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NEWS
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GNU Astronomy Utilities NEWS -*- outline -*-
Copyright (C) 2015-2024 Free Software Foundation, Inc.
See the end of the file for license conditions.
* Noteworthy changes in release X.XX (library XX.X.X) (YYYY-MM-DD)
** New publications
** New features
*** MakeCatalog
--novalinerror: ignore pixel in the values image when calculating the
variance of each label's pixel: only use the pixel's value in the
'--instd' image (which can also be the variance with the '--variance'
option). This is useful in scenarios where the STD/variance image is
not just the sky STD/Variance, but also has the signal's contribution.
--mean-error: Measure the error of the mean for each label (object or
clump).
*** astscript-radial-profile
--azimuth option can be called multiple times so the profile is generated
over discrete azimuthal regions of the input. For example if called
with '--azimuth=30,50 --azimuth=210,250', the profile (or polar plot if
requested) will be generated only using pixels within these two
azimuthal ranges (all other pixels are ignored). Suggested and
implemented by Ignacio Ruiz Cejudo.
*** Library
- gal_units_wavelength_flux_density_to_jy: convert given wavelength flux
density (erg/s/cm^2/A) to Janskys.
** Removed features
** Changed features
** Bugs fixed
- bug #66216: NaN values in MakeProfile outputs for very small profiles
(smaller than a pixel even after accounting for the truncation
factor). Reported by Alejandro Camazón Pinilla.
- bug #66262: color-faint-gray crashes when using --graykernelfwhm. Found
and fixed by Samane Raji.
- bug #66280: Convolve's check images not in same directory as output.
* Noteworthy changes in release 0.23 (library 21.0.0) (2024-07-13)
** New publications
- https://ui.adsabs.harvard.edu/abs/2024RNAAS...8..168E by Eskandarlou
and Akhlaghi describing the newly added polar plot capability of
'astscript-radial-profile' (see the figure in the paper).
** New features
*** Arithmetic
--append: if the output file already exists, don't delete it, add the
outputs as extra HDUs (by default, the output file is deleted). If the
output does not exist, then this option has no affect.
- New operators (also available in "Column Arithmetic" of the Table
program):
- jy-to-wavelength-flux-density: converts Janskys to wavelength flux
density (erg/cm^2/s/Å) at the given wavelength.
- filter-madclip-mean: filter/smooth the input using MAD-clipped mean.
- filter-madclip-median: filter/smooth the input using MAD-clipped
median.
- free: free (from memory) the top operand on the stack of
operands. This is useful in combination with operators that produce
more than one output operand.
- madclip-maskfilled: mask (set to NaN) all input elements that are
outliers (defined by MAD-clipping). Combined with the stacking
operators this allows removing large contiguous outliers in your
final stacked datasets.
- siglclip-maskfilled: similar to 'madclip-maskfilled', but defining
outliers by Sigma-clipping.
- zeropoint-change: change the zero point of the input data set to a
new zero point.
*** Statistics
--concentration: measure the "concentration" of values in a distribution
around the median. See the book for the full description of this
option.
*** astscript-fits-view
--globalhdu: use the same HDU in any number of input files (with the
short format of '-g'); similar to the same option in Arithmetic or
ConvertType.
--ds9region: load any number of DS9 region files (separated by comas and
given to this option) into the DS9 window that will be opened. This was
added by Giacomo Lorenzetti.
- The default DS9 'sls' colormap contrast and bias are adjusted so the
largest value does not have a white color, but is dark red. This was
done because white is DS9's default color for blank pixels and
out-of-image regions; making the pixels with the largest value
invisible.
*** astscript-radial-profile
--polar: generate a 2D polar plot in the same region of the image that
the 1D radial profile has been calculate over. The polar plot is a
mapping/projection of pixels into an azimuthal angle vs. radius grid,
highlighting features that have polar symmetry (for example spiral arms
in galaxies or diffraction spikes in the PSF). This feature was
implemented by Sepideh Eskdandarlou.
*** astscript-psf-scale-factor
--nocentering: disable sub-pixel centering of the desired star before
finding the scale factor; added by Sepideh Eskandarlou and Raul
Infante-Sainz.
*** Makefile extensions
- $(ast-text-prev TARGET, LIST): select the word that is previous to
'TARGET' in a list of words. See the minimal working example in the
book for more.
- $(ast-text-prev-batch TARGET, NUM, LIST): select the previous "batch"
of 'NUM' words (in relation to the batch that contains 'TARGET'). This
is useful for steps in your pipelines were you need to limit the
parallelization to batches. See the minimal working example in the book
for more.
- $(ast-text-prev-batch-by-ram TARGET, NEEDED_RAM_GB, LIST): select the
previous batch of words in 'LIST' such that the total consumed RAM by
all the parallel executions does not exceed the available RAM when Make
starts. Like 'ast-text-prev-batch', this is useful for steps in a
pipeline that require a large amount of RAM (thus not allowing parallel
execution), but this is more generic and adapts to different systems
with very different RAM and/or CPU threads. See the minimal working
example in the book for more.
*** Library
- gal_statistics_concentration: measure the concentration of values
around the median; see the book for the details.
- gal_units_jy_to_wavelength_flux_density: convert Janskys to wavelength
flux density.
- gal_units_zeropoint_change: change the zero point of the input data set
to an output zero point.
** Removed features
** Changed features
*** All programs
- System configuration files are installed in 'PREFIX/etc/gnuastro/',
('PREFIX/' is the installation directory of Gnuastro; when installing
from source, and if no '--prefix' is given to the './configure script,
it is '/usr/local'). Until now, the configuration files of Gnuastro's
programs were installed in 'PREFIX/etc/'. But that was a top-level
directory for the configuration files of all the programs within the
operating system. Therefore the old method would unnecessarily populate
that already crowded directory, and finding Gnuastro's configuration
files could become non-trivial. This was suggested by Phil Wyett.
- User configuration files are installed in '$HOME/.local/etc/gnuastro/'
instead of '$HOME/.local/etc/'. See the description of system
configuration files above for more.
*** Arithmetic
- The following operators will output two operands: the main statistic
and the number of inputs used in each pixel: 'sigclip-mean',
'sigclip-median', 'sigclip-std', 'sigclip-mad', 'madclip-mean',
'madclip-median', 'madclip-std', 'madclip-mad'. See the book for full
examples on how to work with this (in summary: use '--writeall' to also
write the numbers image in the output or use 'swap free' to free it).
- Removed operators:
- 'madclip-number' and 'sigclip-number': because the numbers image will be
returned with any clipping stacking operator.
- 'madclip-fill-mad', 'sigclip-fill-mad', 'madclip-fill-std',
'sigclip-fill-std', 'madclip-fill-mean', 'sigclip-fill-mean',
'madclip-fill-median', 'sigclip-fill-median', 'madclip-fill-std',
'sigclip-fill-std': because the newly added and more general
operators ('madclip-maskfilled' and 'sigclip-maskfilled') can be
combined with any of the stacking operators to produce these as well
as many other useful scenarios.
*** ConvertType
- Standard input (stdin) is only checked when no input file has been
specified. Until now, the 'stdin' would be checked all the time, and if
anything was present there, it would be taken as the first color
channel. But this could cause problems in shell loops that parse the
standard input (for example, see
https://lists.gnu.org/archive/html/help-bash/2024-02/msg00074.html). Also,
it would rarely happen that when the three RGB color channels are
necessary, the first would be from the standard input, and the other
two as files. The new behavior is much more similar to the behavior of
other command-line programs like AWK or SED. This issue was reported by
Jesús Vega and Raul Infante-Sainz and solved with the help of Greg
Wooledge and Dennis Williamson.
*** CosmicCalculator
- The names of spectral lines which include their rest frame wavelength
is rounded to the nearest integer. For example the OIII line at
wavelength of 5006.84 Angstroms is now called O-III-5007. Until now,it
was confusingly/wrongly called O-III-5006!
*** Library
- speclines.h: macros specifying spectral lines have been corrected to
round wavelengths to nearest integer (see description of changes in
CosmicCalculator). For example the old 'GAL_SPECLINES_O_III_5006' is
now called 'GAL_SPECLINES_O_III_5007'.
*** astscript-fits-view
- The short format of the '--ds9geometry' option is '-G' (until now it
was '-g'). This was necessary to allow the '-g' of this script to have
a similar behavior to the other Gnuastro programs that take multiple
inputs (like Arithmetic or ConvertType) and '-g' is short for
'--globalhdu' (so the same HDU is opened in all the inputs).
** Bugs fixed
- bug #65255: description of CosmicCalculator's '--arcsectandist' didn't
specify if it is in physical or comoving coordinates. Found and fixed
by Boud Roukema.
- bug #65267: 'astscript-fits-view' created incorrect call to ds9 when
the number of input files was more than the specified HDUs.
- bug #65269: 'astscript-color-faint-gray' and 'astscript-psf-stamp' use
a coma as the decimal point on some operating systems. Reported by
Jesús Vega and fixed by Raul Infante-Sainz.
- bug #65377: MakeCatalog's suggested command when labeled image has
negative values (and MakeCatalog crashes) is wrong. Reported by Zahra
Sharbaf.
- bug #65382: Radial profile script truncates the azimuthal angle when
the maximum requested azimuthal range is above 360 degrees. Reported by
Fernando Buitrago Alonso and fixed by Raul Infante-Sainz.
- bug #63064: Statistics crashes when all pixels are NaN. Reported by
Raul Infante-Sainz and fixed with help of Thorsten Alteholz.
- bug #65494: Crop segmentation fault with older CFITSIOs (three word
version format). Reported by Giacomo Lorenzetti.
- bug #65571: Crop returns successfully when no output was made. Reported
by Sepideh Eskandarlou.
- bug #65561: Projections to infinity cause very long running time in
Warp. Found and fixed by Giacomo Lorenzetti.
- bug #63026: Warp translation adds one extra pixel even if it is not
requested. Reported by Raul Infante-Sainz and fixed by Giacomo
Lorenzetti.
- bug #65672: ./developer-build exits silently when some options are
given an empty value. Found and fixed by Giacomo Lorenzetti.
- bug #65673: Arithmetic creates a metadata FITS file a HDU with no data)
even when the output is not FITS (plain-text or on the standard
output). Reported by Sepideh Eskandarlou.
- bug #65743: Arithmetic's collapse-number mistakenly calculating
collapse-median instead. Reported by Sepideh Eskandarlou.
- bug #65801: astscript-fits-view could not properly parse the short
versions of the '--ds9geometry', '--ds9extra', '--ds9center' and
'--ds9mode' when the value was touching the short option name. Found
and fixed by Giacomo Lorenzetti.
- bug #65822: MakeProfiles does not write negative values with --replace.
- bug #65833: Convolve crashes when the kernel only has a single element.
- bug #65847: make check FAILs on color-faint-gray script when libjpeg
not found. Reported by Takashi Ichikawa.
- bug #65853: Statistics crashes with the --ontile option.
- bug #65862: Output directory ignored when Statistics is called with
the '--ontile' option.
- bug #65935: Arithmetic crashes with constants like speed of light.
- bug #65939: Column numbers in plain-text table metadata with +100
columns incorrectly written for the first 9 (single-digit) columns;
found with the help of Sepideh Eskandarlou.
- bug #65941: Name of spectral lines with wavelength were not rounded to
smallest nearest integer (see description of change in
CosmicCalculator).
* Noteworthy changes in release 0.22 (library 20.0.0) (2024-02-03)
** New publications
- https://ui.adsabs.harvard.edu/abs/2023RNAAS...7..269E by Eskandarlou et
al. on Gnuastro's zero point measurement script for calibration of
astronomical images ('astscript-zeropoint').
- https://ui.adsabs.harvard.edu/abs/2024RNAAS...8...10I by Infante-Sainz
& Akhlaghi on Gnuastro's script to visualize the full dynamic range of
astronomical images ('astscript-color-faint-gray').
- https://ui.adsabs.harvard.edu/abs/2024RNAAS...8...22I by Infante-Sainz
et al. on Gnuastro's script to measure the radial profile of a given
source ('astscript-radial-profile').
** New features
*** New program
- 'astscript-color-faint-gray': a new installed script to maximize the
visualization of the contents within your astronomical images. It does
this by showing the brighter parts of the image as color, intermediate
regions as black and the noisy/faint regions as gray/white.
*** All programs
- The following options are now available in all programs to allow
customization of which metadata is printed in the 0-th HDU of the FITS
output of all Gnuastro programs. Also see the "Changed features" list
for an important change in this regard to all Gnuastro output FITS
files.
--outfitsnoconfig: do not print any metadata in the 0-th HDU (including
the used options and their values, the date, the versions and git
commit of running directory).
--outfitsnodate: do not write the 'DATE' keyword.
--outfitsnoversions: do not write the versions of Gnuastro and
mandatory dependencies.
--outfitsnocommit: do not write the Git commit.
*** Arithmetic
--arguments: takes the name of plain-text file that contains the list of
arguments to the program. This option is critical if you have very long
(thousands) of operands and operators (which happen in large pipelines
where the arguments are constructed automatically). Without this
option, the shell is going to abort with an "Argument list too long"
error message.
- New operators:
- rotate-coord: given a 2D point's coordinates, return the coordinates
after it has been rotated by your requested angle around your
requested center (see documentation for example).
- mad: Median Absolute Deviation (MAD) stacking.
- madclip-mad: MAD after MAD-clipping stacking.
- madclip-std: Standard deviation after MAD-clipping stacking.
- madclip-mean: Mean after MAD-clipping stacking.
- madclip-median: Median after MAD-clipping stacking.
- madclip-number: Number of elements after MAD-clipping stacking.
- madclip-fill-mad: MAD after filled MAD-clipping stacking: this
involves a two-phase clipping: after the first
clipping, Arithmetic will "fill" the unclipped
holes in each input and masks them for a second
round. This is critical for clipping more
diffuse outliers: where a pixel may not be
clipped individually and will produce biased
results, but due to proximity with many nearby
clipped pixels, it can be discarded and thus its
effect on the final stack be removed.
- madclip-fill-std: Standard deviation after filled MAD-clipping stacking.
- madclip-fill-mean: Mean after filled MAD-clipping stacking.
- madclip-fill-median: Median after filled MAD-clipping stacking.
- madclip-fill-number: Num. of elements after filled MAD-clipping stacking.
- sigclip-fill-mad: MAD after filled MAD-clipping stacking.
- sigclip-fill-std: Standard deviation after filled MAD-clipping stacking.
- sigclip-fill-mean: Mean after filled MAD-clipping stacking.
- sigclip-fill-median: Median after filled MAD-clipping stacking.
- sigclip-fill-number: Num. of elements after filled MAD-clipping stacking.
- sigclip-mad: MAD after sigma-clipping stacking.
- collapse-madclip-mad: Collapse dim. by MAD-clipped MAD.
- collapse-madclip-std: Collapse dim. by MAD-clipped STD.
- collapse-madclip-mean: Collapse dim. by MAD-clipped mean.
- collapse-madclip-median: Collapse dim. by MAD-clipped median.
- collapse-madclip-number: Collapse dim. by MAD-clipped number.
- collapse-madclip-fill-mad: Collapse dim. by filled MAD-clipped MAD.
- collapse-madclip-fill-std: Collapse dim. by filled MAD-clipped STD.
- collapse-madclip-fill-mean: Collapse dim. by filled MAD-clipped mean.
- collapse-madclip-fill-median: Collapse dim. by filled MAD-clipped median.
- collapse-madclip-fill-number: Collapse dim. by filled MAD-clipped num.
- collapse-sigclip-mad: Collapse dim. by sigma-clipped MAD.
- collapse-sigclip-fill-mad: Collapse dim. by filled sigma-clipped MAD.
- collapse-sigclip-fill-std: Collapse dim. by filled sigma-clipped STD.
- collapse-sigclip-fill-mean: Collapse dim. by filled sigma-clipped mean.
- collapse-sigclip-fill-median: Collapse dim. by filled sigma-clip. median.
- collapse-sigclip-fill-number: Collapse dim. by filled sigma-clipped num.
*** Fits
--arguments: takes the name of plain-text file that contains the list of
arguments to the program. Currently this only works with '--keyvalue'
and is necessary when you want to get the keywords of a very long list
of files (~thousands!). Without this option, the shell is going to
abort with an "Argument list too long" error message.
--datasum-encoded: new option that will return an ASCII encoded
16-character string for the value of the 'DATASUM' concept in FITS data
verification.
*** Statistics
--checkskynointerp: similar to '--checksky', but stop as soon as the good
tiles are found (do not continue to interpolation and smoothing of the
tiles which can be time consuming if not needed).
--mad: Median Absolute Deviation (MAD) of input dataset.
--madclip: MAD-clipping, showing intermediate results.
--sigclip-mad: MAD of input after sigma-clipping.
--madclip-number: Number of input elements after MAD-clipping.
--madclip-median: Median of input elements after MAD-clipping.
--madclip-mean: Mean of input elements after MAD-clipping.
--madclip-std: Standard deviation of input elements after MAD-clipping.
--madclip-mad: MAD of input elements after MAD-clipping.
--mclipparams: Parameters of MAD-clipping, similar to sigma-clipping. Note
that in a Gaussian distribution, MAD = 0.67 sigma, so if
you want something similar to 3-sigma (the default), you
should set the MAD multiple to 5 (the default).
*** Makefile extension
- 'ast-text-to-upper': convert input string to upper-case.
- 'ast-text-to-lower': convert input string to lower-case.
*** Library
**** Functions
- gal_dimension_collapse_mclip_mad: MAD-clipped MAD.
- gal_dimension_collapse_mclip_fill_mad: filled MAD-clipped MAD.
- gal_dimension_collapse_mclip_std: MAD-clipped STD.
- gal_dimension_collapse_mclip_fill_std: filled MAD-clipped STD.
- gal_dimension_collapse_mclip_mean: MAD-clipped mean.
- gal_dimension_collapse_mclip_fill_mean: filled MAD-clipped mean
- gal_dimension_collapse_mclip_median: MAD-clipped median.
- gal_dimension_collapse_mclip_fill_median: filled MAD-clipped median.
- gal_dimension_collapse_mclip_number: MAD-clipped number.
- gal_dimension_collapse_mclip_fill_number: filled MAD-clipped number.
- gal_dimension_collapse_sclip_mad: sigma-clipped MAD
- gal_dimension_collapse_sclip_fill_mad: filled sigma-clipped MAD.
- gal_dimension_collapse_sclip_fill_std: filled sigma-clipped STD.
- gal_dimension_collapse_sclip_fill_mean: filled sigma-clipped mean
- gal_dimension_collapse_sclip_fill_median: filled sigma-clipped median.
- gal_dimension_collapse_sclip_fill_number: filled sigma-clipped number.
- gal_fits_hdu_datasum_encoded: the 16-character encoded sting datasum.
- gal_fits_key_list_add_date: add 'DATE' to current list of keywords.
- gal_fits_key_list_add_git_commit: add the Git commit information of the
running directory to the input list of keywords (if built with libgit2).
- gal_fits_key_list_add_software_versions: add versions of Gnustro and
its mandatory dependencies to the input list of keywords.
- gal_statistics_clip_mad: MAD clipping of given input.
- gal_statistics_mad: return median absolute deviation (MAD).
- gal_statistics_median_mad: return median and MAD.
- gal_txt_read_to_list: read all the space-separated words of the input
plain-text file as a separate node in a linked list of strings.
**** Macros
- Used by 'gal_arithmetic':
- GAL_ARITHMETIC_OP_SIGCLIP_MAD: Sigma-clipped MAD.
- GAL_ARITHMETIC_OP_SIGCLIP_MAD: Sigma-clipped STD.
- GAL_ARITHMETIC_OP_SIGCLIP_FILL_NUMBER: MAD-clipped num. of arrays.
- GAL_ARITHMETIC_OP_SIGCLIP_FILL_MEAN: MAD-clipped mean of arrays.
- GAL_ARITHMETIC_OP_SIGCLIP_FILL_MEDIAN: MAD-clipped median of arrays.
- GAL_ARITHMETIC_OP_SIGCLIP_FILL_STD: MAD-clipped STD of arrays.
- GAL_ARITHMETIC_OP_SIGCLIP_FILL_MAD: MAD-clipped STD of arrays.
- GAL_ARITHMETIC_OP_MADCLIP_NUMBER: MAD-clipped number of mult. arrays.
- GAL_ARITHMETIC_OP_MADCLIP_MEAN: MAD-clipped mean of multiple arrays.
- GAL_ARITHMETIC_OP_MADCLIP_MEDIAN: MAD-clipped median of mult. arrays.
- GAL_ARITHMETIC_OP_MADCLIP_STD: MAD-clipped STD of multiple arrays.
- GAL_ARITHMETIC_OP_MADCLIP_MAD: MAD-clipped STD of multiple arrays.
- GAL_ARITHMETIC_OP_MADCLIP_FILL_NUMBER: MAD-clipped num. of arrays.
- GAL_ARITHMETIC_OP_MADCLIP_FILL_MEAN: MAD-clipped mean of arrays.
- GAL_ARITHMETIC_OP_MADCLIP_FILL_MEDIAN: MAD-clipped median of arrays.
- GAL_ARITHMETIC_OP_MADCLIP_FILL_STD: MAD-clipped STD of arrays.
- GAL_ARITHMETIC_OP_MADCLIP_FILL_MAD: MAD-clipped STD of arrays.
- Used by 'gal_statistics_clip_sigma' and 'gal_statistics_clip_mad':
- GAL_STATISTICS_CLIP_OUTCOL_NUMBER_USED: index of final number in output.
- GAL_STATISTICS_CLIP_OUTCOL_MEAN: index of clipped mean in output.
- GAL_STATISTICS_CLIP_OUTCOL_STD: index of clipped STD in output.
- GAL_STATISTICS_CLIP_OUTCOL_MEDIAN: index of clipped median in output.
- GAL_STATISTICS_CLIP_OUTCOL_MAD: index of clipped MAD in output.
- GAL_STATISTICS_CLIP_OUTCOL_NUMBER_CLIPS: index of clipped number in output.
- GAL_STATISTICS_CLIP_OUTCOL_OPTIONAL_MEAN: bit flag for measuring mean.
- GAL_STATISTICS_CLIP_OUTCOL_OPTIONAL_STD: bit flag for measuring STD.
- GAL_STATISTICS_CLIP_OUTCOL_OPTIONAL_MAD: bit flag for measuring MAD.
** Removed features
*** Library
- gal_fits_key_write_version: redundant with the new
'gal_fits_key_list_add_software_versions'.
- gal_fits_key_write_version_in_ptr: as in gal_fits_key_write_version.
- gal_fits_key_write_config: redundant since all configuration (options)
are stored as generic keys.
** Changed features
*** All programs
- Date and versions FITS keywords are only written in the 0-th HDU of
output FITS files (along with the options names and values), not the
HDU(s) containing data. Until now, the data and versions metadata were
written in the data HDU. However, ultimately, these are also metadata
and are better suited for the 0-th HDU. For example when everything
else is identical, you expect an exactly reproducible HDU (to verify
with the FITS 'CHECKSUM' for example), but every time you run, 'DATE'
will be different! Similarly for the versions of the software or Git
commit (they may change, while your dataset doesn't). To disable these
in the 0-th HDU also, see the newly added '--outfitsno*' options in the
new features.
*** Arithmetic
- Binary operators (like '+' or 'x') that are given two integers will
crash with an error if the input operands have the same width but
different signs. Until now, they would just report a warning and print
the output. However, in large scripts, users could miss the warning and
not be aware of a possibly wrong result. Therefore it is more robust to
crash with an error rather than print a warning. This was suggested by
Sepideh Eskandarlou and implemented by Faezeh Bidjarchian after a poll
on Gnuastro's Matrix chat channel (#gnuastro:openastronomy.org).
*** CosmicCalculator
- In a non-FLRW model (when the sum of the densities is not 1.0),
CosmicCalculator no longer crashes with an error since calculations
like the radial comoving distance ('--properdistance') are still valid
in a curved cosmology. Instead a warning is printed informing the user
that with Gnuastro's current implementation angular diameter based
calculations will be wrong. This was implemented by Boud Roukema.
--angulardiamdist is the new name for the old '--angulardimdist'
option. This was necessary to avoid confusion of 'dim' in the old name
with "dimension"; 'diam' makes it clear that this is a "diameter", not
'dimension'. This was suggested by Boud Roukema.
*** Crop
- The 'ICF*' keywords are now written in the 0-th HDU of Crop's outputs
(the extension with no data, only metadata). Therefore, the WCS is now
the only metadata in the HDU containing data.
*** astscript-psf-stamp
- When no name is given to the temporary directory, the default name will
contain the center coordinates as a suffix (to avoid being confused
with other calls for other centers), and the contents of the temporary
directy will have the same filename. Until now, the temporary directory
name would be the same for different calls, and the coordinates suffix
would be in the temporary file names. This could cause confusions and
bugs (for example one call to this script could delete the temporary
directory that was being used by a later call).
*** Library
- gal_cosmology_age: a 'quiet' argument is added to disable warnings.
- gal_cosmology_proper_distance: similar 'gal_cosmology_age'.
- gal_cosmology_comoving_volume: similar 'gal_cosmology_age'.
- gal_cosmology_critical_density: similar 'gal_cosmology_age'.
- gal_cosmology_angular_distance: similar 'gal_cosmology_age'.
- gal_cosmology_luminosity_distance: similar 'gal_cosmology_age'.
- gal_cosmology_distance_modulus: similar 'gal_cosmology_age'.
- gal_cosmology_to_absolute_mag: similar 'gal_cosmology_age'.
- gal_fits_key_write: to generalize, the "title" argument has been
removed (because it is a keyword). It can also create the file if it
doesn't exist and can optionally free the list of keywords (until now,
it would always free them).
- gal_fits_key_write_in_ptr: similar to 'gal_fits_key_write'.
- gal_fits_img_write: no more 'program_name'; it is a keyword title;
added 'freekeys' argument to optionally free the input keyword list.
- gal_fits_img_write_to_type: as in 'gal_fits_img_write'.
- gal_fits_img_write_corr_wcs_str: as in 'gal_fits_img_write'.
- gal_fits_tab_write: as in 'gal_fits_img_write'.
- GAL_STATISTICS_CLIP_MAX_CONVERGE: new name for the old
'GAL_STATISTICS_SIG_CLIP_MAX_CONVERGE'. Since we now also have
MAD-clipping.
- gal_statistics_clip_sigma: new name for 'gal_statistics_sigma_clip'.
- gal_table_write: as in 'gal_fits_img_write'.
- gal_tile_full_values_write: as in 'gal_fits_img_write'.
- gal_wcs_write: as in 'gal_fits_img_write'.
** Bugs fixed
- bug #46225: Programs don't depend on libs in Makefiles; reported by
Mosè Giordano and fixed by Thorsten Alteholz.
- bug #52295: Cosmology library integrals crash for high z; fixed by
Thorsten Alteholz.
- bug #52674: Correcting Clang warnings on macOS during compilation;
fixed with help of Thorsten Alteholz and Raul
Infante-Sainz.
- bug #61476: astscript-ds9-region: output created when input file does
not exist; reported by Sepideh Eskandarlou, fixed by
Thorsten Alteholz.
- bug #64825: astscript-fits-view only takes the last HDU provided;
reported by Teet Kuumta and fixed by Raul Infante-Sainz.
- bug #64852: astscript-zeropoint: crash when input is in 0-th HDU;
reported in https://savannah.gnu.org/support/?110952; fixed
by Sepideh Eskandarlou.
- bug #64915: Segment's SKY_STD output HDU does not have WCS; reported by
Sepideh Eskandarlou.
- bug #64952: Table error message for incorrect column name was not
complete; reported by Sepideh Eskandarlou.
- bug #65005: astscript-psf-unit not accounting for --innerhdu; reported
by Ignacio Ruiz Cejudo.
- bug #65050: Use --libtool option in the TEMPLATE usage; found and fixed
by Faezeh Bidjarchian.
- bug #65055: Columns of empty FITS tables (with no rows) read in
reverse.
- bug #65084: Fits program's --skycoverage prints connected numbers for
cubes; found with help of Rahna Payyasseri Thanduparackal.
- bug #65106: Necessity of --oversample with astscript-radial-profile
when a 2D profile is to be created with '--customtable' of
MakeProfile; reported by Sepideh Eskandarlou.
- bug #65141: MakeCatalog crash when labled image is all blank; reported
by Sepideh Eskandarlou.
- bug #65149: MakeCatalog '--frac-max*-*' measurements done without
'--frac-max'; reported by Helena Domínguez Sánchez.
- bug #65194: --quiet does not disable the warning for un-given
minmapsize; reported by Boud Roukema.
- bug #65195: CosmicCalculator prevents non-flat FLRW models and angular
diameter distance only correct in flat models. Found and
fixed by Boud Roukema.
* Noteworthy changes in release 0.21 (library 19.0.0) (2023-10-20)
** New features
*** New program
- 'astscript-pointing-simulate': a new installed script that will
simplify the process of designing a pointing pattern for your observing
strategy. It takes into account the distortion of the camera, runs in
parallel and allows customizations (for example to account for
vignetting, or large blobs of bad pixels) through hooks at relevant
steps. A new tutorial has been added in the Tutorials chapter of the
book on how to use this new script. The following research note has
also been published for this script:
https://ui.adsabs.harvard.edu/abs/2023RNAAS...7..211A
*** Book
- New tutorial on a low surface brightness optimized design of a pointing
pattern using the newly added installed script in Gnuastro for
simulating the exposure map of a pointing pattern stack (it is called as
'astscript-pointing-simulate' on the command-line).
- Smaller tutorials that were distributed within the documentation of
different programs are brought into the "Tutorials" chapter.
- New "Standard deviation vs. error" sub-section added under the
MakeCatalog section. It uses real examples to clearly show the
fundamental difference between the two (which are sometimes confused
with each other). This was written with the help of Raul Infante-Sainz.
*** Configuration files
- To separate the option name and value, you can now also use the '='
character. This allows your custom configuration files to also be
loaded into a shell (with 'source') or Make (with 'include'). Until
now, only white-space characters were allowed as separators of option
names and values.
--config-prefix=STR: Given string can be a prefix of options in
configuration files. Added with the point above, this allows loading
the different configuration files of different instances of the same
program without overwriting them. See the example in the book.
*** Arithmetic
- New operators (see book for a full description):
- pool-min: Min-pooling to reduce the size of the input by calculating
the minimum of a the pixels within the pooling window
(accounting for a stride). See the new "Pooling operators"
section of the book for more. The pooling operators were
all implemented by Faezeh Bidjarchian.
- pool-max: Similar to 'pool-min' but using maximum.
- pool-sum: Similar to 'pool-min' but using sum.
- pool-mean: Similar to 'pool-min' but using mean.
- pool-median: Similar to 'pool-min' but using median.
- to-1d: convert the input operand into a 1D array, no matter how many
dimensions it has. Suggested by Faezeh Bidjarchian.
- trim: remove all fully-blank outer regions of the input dataset.
- eq-b1950-to-eq-j2000: Convert input equatorial coordinates (RA and
Dec) in the B1950 equinox to equatorial J2000
equinox.
- eq-b1950-to-ec-b1950: Same input as above; to ecliptic B1950.
- eq-b1950-to-ec-j2000: Same input as above; to ecliptic J2000.
- eq-b1950-to-galactic: Same input as above; to Galactic.
- eq-b1950-to-supergalactic: Same input as above; to Supergalactic.
- eq-j2000-to-eq-b1950: Convert input equatorial coordinates (RA and
Dec) in the J2000 equinox to equatorial B1950
equinox.
- eq-j2000-to-ec-b1950: Same input as above; to ecliptic B1950.
- eq-j2000-to-ec-j2000: Same input as above; to ecliptic J2000.
- eq-j2000-to-galactic: Same input as above; to Galactic.
- eq-j2000-to-supergalactic: Same input as above; to Supergalactic.
- ec-b1950-to-eq-b1950: Convert input ecliptic coordinates in the
B1950 equinox to equatorial B1950 equinox.
- ec-b1950-to-eq-j2000: Same input as above; to equatorial B1950.
- ec-b1950-to-ec-j2000: Same input as above; to ecliptic J2000.
- ec-b1950-to-galactic: Same input as above; to Galactic.
- ec-b1950-to-supergalactic: Same input as above; to Supergalactic
- ec-j2000-to-eq-b1950: Convert input ecliptic coordinates in the
J2000 equinox to equatorial B1950 equinox.
- ec-j2000-to-eq-j2000: Same input as above; to equatorial J2000.
- ec-j2000-to-ec-b1950: Same input as above; to ecliptic B1950.
- ec-j2000-to-galactic: Same input as above; to Galactic.
- ec-j2000-to-supergalactic: Same input as above; to Supergalactic.
- galactic-to-eq-b1950: Convert input Galactic coordinates to
equatorial B1950 equinox.
- galactic-to-eq-j2000: Same input as above; to equatorial J2000.
- galactic-to-ec-b1950: Same input as above; to ecliptic B1950.
- galactic-to-ec-j2000: Same input as above; to ecliptic J2000.
- galactic-to-supergalactic: Same input as above; to Supergalactic.
- supergalactic-to-eq-b1950: Convert input Supergalactic coordinates to
equatorial B1950 equinox.
- supergalactic-to-eq-j2000: Same input as above; to equatorial J2000.
- supergalactic-to-ec-b1950: Same input as above; to ecliptic B1950.
- supergalactic-to-ec-j2000: Same input as above; to ecliptic J2000.
- supergalactic-to-galactic: Same input as above; to Galactic.
*** ConvertType
- It is now possible to write TIFF files in the output (until now,
Gnuastro could only read TIFF files). This step was written by Fathma
Mehnoor.
*** Convolve
--conv-on-blank: do not ignore blank pixels in the convolution. This will
effectively expand the non-blank regions of your dataset into the blank
regions and only works in spatial-domain convolution. This was
suggested by Raul Infante-Sainz.
*** MakeCatalog
- New measurements:
--river-min: minimum river value around a clump.
--river-max: minimum river value around a clump.
*** Table
--info-num-cols: print the number of the input table's columns and abort.
--info-num-rows: print the number of the input table's rows and abort.
- '$_all' in column arithmetic: when an arithmetic expression contains
this string, it will be repeated independently for all the columns of
the input table.
- New operators in Table's column arithmetic:
- eq-j2000-to-flat: convert the RA and Dec columns in a table to a
flat-RA and flat-Dec (accounting for a reference point as well as any
type of projection that is available in the FITS WCS standard). This
is necessary when you are plotting points in a report or paper cover
more than a couple of square degrees on the sky. Without this
operator, significant distortions will appear when you plot spherical
coordinates (RA,Dec) on a flat plane (your paper's plot). See the
documentation for this operator in the book for more.
- eq-j2000-from-flat: the inverse of 'eq-j2000-to-flat' (useful when
designin dither patterns for example (where you know the final
shape/distanced after flatting; and want coordinates on the sphere).
*** astscript-zeropoint
--mksrc: use a custom Makefile for estimating the zeropoint, not the
default installed Makefile. This is primarily intended for debugging or
developing this script, not for normal usage.
*** Library
- gal_blank_not_minmax_coords: returns the minimum/maximum coordinates of
non-blank regions of input dataset.
- gal_blank_trim: trim all outer blank regions from the input dataset.
- gal_polygon_area_sky: area of polygon defined on celestial coordinates.
- gal_pool_min: min-pooling function, see 'pool-min' above.
- gal_pool_max: max-pooling function, see 'pool-min' above.
- gal_pool_sum: sum-pooling function, see 'pool-min' above.
- gal_pool_mean: mean-pooling function, see 'pool-min' above.
- gal_pool_median: median-pooling function, see 'pool-min' above.
- gal_statistics_mad: Calculate the Median Absolute Deviation (MAD).
- gal_statistics_median_mad: Calculate the Median and MAD.
- gal_statistics_clip_mad: Median Absolute Deviation (MAD) clipping.
- gal_tiff_write: write 'gal_data_t' to a TIFF file; written by
Fathma Mehnoor.
- gal_wcs_projection_name_to_id: convert projection names to IDs.
- gal_wcs_projection_name_from_id: convert projection IDs to their name.
- gal_wcs_coordsys_convert_points: convert the input set of points from
one celestial coordinate system to another.
- gal_wcs_coordsys_sys1_ref_in_sys2: return the longitude reference point
of the first celestial coordinate system in the second coordinate
system's longitude and latitude.
** Removed features
*** MakeNoise
- MakeNoise (with executable name 'astmknoise') has been removed from
Gnuastro. This is because the 'mknoise-*' operators of Arithmetic do
the same job, but in a much more customizable, modular and manageable
manner; allowing to mix with other operators. The "Noise basics"
sub-section of the book has been moved under the Arithmetic program's
documentation also.
** Changed features
*** Arithmetic
- mknoise-sigma-from-mean: new name for the old 'mknoise-poisson'
random number distribution.
- mknoise-poisson: now produces correct Poisson distribution output,
which can be non-symmetric in low background values and is always
integers. For a complete description and hands-on example of the
differences with 'mknoise-sigma-from-mean' and 'mknoise-sigma', see
the description of these three operators in the "Random number
generators" operators sub-section of the "Arithmetic operators"
section of the Gnuastro book.
*** MakeCatalog
- The dash in the column names of the following measurement names has
been replaced by underscore to conform with the general standard of
using underscores between words in column names (reported by Raul
Infante-Sainz). Also, in the case of '--sigclip-mean-sb-delta' the
column name didn't correspond to the option name.
--------------------------------------------------------------
Option Column name Old column name
--------------------------------------------------------------
--sigclip-mean SIGCLIP_MEAN SIGCLIP-MEAN
--sigclip-median SIGCLIP_MEDIAN SIGCLIP-MEDIAN
--sigclip-number SIGCLIP_NUMBER SIGCLIP-NUMBER
--sigclip-std SIGCLIP_STD SIGCLIP-STD
--sigclip-mean-sb SIGCLIP_MEAN_SB SIGCLIP-MEAN-SB
--sigclip-mean-sb-delta SIGCLIP_MEAN_SB_DELTA SIGCLIP-MEAN-SB-ERR
--------------------------------------------------------------
- The default extension name for the values image ('--valueshdu') is now
'INPUT-NO-SKY'. Until now, it was simply '1' (without any hint on what
what is expected by default). Recall that if the sky is not subtracted
from the values image you can use '--sky' for MakeCatalog to subtract
it before the measurements. Implemented by Sepideh Eskandarlou.
- When the input clump labels do not have the 'NUMLABS' keyword
(specifying how many clumps there are in the image, independent of the
number of objects), MakeCatalog will no longer re-label the input
clumps: the output catalog will have the same clump ids as the
labels. Until now, it would generate new labels for the clumps in such
cases (along with a new FITS image containing the clumps with the new
labels to allow you to match them). The output catalog also had the new
label, not the original labels (the old behavior was therefore very
inconvenient!).
*** Segment
- The default name of the first extension of Segment's output is now
'INPUT-NO-SKY', until now, it was 'INPUT'. This was necessary because
the first extension of the output is not the exact input file (if a
value is given to '--sky' it will be subtracted from the input in the
first extension). Implemented by Sepideh Eskandarlou.
*** astscript-psf-stamp
- After applying the signal-to-noise threshold (if it is requested), any
extra pixels that are not connected to the central target are also
masked. Such pixels can remain in rivers between bright clumps and
would cause problem in the final stack and were not removed until now.
Implemented by Sepideh Eskandarlou
*** Library
- gal_convolve_spatial: new argument to allow convolution over blank
elements.
- gal_convolve_spatial_correct_ch_edge: new argument to allow convolution
over blank elements.
- gal_polygon_area_flat: new name for the old 'gal_polygon_area'
function. This was necessary because this function assumes flat
coordinates and can lead to wrong results when used with a polygon
defined by RA,Dec for example.
- gal_statistics_clip_sigma: new name for 'gal_statistics_sigma_clip',
also, a new argument has been added to measure statistics that were not
automatically calculated during the clipping.
- gal_wcs_distortion_name_to_id: new name of gal_wcs_distortion_from_string.
- gal_wcs_distortion_name_from_id: new name of gal_wcs_distortion_to_string.
- gal_wcs_coordsys_name_to_id: new name of gal_wcs_coordsys_from_string.
** Bugs fixed
bug #64138: Arithmetic's mknoise-poisson only using first pixel value.
Reported by Irene Pintos Castro.
bug #64146: SIGCLIP column names contain dashes instead of
underlines. Reported by Raul Infante-Sainz.
bug #64148: MakeCatalog crash when using the options '--std' and/or
'sigclip-mean-sb-delta' for clumps catalog. Reported by Raul
Infante-Sainz.
bug #64153: astscript-ds9-region: '--namecol' gives a constant zero in
image-mode. Reported by Zahra Sharbaf.
bug #64186: Query: core dump when custom name given to '--dataset'. First
reported by Zohreh Ghaffari as a problem in
'astscript-select-stars' (sr #110874) and identified as a
problem in Query by Sepideh Eskandarlou.
bug #64199: info astscript-zeropoint not working. Reported by Zahra
Sharbaf.
bug #64246: Query's --information gives a crash for Gaia datasets.
Reported by Rashid Yaaqib.
bug #64250: astscript-fits-view: no message printed when input file did
not exist. Reported by Ryan Begley.
bug #64274: MakeProfiles crash for points in 3D. Found by Teet Kuumta.
bug #64303: Statistics fit --fitestimate crash when covariance matrix has
NaN. Reported Sepideh Eskandarlou.
bug #64357: Plain text metadata ignored when no name is present.
bug #64392: Arithmetic's isnotblank operator producing zeros when no
blanks present.
bug #64420: Error message of wrongly specified HDU doesn't give the
problematic option name; reported by Aaron Watkins.
bug #64431: gal_wcs_to_cd does not account for altlin==3. Reported by
Colin Orion Chandler.
bug #64541: Segment's --keepmaxnearriver has no effect.
bug #64544: Arithmetic crashes with tofilefree operator value has a
directory.
bug #64545: Accounting for CFITSIO silently appending '.gz' when file
doesn't exist. Reported by Sepideh Eskandarlou.
bug #64610: --copykeys of Fits program finds wrong key when the first
characters of the keyword names match.
bug #64615: Fits program's '--pixelareaonwcs' only accurate on equator.
bug #64635: astscript-psf-stamp's '--snthresh' option produces fully NaN
valued image when a saturated star is in the center. Found
and fixed by Sepideh Eskandarlou.
bug #64643: MakeCatalog not reporting the actual '--upmaskhdu' that was
used on standard output. Found by S. Zahra Hosseini
Shahisavandi.
* Noteworthy changes in release 0.20 (library 18.0.0) (2023-04-29)
** New features
*** New program
- astscript-zeropoint: this script is used for calibrating the pixel
values in one image (finding its "zero point") based on a reference
catalog or (any number of) reference image(s). The script allows for
checking many apertures in the same command to let you choose the
best; and will operate in parallel where necessary. The documentation
of this script contains two tutorials on how to optimally use it and
interpret its results; please read and run them once before using it.
This script was written as a team effort lead by Sepideh Eskandarlou
and including (in alphabetical order): Elham Saremi, Giulia Golini,
Raul Infante-Sainz, Samane Raji, Zahra Sharbaf, Zohreh Ghaffari.
*** Book
- New tutorial on detection and spectrum extraction from 3D data has
been added in the "Tutorials" chapter. It uses a MUSE cube and
demonstrates how to subtract the continuum, run NoiseChisel, Segment
and MakeCatalog for obtaining spectra and creating pseudo narrow-band
images of emission-lines.
- New "Shell tips" sub-section added (under the "Command-line" section
of the "Common program behavior" chapter). This sub-section contains
useful shell tips and tricks that can be useful when using Gnuastro's
programs.
*** Arithmetic
--writeall: Write all datasets on the stack as separate HDUs in the
output; this is useful in debugging incomplete Arithmetic commands.
- New operators (also available in Table).
- isnotblank: same as 'isblank not', but slightly more efficient.
This was suggested by Sepideh Eskandarlou.
- swap: swap the top two datasets on the stack of operands.
- index: return dataset of same size, with pixel values that are
integers starting from 0 and incrementing one by one. This operator
doesn't pop the top dataset from the stack, it only adds one (to
avoid extra RAM usage in most usage scenarios).
- counter: similar to 'index', but integers start with 1.
- indexonly: similar to 'index', but pops the top stack dataset.
- counteronly: similar to 'counter', but pops the top stack dataset.
- constant: replace all elements of input image or column with the
given constant value (for example to set all pixels in an image to
NaN or zero), or to give identifiers to each source catalog when
adding rows from different catalogs, see the documentation for
complete examples.
- counts-to-nanomaggy: convert counts to Nanomaggy (with fixed
zeropoint of 22.5, used as the pixel units of many surveys like
SDSS). This was suggested by Giulia Golini.
- nanomaggy-to-counts: convert nanomaggy to counts. This was suggested
by Giulia Golini.
- box-vertices-on-sphere: calculate the RA,Dec of vertices of the four
vertices of a rectangle from its center and width along RA and
Dec. This takes into account the curved nature of the coordinate
system. Added after discussion with Martin Kuemmel.
- number-neighbors: Return the number of non-zero neighbors of each
non-zero pixel in a binary image.
- New operators (only in the Arithmetic program):
- interpolate-meanngb: interpolate blank values with mean of the
requested number of nearest neighbors.
- Alternative (shorter) names for existing operators, added after
discussion with Samane Raji.
- u8: same as 'uint8' (to convert to unsigned 8-bit integers).
- i8: same as 'int8' (to convert to signed 8-bit integers).
- u16: same as 'uint16' (to convert to unsigned 16-bit integers).
- i16: same as 'int16' (to convert to signed 16-bit integers).
- u32: same as 'uint32' (to convert to unsigned 32-bit integers).
- i32: same as 'int32' (to convert to signed 32-bit integers).
- u64: same as 'uint64' (to convert to unsigned 64-bit integers).
- i64: same as 'int64' (to convert to signed 64-bit integers).
- f32: same as 'float32' (to convert to 32-bit floating point).
- f64: same as 'float64' (to convert to 64-bit floating point).
*** CosmicCalculator
- Spectral line database has been increased to 235 spectral lines in the
UV and optical (previously only had 41 lines!) from:
http://astronomy.nmsu.edu/drewski/tableofemissionlines.html
To see the full list, run 'astcosmiccal --listlines'.
--lineunit: allows you to specify the units of the displayed spectral
line wavelengths. Currently, it take four units: 'm', 'micron', 'nm'
and 'angstrom'. We can add any other unit easily, just let us know.
*** Crop
--append: if the output file already exists, append the cropped image
HDU to the already existing HDUs of the file. Without this option, any
existing HDUs in the output file will be removed (default behavior).
--metaname: Specify the name of the cropped output HDU (value to the
'EXTNAME' keyword in FITS).
*** MakeCatalog
- Book: with the increasing number of possible measurements the
"MakeCatalog measurements" section of the Gnuastro book has been
broken into separate sub-section and contextually similar measurements
are grouped separately there.
--sigclip-mean-sb: surface brightness (over one pixel's area in
arcsec^2) of the sigma-clipped mean of the values. This is useful in
scenarios where you want to compare surface brightness values
independent of the object's area, and by removing outliers (for
example in a radial profile). See the description of this option in
the book for more. This was added after a discussion by Ignacio
Trujillo and Zahra Sharbaf.
--sigclip-mean-sb-err: the error in '--sigclip-mean-sb' but using the
sigma-clipped standard deviation of the values as the error, not the