Dear all,
We are almost ready for the 11th release of Gnuastro by next week. To
have a clean release, I am making this announcement so you can try
building and using it and report any possible warnings, or failures in
the build on your system.
Many new things have been added and some bugs have been found and
fixed since the last release. For the full list, please see the NEWS
file and see [1] below for the most important changes since version
0.10.39 (last announcement). Here are the most important points:
1) arXiv:1909.11230 ( https://arxiv.org/abs/1909.11230 ) is a new
paper (to be published in the IAU Symposium 355 proceedings) that
describes the significant improvements in NoiseChisel and Segment
since the initial paper in 2015. If you are using NoiseChisel or
Segment after version 0.6, please read this paper, and also cite
it with the 2015 paper (they are complementary). Its BibTeX
information has been added to the output of `--cite' for
NoiseChisel and Segment. By the way, this paper is also fully
reproducible! See the last word in the abstract: its the checksum
of the Git commit that contains the whole source to automatically
and exactly reproduce every figure and number in this paper (a
much improved version of pipeline used in the 2015 paper!). I will
be giving a webinar on it this Wednesday as part of the Research
Data Alliance (RDA) webinars, please join if you are interested in
publishing reproducible scientific papers:
https://www.rd-alliance.org/group/early-career-and-engagement-ig-early-career-networking-group/event/november-ama-call
2) Several programs now also support direct operation on 3D
datacubes: Convolve, MakeCatalog, MakeProfiles and Match. Work in
ongoing to hopefully finalize the 3D work on NoiseChisel and
Segment also.
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 see [3]:
https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.10.61-c417.tar.lz [3.4MB]
https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.10.61-c417.tar.lz.sig
[833B]
Here are the MD5 and SHA1 checksums (other ways to check if the
tarball you download is what we distributed):
097909af3f6a85c3d7bfaefe9f37b149 gnuastro-0.10.61-c417.tar.lz
a678065a365d9539eabae3bf31cbdb1d3c232d53 gnuastro-0.10.61-c417.tar.lz
Since the last announcement, I am very grateful to Stefan Brüns,
Alexey Dokuchaev and Joseph Putko for providing very useful
suggestions and bug fixes.
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). 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 2.69
Automake 1.16.1
Help2man 1.47.11
ImageMagick 7.0.9-4
Gnulib v0.1-2905-gba23291b7
Autoconf archives v2019.01.06-61-g5aaaf3b
The dependencies to build Gnuastro from this tarball on your system
are described here:
https://www.gnu.org/s/gnuastro/manual/html_node/Dependencies.html
Best wishes,
Mohammad
--
Postdoctoral research fellow,
Instituto de Astrofísica de Canarias (IAC),
Calle Vía Láctea, s/n, E38205,
San Cristóbal de La Laguna, Tenerife, Spain.
[1] Major changes since Gnuastro 0.10.39 (last announcement)
New features:
Book:
- The "General program usage tutorial" now has a section on how to
write
scripts effectively to automate your analysis.
Arithmetic:
- The new `add-dimension' operator will stack the popped operands in a
higher-dimensional dataset. For example to build a 3D cube from
individual 2D images/slices.
Convolve:
- Spatial domain convolution now possible on 3D data cubes (with a 3D
kernel).
MakeCatalog:
- Catalogs from 3D inputs now available, with the following new
options,
see book for more.
--spectrum: label's spectrum (across the third dimension).
--z: Flux-weighted position in 3rd dimension.
--geoz: Geometric center in third FITS axis.
--minz: Minimum third FITS axis position.
--maxz: Maximum third FITS axis position.
--clumpsz: Flux weighted center of all clumps in object in 3rd dim.
--clumpsgeoz: Geometric center of all clumps in object in 3rd dim.
--w3: Flux weighted center in third WCS axis.
--geow3: Geometric center in third WCS axis.
--clumpsw3: Flux wheighted center of all clumps in 3rd dim.
--clumpsgeow3: Geometric center of all clumps in 3rd dim.
--areaxy: Projected area in first two dimentions.
--geoareaxy: Projected geoarea in first two dimensions.
--inbetweenints: output will contain one row for all integers between 1
and the largest label in the input (irrespective of their
existance in
the input image). This was the default/only behavior of MakeCatalog
until now. However, there are situations where the labeled input
image
integers may not be contiguous. For example if the input's only
labeled pixel values are 11 and 13 from this release MakeCatalog's
output will only have two rows. If you want the old behavior (of one
row per integer, even if its not in the image), you can use this
option.
MakeProfiles:
- Can produce mock ellipsoids in a datacube (using X-Z-X Euler angles
for 3D orientation), the following options have been added, see the
book for more details.
--p2col: Second Euler angle (X-Z-X order).
--p3col: Third Euler angle (X-Z-X order).
--q2col: Axis ratio (major/dim3 in 3D).
- The `--kernel' option can build 3D kernels, see the description of
this option in the book for examples and details on how to run it.
Match:
- Matching of catalogs now possible using 3 coordinates (on catalogs
generated from 3D data cubes), see book for more.
NoiseChisel:
- arXiv:1909.11230 added in papers to cite (with the `--cite' option):
this paper describes the major changes made to NoiseChisel in the
last
10 stable releases since the 2015 paper, most importantly how Segment
has been separated and the new growth strategy. It is therefore
necessary to cite it along with the initial 2015 paper when using
NoiseChisel.
Segment:
- arXiv:1909.11230 added in papers to cite (with the `--cite' option):
this paper describes why Segment has been separated from NoiseChisel
and some important updates to it compared to the 2015 paper, it is
therefore necessary to cite it along with that paper when using
Segment.
Library:
- gal_blank_remove_realloc: Remove blanks and shrink allocated space.
- gal_box_bound_ellipsoid_extent: Extent of 3D ellipsoid.
- gal_box_bound_ellipsoid: Bounding box for a 3D ellipsoid.
- gal_statistics_unique: Return unique (non-blank) elements of the
input.
Removed feautures:
bug #57101: Crop segmentation fault when no overlap exists in
image-mode.
bug #57164: MakeCatalog crashes when a label isn't in the dataset.
bug #57180: MakeCatalog reporting infinity S/N when --instd isn't an
image.
bug #57200: Generated pkgconfig must request wcslib, not wcs.
[2] Lzip has better compression ratio and archival features compared
to the common `.gz' or `.xz' formats. Therefore Gnuastro's alpha/test
releases are only in this format, 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), you can get it
from your package manager, or download and install it from its
webpage:
https://www.nongnu.org/lzip/lzip.html
If Lzip is present and you use GNU Tar, then the single command below
should uncompress and un-pack the tarball:
$ tar xf gnuastro-0.10.61-c417.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-0.10.61-c417.tar.lz | tar -xf -'):
$ lzip -d gnuastro-0.10.61-c417.tar.lz
$ tar xf gnuastro-0.10.61-c417.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-0.10.61-c417.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 71E899012D174B66
and rerun the 'gpg --verify' command.