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[gnuastro-commits] master 2cda36b: Preparing for version 0.13, new --pix
|
From: |
Mohammad Akhlaghi |
|
Subject: |
[gnuastro-commits] master 2cda36b: Preparing for version 0.13, new --pixelscale in astfits |
|
Date: |
Sun, 6 Sep 2020 20:32:19 -0400 (EDT) |
branch: master
commit 2cda36b6f6578a04a721f1fe1e9f558da925eb93
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Preparing for version 0.13, new --pixelscale in astfits
With this commit, Gnuastro is being prepared for version 0.13.
In the middle, the issue of reading the pixel-scale from any FITS image
came up in another discussion (because some FITS creators don't write the
CDELT keywords!). Since it was very easy to implement, I also added an
option to do this in the FITS program. Ideally those parts should have been
done in a separate commit, but I had already staged some of the changes for
version 0.13 and didn't have the time to re-organize the staged files.
---
NEWS | 6 ++--
bin/fits/args.h | 13 +++++++
bin/fits/fits.c | 61 ++++++++++++++++++++++++++++---
bin/fits/main.h | 1 +
bin/fits/ui.c | 3 +-
bin/fits/ui.h | 1 +
doc/announce-acknowledge.txt | 10 ------
doc/gnuastro.en.html | 8 ++---
doc/gnuastro.fr.html | 8 ++---
doc/gnuastro.texi | 86 +++++++++++++++++++++++++++-----------------
doc/release-checklist.txt | 6 ++--
11 files changed, 141 insertions(+), 62 deletions(-)
diff --git a/NEWS b/NEWS
index 850b179..58253e1 100644
--- a/NEWS
+++ b/NEWS
@@ -3,7 +3,7 @@ GNU Astronomy Utilities NEWS -*-
outline -*-
Copyright (C) 2015-2020 Free Software Foundation, Inc.
See the end of the file for license conditions.
-* Noteworthy changes in release X.XX (library XX.X.X) (XXXX-XX-XX) [stable]
+* Noteworthy changes in release 0.13 (library 11.0.0) (2020-09-06) [stable]
** New features
@@ -40,6 +40,8 @@ See the end of the file for license conditions.
astcosmiccal --obsline=lyalpha,4000 --listlinesatz
FITS:
+ - New '--pixelscale' option will return the size of pixels in each
+ dimension in the "world coordinates".
- New '--wcsdistortion' option allows conversion between the various WCS
distortions. For example if you have a FITS image with the TPV-based
WCS distortion, and you would like to convert it to a SIP-based
@@ -140,7 +142,7 @@ See the end of the file for license conditions.
bug #58696: Warp with --centeroncorner --scale making wrong size.
bug #58774: Warp' s output on a cube is a 2D image or wrong size.
bug #58809: NoiseChisel not removing negative outlier tiles.
- bug #58833: Segment crashes when detetion map has blank pixels
+ bug #58833: Segment crashes when detection map has blank pixels.
bug #58835: Floating point errors when comparing pixel scale in Crop.
bug #58898: Plain text string columns touching next, clear first character.
bug #58901: Blank values for non-standard integer types in FITS tables.
diff --git a/bin/fits/args.h b/bin/fits/args.h
index 254b228..6de69dc 100644
--- a/bin/fits/args.h
+++ b/bin/fits/args.h
@@ -115,6 +115,19 @@ struct argp_option program_options[] =
GAL_OPTIONS_NOT_MANDATORY,
GAL_OPTIONS_NOT_SET
},
+ {
+ "pixelscale",
+ UI_KEY_PIXELSCALE,
+ 0,
+ 0,
+ "Return the pixel-scale of the HDU's WCS.",
+ UI_GROUP_EXTENSION,
+ &p->pixelscale,
+ GAL_OPTIONS_NO_ARG_TYPE,
+ GAL_OPTIONS_RANGE_0_OR_1,
+ GAL_OPTIONS_NOT_MANDATORY,
+ GAL_OPTIONS_NOT_SET
+ },
diff --git a/bin/fits/fits.c b/bin/fits/fits.c
index d0ab3a9..790fdd4 100644
--- a/bin/fits/fits.c
+++ b/bin/fits/fits.c
@@ -27,6 +27,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <string.h>
#include <unistd.h>
+#include <gnuastro/wcs.h>
#include <gnuastro/list.h>
#include <gnuastro/fits.h>
#include <gnuastro/blank.h>
@@ -283,7 +284,7 @@ fits_datasum(struct fitsparams *p)
fitsfile *fptr;
unsigned long datasum, hdusum;
- /* Read the first extension (necessary for reading the rest). */
+ /* Read the desired extension (necessary for reading the rest). */
fptr=gal_fits_hdu_open(p->filename, p->cp.hdu, READONLY);
/* Calculate the checksum and datasum of the opened HDU. */
@@ -302,6 +303,57 @@ fits_datasum(struct fitsparams *p)
static void
+fits_pixelscale(struct fitsparams *p)
+{
+ size_t i, ndim;
+ double *pixelscale;
+ struct wcsprm *wcs;
+ int nwcs=0;
+
+ /* Read the desired WCS. */
+ wcs=gal_wcs_read(p->filename, p->cp.hdu, 0, 0, &nwcs);
+
+ /* If a WCS doesn't exist, let the user know and return. */
+ if(wcs)
+ ndim=wcs->naxis;
+ else
+ error(EXIT_FAILURE, 0, "%s (hdu %s): no WCS could be read by WCSLIB, "
+ "hence the pixel-scale cannot be determined", p->filename,
+ p->cp.hdu);
+
+ /* Calculate the pixel-scale in each dimension. */
+ pixelscale=gal_wcs_pixel_scale(wcs);
+
+ /* If not in quiet-mode, print some extra information. We don't want the
+ last number to have a space after it, so we'll write the last one
+ outside the loop.*/
+ if(p->cp.quiet==0)
+ {
+ printf("Basic information for --pixelscale (remove extra info "
+ "with '--quiet' or '-q')\n");
+ printf(" Input: %s (hdu %s) has %zu dimensions.\n", p->filename,
+ p->cp.hdu, ndim);
+ printf(" Pixel scale in each dimension:\n");
+ for(i=0;i<ndim;++i)
+ printf(" %zu: %g (%s/pixel)\n", i+1, pixelscale[i], wcs->cunit[i]);
+ }
+ else
+ {
+ for(i=0;i<ndim-1;++i)
+ printf("%g ", pixelscale[i]);
+ printf("%g\n", pixelscale[ndim-1]);
+ }
+
+ /* Clean up. */
+ wcsfree(wcs);
+ free(pixelscale);
+}
+
+
+
+
+
+static void
fits_hdu_remove(struct fitsparams *p, int *r)
{
char *hdu;
@@ -428,10 +480,9 @@ fits(struct fitsparams *p)
case FITS_MODE_HDU:
/* Options that must be called alone. */
- if(p->numhdus)
- fits_hdu_number(p);
- else if(p->datasum)
- fits_datasum(p);
+ if(p->numhdus) fits_hdu_number(p);
+ else if(p->datasum) fits_datasum(p);
+ else if(p->pixelscale) fits_pixelscale(p);
/* Options that can be called together. */
else
diff --git a/bin/fits/main.h b/bin/fits/main.h
index a7ea949..cf99137 100644
--- a/bin/fits/main.h
+++ b/bin/fits/main.h
@@ -62,6 +62,7 @@ struct fitsparams
gal_list_str_t *cut; /* Copy ext. to output and remove. */
uint8_t numhdus; /* Print number of HDUs in FITS file. */
uint8_t datasum; /* Calculate and print HDU's datasum. */
+ uint8_t pixelscale; /* Calculate and print HDU's pixelscale. */
uint8_t primaryimghdu; /* Copy/cut HDU into primary HDU. */
uint8_t printallkeys; /* Print all the header keywords. */
uint8_t date; /* Set DATE to current time. */
diff --git a/bin/fits/ui.c b/bin/fits/ui.c
index c1d3d5b..616b164 100644
--- a/bin/fits/ui.c
+++ b/bin/fits/ui.c
@@ -362,7 +362,8 @@ ui_read_check_only_options(struct fitsparams *p)
}
/* Same for the extension-related options */
- if( p->remove || p->copy || p->cut || p->numhdus || p->datasum )
+ if( p->remove || p->copy || p->cut || p->numhdus || p->datasum
+ || p->pixelscale )
{
/* A small sanity check. */
if(p->mode!=FITS_MODE_INVALID)
diff --git a/bin/fits/ui.h b/bin/fits/ui.h
index 9dbb6e0..8b3dc16 100644
--- a/bin/fits/ui.h
+++ b/bin/fits/ui.h
@@ -71,6 +71,7 @@ enum option_keys_enum
automatically). */
UI_KEY_TITLE = 1000,
UI_KEY_DATASUM,
+ UI_KEY_PIXELSCALE,
UI_KEY_OUTHDU,
UI_KEY_COPYKEYS,
UI_KEY_PRIMARYIMGHDU,
diff --git a/doc/announce-acknowledge.txt b/doc/announce-acknowledge.txt
index 9f742ee..8065cab 100644
--- a/doc/announce-acknowledge.txt
+++ b/doc/announce-acknowledge.txt
@@ -1,15 +1,5 @@
Alphabetically ordered list to acknowledge in the next release.
-Marjan Akbari
-Carlos Allende Prieto
-Leindert Boogaard
-Mark Calabretta
-Alexey Dokuchaev
-Raúl Infante Sainz
-Samane Raji
-Joanna Sakowska
-Zahra Sharbaf
-Ole Streicher
diff --git a/doc/gnuastro.en.html b/doc/gnuastro.en.html
index d078a61..ecc29d1 100644
--- a/doc/gnuastro.en.html
+++ b/doc/gnuastro.en.html
@@ -86,9 +86,9 @@ for entertaining and easy to read real world examples of using
<p>
The current stable release
- is <a href="http://ftp.gnu.org/gnu/gnuastro/gnuastro-0.12.tar.gz";>Gnuastro
- 0.12</a> (May 20th, 2020).
- Use <a href="http://ftpmirror.gnu.org/gnuastro/gnuastro-0.12.tar.gz";>a
+ is <a href="http://ftp.gnu.org/gnu/gnuastro/gnuastro-0.13.tar.gz";>Gnuastro
+ 0.13</a> (September 6th, 2020).
+ Use <a href="http://ftpmirror.gnu.org/gnuastro/gnuastro-0.13.tar.gz";>a
mirror</a> if possible.
<!-- Comment the test release notice when the test release is not more
@@ -99,7 +99,7 @@ for entertaining and easy to read real world examples of using
To stay up to date, please subscribe.</p>
<p>For details of the significant changes in this release, please see the
- <a
href="https://git.savannah.gnu.org/cgit/gnuastro.git/plain/NEWS?id=gnuastro_v0.12";>NEWS</a>
+ <a
href="https://git.savannah.gnu.org/cgit/gnuastro.git/plain/NEWS?id=gnuastro_v0.13";>NEWS</a>
file.</p>
<p>The
diff --git a/doc/gnuastro.fr.html b/doc/gnuastro.fr.html
index e7db1b1..f5da5ba 100644
--- a/doc/gnuastro.fr.html
+++ b/doc/gnuastro.fr.html
@@ -85,15 +85,15 @@ h3 { clear: both; }
<h3 id="download">Téléchargement</h3>
<p>La version stable actuelle
- est <a href="https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.12.tar.gz";>Gnuastro
- 0.12</a> (sortie le 20 mai
- 2020). Utilisez <a
href="https://ftpmirror.gnu.org/gnuastro/gnuastro-0.12.tar.gz";>un
+ est <a href="https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.13.tar.gz";>Gnuastro
+ 0.13</a> (sortie le 6 septembre
+ 2020). Utilisez <a
href="https://ftpmirror.gnu.org/gnuastro/gnuastro-0.13.tar.gz";>un
miroir</a> si possible. <br />Les nouvelles publications sont annoncées
sur <a
href="https://lists.gnu.org/mailman/listinfo/info-gnuastro";>info-gnuastro</a>.
Abonnez-vous pour rester au courant.</p>
<p>Les changements importants sont décrits dans le
- fichier <a
href="https://git.savannah.gnu.org/cgit/gnuastro.git/plain/NEWS?id=gnuastro_v0.12";>
+ fichier <a
href="https://git.savannah.gnu.org/cgit/gnuastro.git/plain/NEWS?id=gnuastro_v0.13";>
NEWS</a>.</p>
<p>Le lien
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index c45b1dd..f43e6d7 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -1391,6 +1391,7 @@ Work on improving Gnuastro and making it mature is now
continuing primarily in t
In general, we would like to gratefully thank the following people for their
useful and constructive comments and suggestions (in alphabetical order by
family name):
Valentina Abril-melgarejo,
Marjan Akbari,
+Carlos Allende Prieto,
Hamed Altafi,
Roland Bacon,
Roberto Baena Gall@'e,
@@ -1402,6 +1403,7 @@ Stefan Br@"uns,
Fernando Buitrago,
Adrian Bunk,
Rosa Calvi,
+Mark Calabretta
Nushkia Chamba,
Benjamin Clement,
Nima Dehdilani,
@@ -1438,11 +1440,14 @@ Mamta Pommier,
Marcel Popescu,
Bob Proulx,
Joseph Putko,
+Samane Raji,
Teymoor Saifollahi,
+Joanna Sakowska,
Elham Saremi,
Yahya Sefidbakht,
Alejandro Serrano Borlaff,
Zahra Sharbaf,
+David Shupe
Jenny Sorce,
Lee Spitler,
Richard Stallman,
@@ -1462,7 +1467,7 @@ Johannes Zabl.
The GNU French Translation Team is also managing the French version of the top
Gnuastro webpage which we highly appreciate.
Finally we should thank all the (sometimes anonymous) people in various online
forums which patiently answered all our small (but imporant) technical
questions.
-All work on Gnuastro has been voluntary, but the authors are most grateful to
the following institutions (in chronological order) for hosting us in our
research.
+All work on Gnuastro has been voluntary, but the authors are most grateful to
the following institutions (in chronological order) for hosting/supporting us
in our research.
Where necessary, these institutions have disclaimed any ownership of the parts
of Gnuastro that were developed there, thus insuring the freedom of Gnuastro
for the future (see @ref{Copyright assignment}).
We highly appreciate their support for free software, and thus free science,
and therefore a free society.
@@ -1471,6 +1476,7 @@ Tohoku University Astronomical Institute, Sendai, Japan.@*
University of Salento, Lecce, Italy.@*
Centre de Recherche Astrophysique de Lyon (CRAL), Lyon, France.@*
Instituto de Astrofisica de Canarias (IAC), Tenerife, Spain.@*
+Google Summer of Code 2020
@end quotation
@@ -2135,7 +2141,7 @@ $ astcrop --mode=wcs -h0 --output=flat-ir/xdf-f160w.fits \
The only thing varying in the three calls to Gnuastro's Crop program is the
filter name!
Note how everything else is the same.
-In such cases, you should generally avoid repeating a command manually, it is
prone to many bugs, and as you see, it is very hard to read (didn't you
suddently write a @code{7} as an @code{8}?).
+In such cases, you should generally avoid repeating a command manually, it is
prone to many bugs, and as you see, it is very hard to read (didn't you
suddenly write a @code{7} as an @code{8}?).
To simplify the command, and later allow work on more filters, we can use the
shell's @code{for} loop as shown below.
Notice how the place where the filter names (@file{f105w}, @file{f125w} and
@file{f160w}) are used above, have been replaced with @file{$f} (the shell
variable that @code{for} will update in every loop) below.
@@ -2167,18 +2173,29 @@ Gnuastro has the Arithmetic program for such cases, and
we'll introduce it later
@cindex Scales, coordinate
This is the deepest image we currently have of the sky.
The first thing that comes to mind may be this: ``How large is this field on
the sky?''.
-The FITS world coordinate system (WCS) meta data standard contains the key to
answering this question: the @code{CDELT} keyword@footnote{In the FITS
standard, the @code{CDELT} keywords (@code{CDELT1} and @code{CDELT2} in a 2D
image) specify the scales of each coordinate.
-In the case of this image it is in units of degrees-per-pixel.
-See Section 8 of the
@url{https://fits.gsfc.nasa.gov/standard40/fits_standard40aa-le.pdf, FITS
standard} for more.
-In short, with the @code{CDELT} convention, rotation (@code{PC} or @code{CD}
keywords) and scales (@code{CDELT}) are separated.
+The FITS world coordinate system (WCS) meta data standard contains the key to
answering this question.
+Run the following command to see all the FITS keywords (metadata) for one of
the images (mostly the same with the other filters because they were are scaled
to the same region of Sky):
+
+@example
+astfits flat-ir/xdf-f160w.fits -h1
+@end example
+
+Look into the keywords grouped under the `@code{World Coordinate System
(WCS)}' title.
+These keywords define how the image relates to the outside world.
+In particular, the @code{CDELT*} keywords (or @code{CDELT1} and @code{CDELT2}
in this 2D image) contain the ``Coordinate DELTa'' (or change in coordinate
units) with a change in one pixel.
+But what is the units of each ``world'' coordinate?
+The @code{CUNIT*} keywords (for ``Coordinate UNIT'') have the answer.
+In this case, both @code{CUNIT1} and @code{CUNIT1} have a value of @code{deg},
so both ``world'' coordiantes are in units of degrees.
+We can thus conclude that the value of @code{CDELT*} is in units of
degrees-per-pixel@footnote{With the FITS @code{CDELT} convention, rotation
(@code{PC} or @code{CD} keywords) and scales (@code{CDELT}) are separated.
In the FITS standard the @code{CDELT} keywords are optional.
When @code{CDELT} keywords aren't present, the @code{PC} matrix is assumed to
contain @emph{both} the coordinate rotation and scales.
Note that not all FITS writers use the @code{CDELT} convention.
So you might not find the @code{CDELT} keywords in the WCS meta data of some
FITS files.
However, all Gnuastro programs (which use the default FITS keyword writing
format of WCSLIB) write their output WCS with the @code{CDELT} convention, even
if the input doesn't have it.
-If your dataset doesn't use the @code{CDELT} convention, you can feed it to
any (simple) Gnuastro program (for example Arithmetic) and the output will have
the @code{CDELT} keyword.}.
+If your dataset doesn't use the @code{CDELT} convention, you can feed it to
any (simple) Gnuastro program (for example Arithmetic) and the output will have
the @code{CDELT} keyword.
+See Section 8 of the
@url{https://fits.gsfc.nasa.gov/standard40/fits_standard40aa-le.pdf, FITS
standard} for more}.
-With the commands below, we'll use @code{CDELT} (along with the image size) to
find the answer.
+With the commands below, we'll use @code{CDELT} (along with the image size) to
find the answer of our initial question: ``how much of the sky does this image
cover?''.
The lines starting with @code{##} are just comments for you to read and
understand each command.
Don't type them on the terminal.
The commands are intentionally repetitive in some places to better understand
each step and also to demonstrate the beauty of command-line features like
history, variables, pipes and loops (which you will commonly use as you master
the command-line).
@@ -2937,7 +2954,7 @@ $ ls -lh nc-for-storage.fits.gz
We can get this wonderful level of compression because NoiseChisel's output is
binary with only two values: 0 and 1.
Compression algorithms are highly optimized in such scenarios.
-You can open @file{nc-for-storage.fits.gz} directly in SAO DS9 or feed it to
any of Gnuastro's programs without having to uncompress it.
+You can open @file{nc-for-storage.fits.gz} directly in SAO DS9 or feed it to
any of Gnuastro's programs without having to decompress it.
Higher-level programs that take NoiseChisel's output (for example Segment or
MakeCatalog) can also deal with this compressed image where the Sky and its
Standard deviation are one pixel-per-tile.
You just have to give the ``values'' image as a separate option, for more, see
@ref{Segment} and @ref{MakeCatalog}.
@@ -3019,7 +3036,7 @@ asttable cat/xdf-f160w.fits -hCLUMPS -i
Matching the catalogs is possible (for example with @ref{Match}).
However, the measurements of each column are also done on different pixels:
the clump labels can/will differ from one filter to another for one object.
Please open them and focus on one object to see for your self.
-Thiscan bias the result, if you match catalogs.
+This can bias the result, if you match catalogs.
An accurate color calculation can only be done when magnitudes are measured
from the same pixels on both images.
Fortunately in these images, the Point spread function (PSF) are very similar,
allowing us to do this directly@footnote{When the PSFs between two images
differ largely, you would have to PSF-match the images before using the same
pixels for measurements.}.
@@ -3115,7 +3132,7 @@ $ asttable two-in-one.fits -i
Looking at the two metadata outputs (called with @option{-i}), you may have
noticed that both tables have the same number of rows.
But what might have attracted your attention more, is that
@file{both-mags.fits} has double the number of columns (as expected, after all,
you merged both tables into one file).
-Infact, in one command, you can concatenate any number of other tables, for
example:
+In fact you can concatenate any number of other tables in one command, for
example:
@example
$ asttable cat/xdf-f160w.fits -hCLUMPS --output=three-in-one.fits \
@@ -3178,7 +3195,7 @@ $ asttable three-in-one-3.fits -i
We now have both magnitudes in one table and can start doing arithmetic on
them (to estimate colors, which are just a subtraction of magnitudes).
To use column arithmetic, simply call the column selection option
(@option{--column} or @option{-c}), put the value in single quotations and
start the value with @code{arith} (followed by a space) like the example below.
-Column arithmetic uses the same notation as the Arithmetic program (see
@ref{Reverse polish notation}), with almost all the same operators (see
@ref{Arithmetic operators}), and some column-specific opertors (that aren't
available for images).
+Column arithmetic uses the same notation as the Arithmetic program (see
@ref{Reverse polish notation}), with almost all the same operators (see
@ref{Arithmetic operators}), and some column-specific operators (that aren't
available for images).
In column-arithmetic, you can identify columns by number (prefixed with a
@code{$}) or name, for more see @ref{Column arithmetic}.
So let's estimate one color from @file{three-in-one-3.fits} using column
arithmetic.
@@ -3240,7 +3257,7 @@ $ asttable three-in-one-3.fits --range=SN,5,inf
-c1,2,RA,DEC,SN \
$ asttable cat/mags-with-color.fits -i
@end example
-The table now has all the columns we need and it has the proper metadata to
let us safely use it later (without frustrating over column orders!) or passing
it to colleages.
+The table now has all the columns we need and it has the proper metadata to
let us safely use it later (without frustrating over column orders!) or passing
it to colleagues.
You can now inspect the distribution of colors with the Statistics program.
@example
@@ -3262,7 +3279,7 @@ We won't go much deeper into the Statistics program here,
but there is so much m
Let's finish this section of the tutorial with a useful tip on modifying
column metadata.
Above, updating/changing column metadata was done with the
@option{--colmetadata} in the same command that produced the newly created
Table file.
-But in many sitations, the table is already made and you just want to update
the metadata of one column.
+But in many situations, the table is already made and you just want to update
the metadata of one column.
In such cases using @option{--colmetadata} is over-kill (wasting CPU/RAM
energy or time if the table is large) because it will load the full table data
and metadata into memory, just change the metadata and write it back into a
file.
In scenarios when the table's data doesn't need to be changed and you just
want to set or update the metadata, it is much more efficient to use basic FITS
keyword editing.
@@ -3275,7 +3292,7 @@ $ astfits two-in-one.fits -h1 | grep TTYPE
Changing/updating the column names is as easy as updating the values to these
keywords.
You don't need to touch the actual data!
-With the command below, we'll just update the @code{MAGNITUDE} and
@code{MAGNITUDE-1} columns (which are respectively stored in the @code{TTYPE5}
and @code{TTYPE11} keywords) by modifying the keyword values and checking the
effect by listingthe column metadata again:
+With the command below, we'll just update the @code{MAGNITUDE} and
@code{MAGNITUDE-1} columns (which are respectively stored in the @code{TTYPE5}
and @code{TTYPE11} keywords) by modifying the keyword values and checking the
effect by listing the column metadata again:
@example
$ astfits two-in-one.fits -h1 \
@@ -3299,7 +3316,7 @@ rm *.fits
@subsection Aperture photometry
The colors we calculated in @ref{Working with catalogs estimating colors} used
a different segmentation map for each object.
This might not satisfy some science cases that need the flux within a fixed
area/aperture.
-Fortunately the modularity of Gnuastro's modular programs make it very easy to
alo do this type of measurement/photometry.
+Fortunately Gnuastro's modular programs make it very easy do this type of
measurement (photometry).
To do this, we can ignore the labeled images of NoiseChisel of Segment, we can
just built our own labeled image!
That labeled image can then be given to MakeCatalog
@@ -3329,7 +3346,7 @@ $ astmkprof apertures.txt
--background=flat-ir/xdf-f160w.fits \
The first thing you might notice in the printed information is that the
profiles are not built in order.
This is because MakeProfiles works in parallel, and parallel CPU operations
are asynchronous.
-You can try running MakeProfiles with one thread (using
@option{--numthreads=1}) to see how order is respected in that case, but slower
(note that the mult-threaded run will be much more faster when more
mathematically-complicated profiles are built, like S@'eric profiles).
+You can try running MakeProfiles with one thread (using
@option{--numthreads=1}) to see how order is respected in that case, but slower
(note that the multi-threaded run will be much more faster when more
mathematically-complicated profiles are built, like S@'eric profiles).
Open @file{apertures.fits} with a FITS viewer and look around at the circles
placed over the targets.
Also open the input image and Segment's clumps image and compare them with the
positions of these circles.
@@ -3338,7 +3355,7 @@ In the future, MakeCatalog will be able to work with
overlapping labels, but cur
If you are interested, please join us in completing Gnuastro with added
improvements like this (see task 14750
@footnote{@url{https://savannah.gnu.org/task/index.php?14750}}).
We can now feed the @file{apertures.fits} labeled image into MakeCatalog
instead of Segment's output as shown below.
-In comparison with the previous MakeCatalog call, you will notice that there
is no more @option{--clumpscat} option, since there is no more separarate
``clump'' imge now, each aperture is treated as a separate ``object''.
+In comparison with the previous MakeCatalog call, you will notice that there
is no more @option{--clumpscat} option, since there is no more separate
``clump'' image now, each aperture is treated as a separate ``object''.
@example
$ astmkcatalog apertures.fits -h1 --zeropoint=26.27 \
@@ -3359,7 +3376,7 @@ You can also change the filter name and zeropoint
magnitudes and run this comman
In the example above, we had the luxury to generate the catalogs ourselves,
and where thus able to generate them in a way that the rows match.
But this isn't generally the case.
-In many situations, you need to use catalogs from many different telescopes,
or catalogs with high-level calculations that you can't simply regenrate with
the same pixels without spending a lot of time or using heavy computation.
+In many situations, you need to use catalogs from many different telescopes,
or catalogs with high-level calculations that you can't simply regenerate with
the same pixels without spending a lot of time or using heavy computation.
In such cases, when each catalog has the coordinates of its own objects, you
can use the coordinates to match the rows with Gnuastro's Match program (see
@ref{Match}).
As the name suggests, Gnuastro's Match program will match rows based on
distance (or aperture in 2D) in one, two, or three columns.
@@ -3384,7 +3401,7 @@ $ astfits matched.fits
@end example
From the second command, you see that the output has two extensions and that
both have the same number of rows.
-The rows in each extenion correspond with the rows in the other.
+The rows in each extension correspond with the rows in the other.
You can also see which objects didn't match with the @option{--notmatched},
like below.
Note how each extension now has a different number of rows.
@@ -3448,7 +3465,7 @@ $ asttable cat/mags-with-color.fits
--range=F105W-F160W,1.5,inf \
We can now feed @file{reddest.txt} into Gnuastro's Crop program to see what
these objects look like.
To keep things clean, we'll make a directory called @file{crop-red} and ask
Crop to save the crops in this directory.
We'll also add a @file{-f160w.fits} suffix to the crops (to remind us which
filter they came from).
-The width of the crops will be 15 arcseconds (or 15/3600 degrees, which is the
units of the WCS).
+The width of the crops will be 15 arc-seconds (or 15/3600 degrees, which is
the units of the WCS).
@example
$ mkdir crop-red
@@ -8278,7 +8295,10 @@ For more on the datasum feature of the FITS standard,
see @ref{Keyword manipulat
You can use this option to confirm that the data in two different HDUs
(possibly with different keywords) is identical.
Its advantage over @option{--write=datasum} (which writes the @code{DATASUM}
keyword into the given HDU) is that it doesn't require write permissions.
-
+@item --pixelscale
+Print the HDU's pixel-scale (change in world coordinate for one pixel along
each dimension).
+Without the @option{--quiet} option, the output of @option{--pixelscale} is
more human-friendly by printing the file/HDU name, number of dimensions, and
the units of each number along with the actual pixel scales.
+However, in scripts (that are to be run automatically), this human-friendly
format is annoying, so when called with the @option{--quiet} option, only the
pixel-scale value(s) along each dimension is(are) printed in one line.
@item -C STR
@itemx --copy=STR
@@ -9220,7 +9240,7 @@ Viridis is the default colormap of the popular Matplotlib
module of Python and a
@cindex SLS Color
@cindex Colormap: SLS
The SLS color range, taken from the commonly used @url{http://ds9.si.edu,SAO
DS9}.
-The advantage of this color range is that it starts with black, going into
dark blue and comes to brighter colors, finishings with red and white.
+The advantage of this color range is that it starts with black, going into
dark blue and finishes with the brighter colors of red and white.
So unlike the HSV color range, it includes black and white and brighter colors
(like yellow, red) show the larger values.
@item sls-inverse
@@ -9812,7 +9832,7 @@ Look into that file's metadata (with @command{asttable
temp.fits -i}) to see the
Recall that when a name is given, this option will update the metadata of the
first column that matches, so if you have multiple columns with the same name,
you can call this options multiple times with the same first argument to change
them all.
Finally, if you already have a FITS table by other means (for example by
downloading) and you merely want to update the column metadata and leave the
data intact, it is much more efficient to directly modify the respective FITS
header keywords with @code{astfits}, using the keyword manipulation features
described in @ref{Keyword manipulation}.
-@option{--colmetadata} is mainly intended for scenarios where you want to edit
the data so it will always load the full/partial dataset into memory, then
write out the resulting datasets with updated/correced metadata.
+@option{--colmetadata} is mainly intended for scenarios where you want to edit
the data so it will always load the full/partial dataset into memory, then
write out the resulting datasets with updated/corrected metadata.
@end table
@@ -17866,7 +17886,7 @@ In this case, no description or units will be printed.
See @ref{CosmicCalculator basic cosmology calculations} for the full list of
these options along with some explanations how when/how they can be useful.
Another common operation in observational cosmology is dealing with spectral
lines at different redshifts.
-CosmicCalculator also has features to help in such sitatuions, please see
@ref{CosmicCalculator spectral line calculations}.
+CosmicCalculator also has features to help in such situations, please see
@ref{CosmicCalculator spectral line calculations}.
@menu
* CosmicCalculator input options:: Options to specify input conditions.
@@ -18213,7 +18233,7 @@ The comoving volume in Megaparsecs cube
(Mpc@mymath{^3}) until the desired redsh
@subsubsection CosmicCalculator spectral line calculations
@cindex Rest frame wavelength
-At different redhifts, observed spectral lines are shifted compared to their
rest frame wavelengths with this simple relation:
@mymath{\lambda_{obs}=\lambda_{rest}(1+z)}.
+At different redshifts, observed spectral lines are shifted compared to their
rest frame wavelengths with this simple relation:
@mymath{\lambda_{obs}=\lambda_{rest}(1+z)}.
Although this relation is very simple and can be done for one line in the head
(or a simple calculator!), it slowly becomes tiring when dealing with a lot of
lines or redshifts, or some precision is necessary.
The options in this section are thus provided to greatly simplify usage of
this simple equation, and also helping by storing a list of pre-defined
spectral line wavelengths.
@@ -20240,7 +20260,7 @@ container}.
@end deftypefun
@deftypefun {gal_data_t **} gal_data_array_ptr_calloc (size_t @code{size})
-Allocate an array of pointers to Gnuastro's generic data structure and
initalize all pointers to @code{NULL}.
+Allocate an array of pointers to Gnuastro's generic data structure and
initialize all pointers to @code{NULL}.
This is useful when you want to allocate individual datasets later (for
example with @code{gal_data_alloc}).
@end deftypefun
@@ -22842,12 +22862,12 @@ the rotation.
@deftypefun int gal_wcs_distortion_from_string (char @code{*distortion})
Convert the given string (assumed to be a FITS-standard, string-based
distortion identifier) to a Gnuastro's integer-based distortion identifier (one
of the @code{GAL_WCS_DISTORTION_*} macros defined above).
-The sting-based distortion identifiers have three characters and are all in
captial letters.
+The sting-based distortion identifiers have three characters and are all in
capital letters.
@end deftypefun
@deftypefun int gal_wcs_distortion_to_string (int @code{distortion})
Convert the given Gnuastro integer-based distortion identifier (one of the
@code{GAL_WCS_DISTORTION_*} macros defined above) to the string-based
distortion identifier) of the FITS standard.
-The sting-based distortion identifiers have three characters and are all in
captial letters.
+The sting-based distortion identifiers have three characters and are all in
capital letters.
@end deftypefun
@cindex WCS distortion
@@ -24285,7 +24305,7 @@ INDEX INPUT OUTPUT
K-D Tree
This format is therefore scalable to any number of dimensions: the number of
dimensions are determined from the number of nodes in the input list of
@code{gal_data_t}s (for example, using @code{gal_list_data_number}).
In Gnuastro's k-d tree implementation, there are thus no special structures to
keep every tree node (which would take extra memory and would need to be moved
around as the tree is being created).
Everything is done internally on the index of each point in the input dataset:
the only thing that is flipped/sorted during tree creation is the index to the
input row for any number of dimensions.
-As a result, Gnuastro's k-d tree implementation is very memory and CPU
efficient and its two output columns can directly be written into a standrad
table (without having to define any special binary format).
+As a result, Gnuastro's k-d tree implementation is very memory and CPU
efficient and its two output columns can directly be written into a standard
table (without having to define any special binary format).
@deftypefun {gal_data_t *} gal_kdtree_create (gal_data_t @code{*coords_raw},
size_t @code{*root})
Create a k-d tree in a bottom-up manner (from leaves to the root).
@@ -24336,7 +24356,7 @@ main (void)
@deftypefun size_t gal_kdtree_nearest_neighbour (gal_data_t
@code{*coords_raw}, gal_data_t @code{*kdtree}, size_t @code{root}, double
@code{*point}, double @code{*least_dist})
Returns the index of the nearest input point to the query point (@code{point},
assumed to be an array with same number of elements as @code{gal_data_t}s in
@code{coords_raw}).
The distance between the query point and its nearest neighbor is stored in the
space that @code{least_dist} points to.
-This search is efficient due to the constantly checking for the presence of
possible best points in other brances.
+This search is efficient due to the constantly checking for the presence of
possible best points in other branches.
If it isn't possible for the other branch to have a better nearest neighbor,
that branch is not searched.
For example the function below reads the input, and the k-d tree file created
in the example of @code{gal_kdtree_create} (so you won't have to re-create the
k-d tree every time) and finds the input point that is closest to a given query
point.
@@ -25469,7 +25489,7 @@ A manhattan metric will always be an integer and is
like steps (but is also much
@deffnx Macro GAL_INTERPOLATE_NEIGHBORS_FUNC_MEDIAN
@deffnx Macro GAL_INTERPOLATE_NEIGHBORS_FUNC_INVALID
@cindex Saturated stars
-The various types of nearest-neighbor interporation functions for
@code{gal_interpolate_neighbors}.
+The various types of nearest-neighbor interpolation functions for
@code{gal_interpolate_neighbors}.
The names are descriptive for the operation they do, so we won't go into much
more detail here.
The median operator will be one of the most used, but operators like the
maximum are good to fill the center of saturated stars.
@end deffn
@@ -25480,7 +25500,7 @@ Interpolate the values in the input dataset using a
calculated statistics from t
The desired statistics is determined from the @code{func} argument, which
takes any of the @code{GAL_INTERPOLATE_NEIGHBORS_FUNC_} macros (see above).
This function is non-parametric and thus agnostic to the input's number of
dimension or shape of the distribution.
-Distance can be defined on different metrics that are dentified through
@code{metric} (taking values determined by the
@code{GAL_INTERPOLATE_NEIGHBORS_METRIC_} macros described above).
+Distance can be defined on different metrics that are identified through
@code{metric} (taking values determined by the
@code{GAL_INTERPOLATE_NEIGHBORS_METRIC_} macros described above).
If @code{onlyblank} is non-zero, then only blank elements will be interpolated
and pixels that already have a value will be left untouched.
This function is multi-threaded and will run on @code{numthreads} threads (see
@code{gal_threads_number} in @ref{Multithreaded programming}).
diff --git a/doc/release-checklist.txt b/doc/release-checklist.txt
index c5126a9..75d3ca0 100644
--- a/doc/release-checklist.txt
+++ b/doc/release-checklist.txt
@@ -21,7 +21,7 @@ all the commits needed for this release have been completed.
added in the 'THANKS' file since the last stable release (to add in the
book), you can use this command:
- $ git diff gnuastro_vP.P..HEAD THANKS
+ $ git diff gnuastro_vX.X..HEAD THANKS
- Build the Debian distribution (just for a test) and correct any build or
@@ -56,7 +56,7 @@ all the commits needed for this release have been completed.
code and those that must be acknowledged for the announcement ('P.P' is
the previous version).
- $ git shortlog gnuastro_vP.P...HEAD --numbered --summary > ~/people.txt
+ $ git shortlog gnuastro_vX.X...HEAD --numbered --summary > ~/people.txt
$ cat doc/announce-acknowledge.txt >> ~/people.txt
[STABLE] Remove the names in 'doc/announce-acknowledge.txt'.
@@ -405,7 +405,7 @@ Steps necessary to Package Gnuastro for Debian.
Streicher (olebole@debian.org) mentioned privately: "this links all
Debian Astro packages together".
- $ lintian -E -I --pedantic \
+ $ lintian -E -I --pedantic \
/var/cache/pbuilder/result/gnuastro_$ver-1_amd64.changes
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