[info-gnuastro] Gnuastro 0.5.132 (alpha) released

[Mohammad Akhlaghi]

Dear all,

I am happy to say that the sixth release of Gnuastro is almost ready
and will be released in the next week or two. To make sure the sixth
release will be as smooth as possible for your work (bug-free), we are
making this alpha-release (version 0.5.132-60d5).

It would be great if you could try compiling and using this release
and informing us of any compilation warnings or errors along with
crashes or unexpected behavior after installation.

Below, you can get the compressed source of this release. See [2] for
uncompressing Lzip tarballs.
  https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.5.132-60d5.tar.lz (3.1Mb)

The GPG detached signature is also available below. See [3] for how to
verify the integrity of this tarball with the signature.
  https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.5.132-60d5.tar.lz.sig 
(833 b)

Here are the MD5 and SHA1 checksums of the source tarball:
  240a173252bb5a1e1d99f014b555bd7f  gnuastro-0.5.132-60d5.tar.lz
  24b13237c8cefbbd4aebf16b3c04c5881a400e12  gnuastro-0.5.132-60d5.tar.lz

Many new features have been added since the fifth 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].

The most important feature in this release is this: for improved
modularity (creativity in using Gnuastro), NoiseChisel's segmentation
features have been moved to a new program called Segment. Therefore
NoiseChisel is now ONLY in charge of detection and will return a
binary (0 or 1 valued) output marking detections. As described in the
tutorials, you can then feed this into Segment for segmentation. As
always, the book/manual is fully up to date with this and all other
changed/new features. Also, by popular demand, a new tutorial has been
added for detecting large objects to very low surface brightness
limits: 1/20th of the noise level in the case of the dataset used in
the demonstration.

Just as a reminder, the best place to start with Gnuastro is the
"General program usage tutorial" which you can access with the
following command after installing Gnuastro (the webpage will be
updated after the sixth release):

  $ info gnuastro "general program usage tutorial"

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.

I am finally very grateful to (in alphabetic order) Leindert Boogaard,
Nushkia Chamba, Nima Dehdilani, Antonio Diaz Diaz, Lee Kelvin, Brandon
Kelly, Guillaume Mahler, Bertrand Pain, Ole Streicher, Michel Tallon,
Juan C. Tello, Éric Thiébaut, David Valls-Gabaud, Aaron Watkins, Sara
Yousefi Taemeh, and Johannes Zabl who provided many great comments,
suggestions and bug reports to this release.

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 1.47.6
  Gnulib v0.1-1937-g0c0117674
  Autoconf archives v2018.03.13-27-g5b16a3e
For installation dependencies, please see:
https://www.gnu.org/software/gnuastro/manual/html_node/Dependencies.html

Cheers,
Mohammad
--
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 0.5.132-60d5

** New features

  All programs:
    - Input image dataset(s) can be in any of the formats recognized by
      Gnuastro (e.g., FITS, TIFF, JPEG), provided that their libraries
      (optional dependencies) were present at installation time.

  New program:
    - Segment: new program in charge of segmentation over detections. This
      operation was previously done by NoiseChisel. NoiseChisel is now ONLY
      in charge of detection.

  Arithmetic:
    - erode: Erode the foreground of a binary dataset.
    - dilate: Dilate the foreground of a binary dataset.
    - filter-sigclip-mean: sigma-clipped, mean filter operator.
    - filter-sigclip-median: sigma-clipped, median filter operator.
    - connected-components: label the connected elements of the input.
    - invert: subtract the maximum of unsigned types (absorption to 
emission).
    - interpolate-medianngb: Interpolate (only blanks) with nearest 
neighbors.

  ConvertType:
    - TIFF images can also be used as input.

  MakeCatalog:
    MakeCatalog will only read the datasets necessary for the requested
    columns. Until now, it would read all the possible datasets and all the
    intermediate measurements. This is thus major improvement in memory and
    CPU usage. As a result, the input argument is no longer assumed to be
    the values file, but the object labels file. Please see the
    "MakeCatalog inputs and basic settings" section of the book for
    more. Here is the summary of the new options:
    --insky: Sky value as a single value or file (dataset).
    --instd: Sky standard deviation as a single value or file (dataset).
    --valuesfile: filename containing the values dataset.
    --valueshdu: HDU/extension containing the values dataset.
    --clumpscat: Make a clumps catalog also.
    --noclumpsort: Don't sort the clumps catalog by host object ID.
    --subtractsky: Subtract the given Sky from the values dataset.
    --variance: input standard deviation image is actually variance.
    --checkupperlimit: make a table for random positions and measurements.
    --geoarea: the number of labeled pixels (irrespective of value).
    --brightnesserr: error in estimating the brightness.
    --mean: calculate the mean pixel value within an object or clump.
    --median: calculate the median pixel value within an object or clump.
    --upperlimitsigma: position in random distribution (in units of sigma).
    --upperlimitquantile: position in random distribution (quantile).
    --upperlimitonesigma: 1sigma value of the random distribution.
    --upperlimitskew: (mean-median)/sigma or skewness of random 
distribution.

  NoiseChisel:
    - New tutorial on detecting large and extended targets.
    --rawoutput: only output the detection labels and Sky and its STD.
    --ignoreblankinsky: don't set the pixels that are blank in the input to
      blank in the Sky and Sky standard deviation outputs (when
      `--oneelempertile' is not called).
    --label: label the connected detections. Until now this was the default
      behavior. However, from this release, NoiseChisel is only in charge
      of detection. Segmentation is done by a new program (Segment). Since
      detection is ultimately just a binary operator, the default output
      now has an 8-bit unsigned integer type with values of 0 or 1. With
      this option, you can ask for it to label/count the connected
      detections instead of the default binary output.

  Statistics:
    --manualbinrange: histogram or CFP range can be outside of 
distribution.
    --ignoreblankinsky: similar to same option in NoiseChisel.

  Libraries:
    gal_array_read: read array from any of known formats (FITS, TIFF, 
JPEG,...).
    gal_array_read_to_type: similar to `gal_array_read', but to given type.
    gal_array_read_one_ch: Read a dataset, abort if it has multiple 
channels.
    gal_array_read_one_ch_to_type: Make sure input is in one channel 
and type.
    gal_binary_label_holes: label the holes within the foreground.
    gal_blank_is: check to see if argument is blank in its type or not.
    gal_eps_name_is_eps: Returns 1 if given filename is EPS.
    gal_eps_suffix_is_eps: Returns 1 if given suffix is EPS.
    gal_eps_to_pt: Converts dataset size to PostScript points.
    gal_eps_write: Writes a dataset into an EPS file.
    gal_jpeg_name_is_jpeg: Returns 1 if given filename is JPEG.
    gal_jpeg_suffix_is_jpeg: Returns 1 if given suffix is JPEG.
    gal_jpeg_read: Reads input JPEG image into `gal_data_t'.
    gal_jpeg_write: Writes a `gal_data_t' into a JPEG file.
    gal_label_grow_indexs: grow known indexs into desired areas.
    gal_label_watershed: apply watershed algorithm on desired region.
    gal_label_clump_significance: measure significance of all clumps in 
region.
    gal_pdf_name_is_pdf: Returns 1 if given filename is PDF.
    gal_pdf_suffix_is_pdf: Returns 1 if given suffix is PDF.
    gal_pdf_write: Writes a dataset into an PDF file.
    gal_pointer_allocate_mmap: Allocate space in a file, not in RAM.
    gal_qsort_index_single_d: Sort indexs of single array in decreasing 
order.
    gal_qsort_index_single_i: Sort indexs of single array in decreasing 
order.
    gal_qsort_index_multi_d: Sort indexs in multiple arrays (on 
different threads).
    gal_qsort_index_multi_i: Sort indexs in multiple arrays (on 
different threads).
    gal_tiff_name_is_tiff: check if name contains a TIFF suffix.
    gal_tiff_suffix_is_tiff: check if suffix is a TIFF suffix.
    gal_tiff_dir_string_read: convert a string to a TIFF directory number.
    gal_tiff_read: Read the contents of a TIFF "directory" to `gal_data_t'.


** Removed features

  NoiseChisel:
    - Segmentation (and thus the options below) moved to the new Segment
      program: --onlydetection, --segsnminarea, --checkclumpsn, --segquant,
      --keepmaxnearriver, --gthresh, --minriverlength, --objbordersn,
      --grownclumps, --checksegmentation.

    --skysubtracted: no longer necessary, included in noise measuremnts.

  MakeCatalog:
    --skysubtracted: no longer necessary, included in noise measuremnts.

  Library:
    - The macros `GAL_STATISTICS_SORTED_NOT',
      `GAL_STATISTICS_SORTED_INVALID', `GAL_STATISTICS_SORTED_INCREASING',
      `GAL_STATISTICS_SORTED_DECREASING': these macros are removed because
      we already have the `GAL_DATA_FLAG_SORT*'' bit-flags in `gal_data_t'.


** Changed features

  Arithmetic:
    - filter-mean: a blank value in the input can be non-blank in the
         output when non-blank elements present in filter.
    - filter-median: similar to filter-mean.

  Fits:
    --history: can be called/written multiple times in one run.
    --comment: can be called/written multiple times in one run.

  MakeCatalog:
    - The `WCLUMPS' keyword in the objects labeled image is no longer used
         to see if a clumps catalog should also be made. To build a clumps
         catalog, you can now use the `--clumpscat' option.
    - Estimation of noise-level is now done per-pixel over the whole
         label. Until now the average noise level was used.
    --objectsfile has been removed. The main input argument is now assumed
         to be the objects file.

  NoiseChisel:
    From this release, NoiseChisel is only in charge of detection and won't
    do segmentation any more. The new Segment program is in charge of
    segmentation. Many of the changes below are due to this new limited
    scope of NoiseChisel.
    --kernel: value `none' will disable convolution.
    - Renamed options:
      --convolvedhdu ==> --chdu
      --wkhdu        ==> --whdu
      --detsnminarea ==> --snminarea
      --checkdetsn   ==> --checksn
      --detquant     ==> --snquant
    - By default the output detection map is a binary image (values of 
0 or 1).
    - With no output name, the output has a `_detected.fits' suffix.

  Segment:
    - [Previously in NoiseChisel]: For finding true clumps, the difference
      in the peak of the clump and the highest valued river pixel, divided
      by the noise standard deviation are used. Until now, the total
      signal-to-noise ratio was used as a criteria. In initial tests, this
      algorithm was much more promising in detecting clumps over strong
      gradients and also on flatter gradients.

  Table:
    --column: multiple columns (comma separated) can be used in one
         instance of this option (multiple instances of this option are
         still acceptable also).

  Libraries:
    gal_binary_holes_fill: new name for `gal_binary_fill_holes'.
    gal_dimension_is_different: new name for `gal_data_dsize_is_different'.
    gal_fits_img_read: now only reads the data not the WCS, therefore it no
        longer needs the last two arguments. A subsequent call to
        `gal_wcs_read' can be used to read the WCS information in the file.
    gal_pointer_increment: new name for `gal_data_ptr_increment'.
    gal_pointer_num_between: new name for `gal_data_ptr_dist'.
    gal_pointer_allocate: replaces `gal_data_malloc_array' and
        `gal_data_calloc_array', through an argument you can ask for the
        allocated memory to be cleared or not.
    gal_qsort_TYPE_i: new name for gal_qsort_TYPE_increasing.
    gal_qsort_TYPE_d: new name for gal_qsort_TYPE_decreasing.
    gal_statistics_is_sorted: can now also update the bit-flags regarding
        the sorted nature of the input (to optimize future calls to the
        function).
    gal_statistics_quantile_function: returns `inf' or `-inf' if the given
        value is smaller than the minimum or larger than the maximum of the
        input dataset's range. Until now, it would return blank in such
        cases.
    gal_statistics_number: the output dataset now has a `size_t' type. 
Until
        now it was `uint64_t'.


** Bug fixes

  bug #52979: Many unused result warnings for asprintf in some compilers.
  bug #53122: Configure time CPPFLAGS and LDFLAGS don't pass to 
BuildProgram.
  bug #53142: Crash when printing values with the `--onlyversion' option.
  bug #53147: NULL value of onlyversion option causing a crash.
  bug #53226: Match output directory ignored when making multiple files.
  bug #53230: Statistics program bad results on integer columns with 
limits.
  bug #53268: NoiseChisel crash when no growth is possible.
  bug #53295: MakeCatalog parses area larger than clump.
  bug #53304: NoiseChisel crash when there is no detection.
  bug #53312: Fits crash on keyword editing (except --delete).
  bug #53407: Instrumental noise in MakeNoise should be squared.
  bug #53424: Sigma-clipping seg-faults when there are no more elements.
  bug #53580: Warp crash when no WCS present.
  bug #53825: NoiseChisel not accounting for fully zero-valued tiles.





[2] 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:

  https://www.nongnu.org/lzip/lzip.html

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

  $ tar xf gnuastro-0.5.132-60d5.tar.lz

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

  $ lzip -d gnuastro-0.5.132-60d5.tar.lz
  $ tar xf gnuastro-0.5.132-60d5.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 this command:

  $ gpg --verify gnuastro-0.5.132-60d5.tar.lz.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 1849814357EFB73A

and rerun the above 'gpg --verify' command.