift is given, it will only print the input parameters (cosmology) and abort.
  • MakeCatalog: when the output is a FITS file, the two object and clumps catalogs will be stored as multiple extensions of a single file. Until now, two separate FITS files would be created. Plain text outputs are the same as before (two files will be created).
  • `gal_binary_fill_holes' now accepts a `connectivity' and `maxsize' argument to specify the connectivity of the holes and the maximum size of acceptable holes to fill.
  • `gal_fits_img_read' and `gal_fits_img_read_to_type' now also read the WCS structure of the extension/HDU in a FITS file and have two extra arguments: `hstartwcs' and `hendwcs'. With these options it is possible to limit the range of header keywords to read the WCS, similar to how they are used in `gal_wcs_read'.
  • `gal_txt_write', `gal_table_write_log', `gal_fits_tab_write' and `gal_txt_write' don't have the `dontdelete' argument any more. The action they take if the file already exists depends on the file: for FITS, a new extension will be added and for text, they will abort with an error.
  • `gal_tile_block_write_const_value' and `gal_tile_full_values_write' now accept a new `withblank' option to set all pixels that are blank in the tile's block to be blank in the check image.
  • `gal_wcs_pixel_area_arcsec2' will return NaN (instead of aborting) when input is unreasonable (not two dimensions or not in units of degrees).
  • `gal_wcs_world_to_img' and `gal_wcs_img_to_world': Until now, these two WCS conversion functions would explicitly assume RA and Dec and work based on input arrays (so for example it was also necessary to give the number of elements and etc). They now accept `gal_data_t' as input for the input coordinates, thus their API has been greatly simplified and their functionality increased.

Bug fixes

  • ConvertType crash when changing values (bug #52010).
  • Arithmetic not accounting for integer blank pixels in binary operators (bug #52014).
  • NoiseChisel segfault when memory mapping to a file (bug #52043).
  • CFITSIO 3.42 and libcurl crash at Gnuastro configure time (bug #52152).
  • MakeCatalog crash in upper-limit with full size label (bug #52281).
  • NoiseChisel leaving unlabeled regions after clump growth (bug #52327).
  • Libtool checks only in non-current directory (bug #52427).

[2] Using Lzip

Lzip has a much better compression ratio and much better archival features than the common `.gz' or `.xz'. Therefore Gnuastro's stable releases are made in `.gz' (for historical reasons) and `.lz'. The alpha/test releases are only in `.lz'. If you don't have Lzip, can download and install it from its webpage.

If you have GNU Tar, then the single command below should uncompress and un-pack the tarball:

If the command above doesn't work, you have to un-compress and un-pack it with two separate commands:

[3] Verifying tarballs

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:

If that command fails because you don't have the required public key, then run this command to import it:

and rerun the 'gpg --verify' command.

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