Until now, the copyright on all the Gnuastro source files was 2024. But
today, we entered 2025!

With this commit, the copyright statement of all the files have been
updated to an ending year of 2025.

Until now, the copyright date on all the files ended in 2023. However, In
the last couple of hours we have entered 2024 and 2023 is no longer up to
date!

With this commit, all the copyright years now end in 2024.

Until now, the latest copyright year on all the files was 2022. But it is
one month that we have moved into 2023.

With this commit, the latest year in the copyright statements is 2023.

Until now, the ending years in the copyright statements of Gnuastro's
source were 2021. But 2022 has started from today, so it was time for an
update!

With this commit, all the ending copyright years in all the Gnuastro source
files have been changed to 2022.

Since the first commit of Gnuastro (09ac8974) was on the 1st of January
in 2015, Gnuastro is now officially 7 years old! Unofficially (before that
first commit), its one year older!

Having entered 2021, it was necessary to correct the copyright year.

I also noticed that in the French webpage, we still had a notice for GSoC
2020, so that was also commented.

Until now, Gnuastro's quoted strings used a grave accent (`) for opening a
quote and an apostrophe for closing it, something like `this'. But as noted
by Rafael Morales, this is not very clear to the eye.

So I had a look at the GNU Coding Standards, and noticed that under the
section "Quote Characters", it also recommends this style: "Although GNU
programs traditionally used 0x60 (`) for opening and 0x27 (') for closing
quotes, nowadays quotes `like this' are typically rendered asymmetrically,
so quoting "like this" or 'like this' typically looks better."

With this commit, this has been corrected in all of Gnuastro, both in the
printed messages and also the comments in the code.

Also, again as suggested by Rafael, to give a unified interface for quoting
strings, all the double quotations have been removed in the printed
messages (in the C source they looked like '\"'). They are now also shown
with an apostrophe.

In a few hours the year 2020 will start, so I updated all the copyright
notices in the source files (and also the outputs of programs with
`--version') from 2019 to 2020.

A copyright statement was missing on the ChangeLog and the two figures in
the version controlled source. So it was added.

From this commit, the top level `src/' directory is called `bin/' and all
occurances of `src/' within the Gnuastro files were also corrected. This
change was done since `src' is too generic and could cause confusion: is it
the source of the programs and utilities? How does it relate to `lib/'?

This new name was chosen based on the final installation directory of its
(main) contents: the executables of the programs within this directory are
installed in `prefix/bin/', similar to how the libraries (in the top level
`lib/' directory) are installed in `prefix/lib/'.

The ChangeLog update was stopped in each commit following the discussion in
task #13779. However, this choice was not reflected in the ChangeLog its
self. So if someone would open the ChangeLog, they would think the last
change was on November 5th, 2015! To avoid such confusions, an item was
added to the top of the ChangeLog explaining how we have stopped updating
it. Two new tasks have thus been defined:

 - task #14007: to automatically generate the ChangeLog from the version
   controlled history.

 - task #14008: to discuss if it is good to adopt the ChangeLog formatting
   in the commit messages.

This finishes task #13779.

We are planning on removing the ChangeLog (task #13779), but until
then, it has to be updated. The only change was in the "Why C
programming language?" section. The newly added sections are totally
new and are thus not included in the ChangeLog.

Fixes taks#13767.  Relying on CFITSIO, Gnuastro was already able to read
files compressed with fpack, it was just that it did not accept the
standard extension.

Fixes bug#45380: if optimization flag -O2 or higher is used, a bus error
is signaled when trying to access "p->cp.nolog" after calling the
function pointed to by modefunction.  Not using modefunction and calling
the appropriate function "by hand" avoids this crash.

Fixes bug#46212.

Until now the maximum standard deviation in the meshes was used as the
depth. However, the maximum has a strong scatter such that one outling
mesh can completely shift to unreasonable values. So, although the
maximum standrard deviation is still reported by NoiseChisel, but
Makecatalog uses the median standard deviation.

I also added a median function to `statistics.[ch]'.

A tiny spelling mistake was also fixed in MakeCatalog's `--help'
output.

Since ImageWarp is also a starting point in reading images with
non-standard WCS information, I also added this option to
ImageWarp. If it is needed in all applications, these options can be
added to the common arguments easily now. The main readfitswcs
function in lib/fitsarrayvv.[ch] was changed to allow these two values
for easy generalization if needed.

Previously the surface brightness limit and magnitude limit were
defined in terms of a fixed projected area (arcsec^2) and the S/N of
the objects or clumps. But in the first case, the projected area
should not be used since noise is only dependent on the pixel and the
pixel is the unit of our data-collection. Its physical or projected
size are irrelevant. In the latter case, the area used to find the S/N
was not clear and thus this value was very unrealistic. Therefore I
tried to explain how to use number counts (from the outputs of
MakeCatalog) in order to estimate the limiting magnitude.

When the scripts are run in parallel (for example within a Makefile
called with the -j option) then the log files can cause problems when
you want to clean them up in the end. One option was to set the log
file name to be based on the output file name, but I have not seen
that commonly and it would require a lot of extra code. But now, when
the log file doesn't matter, the user can simply igore it being made.

Convolve was not reading the WCS information of the input. A line is
now added in the ui.c to do the job.

The individual outputs of MakeProfiles were simply named as, for
example, 0.fits, 1.fits and so on. But this would not work when
MakeProfiles is to be run in parallel and is also ambiguous. So now
the row numbers are suffixed by the output file name and put into the
output directory.

The output directory and file name fixing in MakeProfiles was also
bugy with problems I hadn't noticed before, so I fixed it.

In order to do this job, two functions were added in checkset.c:
`dirpart' and `notdirpart'.

A new subsection was also added to the manual explaining the two basic
methods to run processes simultaneously.

It was necessary that the branch for the NoiseChisel paper
reproduction (version 0.0) would be separate from all the work that
was done on the programs after the last proof submission of the
paper.

After the paper was published, I completed the reproduction system and
in the process, some issues needed to be added or fixed in the
programs. They were all applied to that branch. But they are all also
necessary for the future versions of Gnuastro, so they were done
independently here.

The following changes were made to make the first reproducible arXiv
release (arxiv:1505.01664, v2). The major additions are:

  - The `--onlydirconf' option was added to the common options. When
    called, only the current directory configuration files are read
    (not the system or user wide configuration options). This will
    allow much easier control over what parameters go into the running
    of a program, which is very useful when reproducibility is
    concerned.

 - The `--onlyversion' option was added to the common options. When
   called, the version of the program is checked with the value to
   this option, and if they aren't exactly equal, the program will not
   run. This is crucial for reproducibility.

 - Added the READ_COMMONOPTIONS_FROM_CONF macro to configfiles.h to
   read common configuration options from a configuration file. Until
   now, there was only the `--numthreads' option, and each program had
   a step to read it, but with the new `--onlydirconf' option, it
   required now too much repetition to be read in each program
   independantly. So this macro was defined and is used by all the
   programs.

 - Added the macro PRINT_COMMONOPTIONS, similar to above, this is done
   to make things more clearer and remove bugs.

 - Added the `astrthreads.h' headers to `spatialconvolve.h' to avoid
   problems with systems that don't support pthread_barrier_t.

 - Added the `--mirrordist' option to ImageStatistics to set the
   maximum distance beyond the mirror.

 - Added the `--maxblankfrac' option to ImageWarp so if a large
   fraction of an output pixel is covered by blank pixels, it is set
   to blank. Before the blank fraction was ignored.

The --makekernel option in Convlve, now gets an argument that is the
maximum radius to keep non-zero kernel values. The output kernel will
also be cropped to only be large enough to have no only-zero rows or
columns.

This was done because the high frequencies were set to zero during the
division and so the larger radii would become too flat. So the user
can specify how far out the final kernel should be.

Also a minor bug fix in NoiseChisel: The check to see if the number of
clumps or detections is more than the minimum specified by the user is
now done before anything else. In the case of zero good S/N values,
this would cause a problem in the next steps.

Convolve now has a `--makekernel' option which will find the kernel
which can be used to match the PSFs of two images.

Two new sections were added to explain the Discrete Fourier transform
and how they change in 2 dimensions. I also went through all the other
explanations and made the whole frequency space explanations more
cogent.

There were two bugs that are now fixed:

  - MakeCatalog: In a grown clump label image, the detections that
    have one or no clumps are fully filled. So there is no river
    pixels for them. I had not corrected the clump S/N calculations in
    MakeCatalog also consider this. Now this issue is corrected.

  - MakeCatalog: Although brightness was correctly calculated, in the
    final printing, it would be divided by the area! It is now fixed.

  - NoiseChisel: When finding the S/N quantile for clumps, it was
    mistakenly using the detection S/N quantile for both clumps and
    detections! Now it uses the correct value. Until now, these two
    were always the same, so I hadn't noticed this!

With this new option, the user can ask to save the grown clumps image
instead of the original clumps image in the output.

Additions
=========

- ImageCrop: Added the two options `--hstartwcs' and `--hendwcs' to
  read specific portions of the input file's header. As explained in
  the manual this is necessary now that WCSLIB includes distortion in
  the coordinates but old FITS files were written with the assumption
  that WCSLIB does not support them.

Bug fixes
=========

- NoiseChisel: The flux weighted center of the detections (which are
  used to find the sky standard deviation on the mesh grid) used the
  flux of all the pixels. But a weight can only have a positive value!
  So the negative values would make the result go wrong. Now, the xys
  array has a third column to keep the sum of positive flux pixels
  which were used as weights in finding the flux weighted center.

To get the river information of each clump, I had mistakenly just
copied from the getclumpinfo function in NoiseChisel's
clumps.c. However, over there all the clumps were within one
detection. So the IDs of neighboring clumps (to a river pixel) were
unique. But in MakeCatalog, two clumps can be separated by one river
pixel and belong to separate objects with different object IDs.

Another consequence was to use the object ID from the neighbor of the
river pixel and not the object on which the river lies.

The total brightness of the clump is also stored internally. Only when
we want to write it to the catalog, do we subtract the average river
flux multiplied by the number of clump pixels.

In the fitsarrayvv.c functions, I had mistakenly used a variable
called `numblank'. Some time in the past, this variable probably
actually did mean the number of blanks. But now it was only a boolean
value specifying if there are any blanks in the input or not. So I
renamed all wrong occurances of `numblank' (as relates to the input
image and FITS blank pixels) to `anyblank' which correctly represents
what this variable holds.

Note that NoiseChisel's segmentation does make use of a similarly
termed variable for the number of pixels left to grow. That is a
different usage and those variable names were left unchanged.

Until now, in labeling the dilated image, I used 4-connected
components. However, in the segmentation step, the 8-connected
neighbors of each river pixel are checked. When the rivers of the
edges of the detections are checked, these two different neighbor
definitions would cause a problem: two separate 4-connected regions
can be 8-connected.

The fix of this bug was a simple change of `4' to `8' in the main
NoiseChisel function. However it took me several (very frustrating)
hours to find it! While Valgrind's messages are usually very useful,
in this case (because they resulted from my own convention), they
caused even more confusion. The valgrind error said something like
this: "You are trying to reference an internal array of another
function that was allocated and freed in another funciton". In short
the array it was complaining about didn't exist when the function
giving the error was called!!! This really confused me! I finally
found it through individual checks of all the detections without using
Valgrind.

In the meantime, I also removed all the checks for NaN (masked) pixels
in oversegment (clumps.c). Since NaN pixels are no longer in the
indexs that are fed to this function.

Throughout Gnuastro, until now, I had used flux and brightness
interchangeably while this is only true for one pixel. So for example
using terms like "total flux" for the sum of pixels is wrong. I have
explained everything completely in the "Flux Brightness and magnitude"
subsection of the manual. All the programs (mainly variable names and
option explanations) and the manual were corrected to make the proper
distinction between these two terms.

Also the other MathJax scripts that might be necessary for the HTML
webpages to be run with LibreJS were also added. However, LibreJS
still doesn't recognize the scripts. I have asked
help-librejs@gnu.org.

The detection limit of the image for clumps and objects is now
reported in the output of MakeCatalog. In order to do this, I had to
save the S/N thresholds in NoiseChisel to header keywords in the
NoiseChisel outputs. MakeCatalog then reads those headers and makes
the information. The manual also contains a complete explanation.

I also had to update the old "readkeyword" function in fitsarrayvv.c
to "readkeywords". Now it can read as many keywords as the user wants.

Until now, MakeCatalog was not prepared to handle blank pixels in the
labeled images. But now, the labeled pixels are easily ignored.

I also added the names of the input files in the catalogs and also a
column specifying the 5 sigma magnitude in the input image.

NoiseChisel underwent to large changes. Mainly as a result of the
previous addition to ImageCrop where an arbitary polygon could be
cropped. So I had to find a way to treat large blank areas in a the
image.

  1. The S/N value was previously found on each large mesh separately
     and would be interpolated and smoothed! On each mesh there
     usually isn't enough area to provide the right number of
     points. Unlike the sky and its standard deviation (noise) which
     can vary over the image, the Signal to noise ratio will only
     change when the data have different noise properties, for example
     more or less correlated noise. This can happen in an image,
     especially in surveys but it doesn't have to be on the same grid,
     so there will be problems.

     Now that ImageCrop can crop out an arbitary polygon, we can crop
     out the parts that have similar noise properties and work on
     them. Over the image the number statistics will be much better
     (for example in estimating the quantile). So NoiseChisel will now
     calculate the detection and segmentation Signal to noise ratios
     over the full image, not within one mesh.

  2. Since I wanted to work on a random polygon a large area of the
     image would be blank. Until now, I had not really put too much
     emphasis on blank pixels, but since their number significantly
     increased I had to find a solution. Now NoiseChisel's functions
     also account for unsigned char and long type blank values too.

I had forgot to confirm if the old `--inpolygon' option actually
worked! So I tried it out and saw that it is much better if it is
`--outpolygon'! Since by default only the region inner to the polygon
is shown, so the old method was mostly redundant. In the few cases
that the user would want to keep the outer parts, they would have to
go and change all their configuration files! Now this option is not in
configuration files any more.

A test was also written for this option.

The polygon mode was tested in the WCS mode and some corrections
needed to be made for the steps I wrote last night. It now works very
nicely both in image mode and WCS mode.

Two tests were also added to accompany this new feature.

MakeCatalog's ui.c is complete for now (all the inputs are read). In
order to make things clear and elegant, I made a clear function to
check for data in other extensions of an image or in another file
depending on the user input.

Until now, there was a macro in checkset.h and also a function in
fitsarrayvv.c which done the job almost similarly. The mask checking
functions of all the programs were updated.