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[gnuastro-commits] master 9af5d8ad: Warp: new --gridfile option to warp
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From: |
Mohammad Akhlaghi |
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Subject: |
[gnuastro-commits] master 9af5d8ad: Warp: new --gridfile option to warp one image to grid of another |
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Date: |
Wed, 5 Oct 2022 10:01:24 -0400 (EDT) |
branch: master
commit 9af5d8ad6e58aa4997f61f70f2da7eb49dd18b61
Author: Pedram Ashofteh Ardakani <pedramardakani@pm.me>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Warp: new --gridfile option to warp one image to grid of another
Until now, when you already had one image with a certain WCS, it was
annoying (when it was aligned: using the three '--center', '--cdelt' and
'--widthinpix') or impossible (when it wasn't aligned and had distortions)
to map another image to that grid using Warp.
With this commit, a new option has been added for this job: '--gridfile'
(and a corresponding '--gridhdu'). When this is given, the WCS and pixel
grid of the output will exactly match that to of the input. This has been
implemented in a library level, so it was necessary to make some changes
there also.
In the process, it was also recognized that there were several cases where
'etc.' came without the last 'period'. Also, since 'etc.' stands for 'et
cetera' which means 'and the rest', using 'and' before 'etc.' is
redundant. One last case, is where there is a 'for example' or 'like' or
'such as' in the sentence; Using 'etc.' while counting examples or cases is
incorrect (see [1] and [2]). For example:
(INCORRECT) Fruits such as apples, oranges, strawberries, etc.
(CORRECT) Fruits such as apples, oranges, and strawberries.
(CORRECT) Apples, oranges, strawberries, etc.
References:
[1] https://www.grammarly.com/blog/et-cetera-etc/
[2] https://www.wikihow.com/Use-%22Etc.%22-Correctly
---
NEWS | 6 +
bin/warp/args.h | 26 +++
bin/warp/astwarp.conf | 1 +
bin/warp/main.h | 2 +
bin/warp/ui.c | 114 ++++++++++--
bin/warp/ui.h | 4 +-
doc/gnuastro.texi | 479 +++++++++++++++++++++++++++++++++++---------------
lib/gnuastro/warp.h | 28 +--
lib/warp.c | 141 +++++++++++----
9 files changed, 599 insertions(+), 202 deletions(-)
diff --git a/NEWS b/NEWS
index 0f8609bc..8c21c22e 100644
--- a/NEWS
+++ b/NEWS
@@ -117,6 +117,12 @@ See the end of the file for license conditions.
Gnomonic or 'TAN').
--edgesampling: extra sampling of pixel polygon to account for strong
non-linear projection or distortion effects, when necessary.
+ --gridfile: warp the input to the exact WCS and pixel grid of the file
+ given to this option. This is very useful when matching images from
+ differetn surveys. Using this option, you can also insert distortions
+ in an image (for example on a mock image, to make it match an
+ observed exposure with dithering+distortion).
+ --gridhdu: HDU containing image to be matched in '--gridfile'.
astscript-fits-view:
--ds9colorbarmulti: show a separate color-bar for each image in DS9. By
diff --git a/bin/warp/args.h b/bin/warp/args.h
index 5d476ea4..47b90f61 100644
--- a/bin/warp/args.h
+++ b/bin/warp/args.h
@@ -171,6 +171,32 @@ struct argp_option program_options[] =
GAL_OPTIONS_MANDATORY,
GAL_OPTIONS_NOT_SET,
},
+ {
+ "gridfile",
+ UI_KEY_GRIDFILE,
+ "FITS",
+ 0,
+ "File to use for output grid.",
+ UI_GROUP_ALIGN,
+ &p->gridfile,
+ GAL_TYPE_STRING,
+ GAL_OPTIONS_RANGE_ANY,
+ GAL_OPTIONS_NOT_MANDATORY,
+ GAL_OPTIONS_NOT_SET
+ },
+ {
+ "gridhdu",
+ UI_KEY_GRIDHDU,
+ "STR",
+ 0,
+ "HDU/extension to use for output grid.",
+ UI_GROUP_ALIGN,
+ &p->gridhdu,
+ GAL_TYPE_STRING,
+ GAL_OPTIONS_RANGE_ANY,
+ GAL_OPTIONS_NOT_MANDATORY,
+ GAL_OPTIONS_NOT_SET
+ },
diff --git a/bin/warp/astwarp.conf b/bin/warp/astwarp.conf
index 86c004b0..dd681da9 100644
--- a/bin/warp/astwarp.conf
+++ b/bin/warp/astwarp.conf
@@ -21,6 +21,7 @@
# Input:
edgesampling 0
+ gridhdu 1
# Output:
coveredfrac 1.0
diff --git a/bin/warp/main.h b/bin/warp/main.h
index c0ba6e0b..d2d82ff5 100644
--- a/bin/warp/main.h
+++ b/bin/warp/main.h
@@ -52,6 +52,8 @@ struct warpparams
uint8_t centeroncorner; /* Shift center by 0.5 before and after. */
double coveredfrac; /* Acceptable fraction of output covered. */
gal_data_t *cdelt; /* Pixel scale of the output image. */
+ char *gridhdu; /* Extension to use for output's WCS. */
+ char *gridfile; /* File to use for output's WCS. */
/* Internal parameters: */
gal_data_t *input; /* Input data structure. */
diff --git a/bin/warp/ui.c b/bin/warp/ui.c
index e88ed0f8..5b11d2fb 100644
--- a/bin/warp/ui.c
+++ b/bin/warp/ui.c
@@ -322,15 +322,102 @@ ui_add_to_modular_warps_ll(struct argp_option *option,
char *arg,
/*************** Sanity Check *******************/
/**************************************************************/
static void
-ui_check_options_and_arguments_nonlinear(struct warpparams *p)
+ui_check_gridfile(struct warpparams *p)
+{
+ int nwcs;
+ size_t ndim, *dsize=NULL;
+ gal_warp_wcsalign_t *wa=&p->wa;
+
+ /* Make sure that the file given to '--gridfile' is a recognized FITS
+ file. */
+ if(gal_fits_file_recognized(p->gridfile)==0)
+ error(EXIT_FAILURE, 0, "'%s' (given to '--gridfile') must be "
+ "in FITS format with a recognizable FITS format suffix",
+ p->gridfile);
+ if(p->gridhdu==NULL)
+ error(EXIT_FAILURE, 0, "%s no HDU/extension specified (file given "
+ "to '--gridfile')! Please use '--gridhdu' to specify a "
+ "HDU/extension to read from", p->gridfile);
+
+ /* Read the WCS and save to a standard PC convention WCS struct. */
+ wa->twcs=gal_wcs_read(p->gridfile, p->gridhdu,
+ GAL_WCS_LINEAR_MATRIX_PC, 0, 0, &nwcs);
+ if(wa->twcs==NULL)
+ error(EXIT_FAILURE, 0, "%s (hdu %s): no readable WCS structure",
+ p->gridfile, p->gridhdu);
+
+ /* Correct the WCS dimensions if necessary. */
+ dsize=gal_fits_img_info_dim(p->gridfile, p->gridhdu, &ndim);
+ ndim=gal_dimension_remove_extra(ndim, dsize, wa->twcs);
+ if(ndim!=2)
+ error(EXIT_FAILURE, 0, "%s (hdu %s): the target WCS must "
+ "contain 2 dimensions, but warp detected %zu dimensions",
+ p->gridfile, p->gridhdu, ndim);
+
+ /* If '--widthinpix' has already been given, inform the user that it will
+ be ignored (because '--gridfile' has been given). */
+ if(wa->widthinpix)
+ {
+ error(EXIT_SUCCESS, 0, "WARNING: '--widthinpix' will be ignored "
+ "because '--gridfile' takes precedence");
+ gal_data_free(wa->widthinpix);
+ }
+
+ /* We don't need to free the input 'dsize' array since it will be freed
+ by gal_data_free at the clean up stage. */
+ wa->widthinpix=gal_data_alloc(dsize, GAL_TYPE_SIZE_T, 1, &ndim, NULL, 1,
+ p->cp.minmapsize, p->cp.quietmmap, NULL, NULL,
+ NULL);
+
+ /* If any of the non-default WCS-defining options are given, free them
+ and print a warning. We don't want to print any warning for the
+ default one ('--ctype') because most users may not set it. */
+ if(wa->ctype) { gal_data_free(wa->ctype); wa->ctype=NULL; }
+ if(wa->cdelt)
+ {
+ error(EXIT_SUCCESS, 0, "WARNING: '--cdelt' will be ignored "
+ "because '--gridfile' takes precedence");
+ gal_data_free(wa->cdelt);
+ wa->cdelt=NULL;
+ }
+ if(wa->center)
+ {
+ error(EXIT_SUCCESS, 0, "WARNING: '--center' will be ignored "
+ "because '--gridfile' takes precedence");
+ gal_data_free(wa->center);
+ wa->center=NULL;
+ }
+}
+
+
+
+
+
+static void *
+ui_check_options_and_arguments_wcsalign(struct warpparams *p)
{
gal_warp_wcsalign_t *wa=&p->wa;
size_t two=2, *sarray=NULL, stemp, indim=0;
double *icenter=NULL, *iwidth=NULL, *imin=NULL, *imax=NULL, *tmp=NULL;
- /* Put the number of threads into the non-linear structure. */
+ /* Copy necessary parameters for the nonlinear warp (independent of
+ having a WCS or not). */
+ wa->input=p->input;
+ wa->coveredfrac=p->coveredfrac;
wa->numthreads=p->cp.numthreads;
+ /* If using a WCS file for the target grid (with '--gridfile' and
+ '--gridhdu' options) check the file and ignore the other given
+ parameters. */
+ if(p->gridfile)
+ {
+ ui_check_gridfile(p);
+ return NULL;
+ }
+
+ /* Not using a WCS file, so put cdelt into the non-linear structure. */
+ p->wa.cdelt=p->cdelt;
+
/* Sanity check user's possibly given '--center'. */
if(wa->center)
{
@@ -392,7 +479,7 @@ ui_check_options_and_arguments_nonlinear(struct warpparams
*p)
if( sarray[0]%2==0 || sarray[1]%2==0 )
{
/* Let the user know that we are updating the output size. */
- error(EXIT_SUCCESS, 0, "WARNING: '--width' must be odd: "
+ error(EXIT_SUCCESS, 0, "WARNING: '--widthinpix' must be odd: "
"updating %zux%zu to %zux%zu", sarray[0], sarray[1],
sarray[0]%2 ? sarray[0] : sarray[0]+1,
sarray[1]%2 ? sarray[1] : sarray[1]+1);
@@ -422,17 +509,13 @@ ui_check_options_and_arguments_nonlinear(struct
warpparams *p)
if(wa->ctype->size != p->input->ndim)
error(EXIT_FAILURE, 0, "%zu value(s) given to '--ctype', but it "
"takes exactly 2 values", wa->ctype->size);
-
-
- /* Copy necessary parameters for the nonlinear warp to work */
- wa->input=p->input;
- wa->cdelt=p->cdelt;
- wa->coveredfrac=p->coveredfrac;
+ return NULL;
}
+
static void
ui_check_cdelt(struct warpparams *p)
{
@@ -546,7 +629,7 @@ ui_check_options_and_arguments(struct warpparams *p)
/* Do all the distortion correction sanity-checks.*/
if(p->nonlinearmode)
- ui_check_options_and_arguments_nonlinear(p);
+ ui_check_options_and_arguments_wcsalign(p);
}
@@ -990,7 +1073,6 @@ ui_preparations(struct warpparams *p)
/**************************************************************/
/************ Set the parameters *************/
/**************************************************************/
-
void
ui_read_check_inputs_setup(int argc, char *argv[], struct warpparams *p)
{
@@ -1052,7 +1134,8 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
warpparams *p)
printf(" Using %zu CPU thread%s\n", p->cp.numthreads,
p->cp.numthreads==1 ? "." : "s.");
printf(" Input: %s (hdu: %s)\n", p->inputname, p->cp.hdu);
-
+ if(p->gridfile)
+ printf(" Pixel grid: %s (hdu %s)\n", p->gridfile, p->gridhdu);
if(p->nonlinearmode)
{
disttype=gal_wcs_distortion_identify(p->input->wcs);
@@ -1100,14 +1183,18 @@ void
ui_free_report(struct warpparams *p, struct timeval *t1)
{
/* Free the allocated arrays: */
- if(p->inverse) free(p->inverse);
if(p->wa.cdelt) p->wa.cdelt=NULL;
if(p->cdelt) gal_data_free(p->cdelt);
+
+ if(p->inverse) free(p->inverse);
+ if(p->gridhdu) free(p->gridhdu);
+ if(p->gridfile) free(p->gridfile);
if(p->matrix) gal_data_free(p->matrix);
if(p->inwcsmatrix) free(p->inwcsmatrix);
if(p->modularll) gal_data_free(p->modularll);
if(p->wa.input) p->wa.input=NULL;
+ if(p->wa.twcs) gal_wcs_free(p->wa.twcs);
if(p->wa.ctype) gal_data_free(p->wa.ctype);
if(p->wa.center) gal_data_free(p->wa.center);
if(p->wa.widthinpix) gal_data_free(p->wa.widthinpix);
@@ -1117,7 +1204,6 @@ ui_free_report(struct warpparams *p, struct timeval *t1)
gal_data_free(p->input);
gal_data_free(p->output);
-
/* Report how long the operation took. */
if(!p->cp.quiet)
gal_timing_report(t1, PROGRAM_NAME" finished in: ", 0);
diff --git a/bin/warp/ui.h b/bin/warp/ui.h
index f976e6cb..b976039c 100644
--- a/bin/warp/ui.h
+++ b/bin/warp/ui.h
@@ -45,7 +45,7 @@ enum program_args_groups
/* Available letters for short options:
a b d g i j l n u v z
- A B E G H J L O Q R W X Y
+ A B E J L O Q R W X Y
*/
enum option_keys_enum
{
@@ -63,6 +63,8 @@ enum option_keys_enum
UI_KEY_INTERPSAMPLING = 'y',
UI_KEY_CENTER = 'c',
UI_KEY_WIDTHINPIX = 'w',
+ UI_KEY_GRIDFILE = 'G',
+ UI_KEY_GRIDHDU = 'H',
/* Only with long version (start with a value 1000, the rest will be set
automatically). */
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index 0b3a893f..2aaf444b 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -505,8 +505,8 @@ Arithmetic
Arithmetic operators
-* Basic mathematical operators:: for example, +, -, /, log, pow, and etc.
-* Trigonometric and hyperbolic operators:: sin, cos, atan, asinh, and etc
+* Basic mathematical operators:: For example, +, -, /, log, and pow.
+* Trigonometric and hyperbolic operators:: sin, cos, atan, asinh, etc.
* Constants:: Physical and Mathematical constants.
* Unit conversion operators:: Various unit conversions necessary.
* Statistical operators:: Statistics of a single dataset (for example,
mean).
@@ -559,8 +559,8 @@ Warp
Invoking Warp
-* Align pixels with WCS and remove distortions:: Default operation.
-* Linear warps to be called explicitly:: Other waprs.
+* Align pixels with WCS account for distortions:: Default operation.
+* Linear warps to be called explicitly:: Other warps.
Data analysis
@@ -623,7 +623,7 @@ Invoking Segment
MakeCatalog
* Detection and catalog production:: Discussing why/how to treat these
separately
-* Brightness flux magnitude:: More on Magnitudes, surface brightness and etc.
+* Brightness flux magnitude:: More on Magnitudes, surface brightness, etc.
* Quantifying measurement limits:: For comparing different catalogs.
* Measuring elliptical parameters:: Estimating elliptical parameters.
* Adding new columns to MakeCatalog:: How to add new columns.
@@ -704,7 +704,7 @@ CosmicCalculator
Invoking CosmicCalculator
* CosmicCalculator input options:: Options to specify input conditions.
-* CosmicCalculator basic cosmology calculations:: Like distance modulus,
distances and etc.
+* CosmicCalculator basic cosmology calculations:: Such as distance modulus
and distances.
* CosmicCalculator spectral line calculations:: How they get affected by
redshift.
Installed scripts
@@ -852,7 +852,8 @@ Library demo programs
* Library demo - inspecting neighbors:: Inspect the neighbors of a pixel.
* Library demo - multi-threaded operation:: Doing an operation on threads.
* Library demo - reading and writing table columns:: Simple Column I/O.
-* Library demo - resampling an image to a new grid::
+* Library demo - Warp to another image:: Output pixel grid and WCS from
another image.
+* Library demo - Warp to new grid:: Define a new pixel grid and WCS to
resample the input.
Developing
@@ -1323,7 +1324,7 @@ It is GNU Bash that then talks to kernel.
To better clarify, let's use this analogy inspired from one of the links
above@footnote{https://www.gnu.org/gnu/gnu-users-never-heard-of-gnu.html}:
saying that you are ``running Linux'' is like saying you are ``driving your
engine''.
The car's engine is the main source of power in the car, no one doubts that.
But you do not ``drive'' the engine, you drive the ``car''.
-Without the radiator, battery, transmission, wheels, chassis, seats,
wind-shield and etc, the engine alone is useless for transportation!
+The engine alone is useless for transportaion without the radiator, battery,
transmission, wheels, chassis, seats, wind-shield, etc.
@cindex Window Subsystem for Linux
To have an operating system, you need lower-level tools (to build the kernel),
and higher-level (to use it) software packages.
@@ -2031,7 +2032,7 @@ $ astscript-fits-view \
After running this command, you will see that the DS9 window fully covers the
height of your monitor, it is showing the whole image, using a more clear
color-map, and many more useful things.
Infact, you see the DS9 command that is used in your terminal@footnote{When
comparing DS9's command-line options to Gnuastro's, you will notice how SAO DS9
does not follow the GNU style of options where ``long'' and ``short'' options
are preceded by @option{--} and @option{-} respectively (for example,
@option{--width} and @option{-w}, see @ref{Options}).}.
-On GNU/Linux operating systems (like Ubuntu, Fedora and etc), you can also set
your graphics user interface to use this script for opening FITS files when you
click on them.
+On GNU/Linux operating systems (like Ubuntu, and Fedora), you can also set
your graphics user interface to use this script for opening FITS files when you
click on them.
For more, see the instructions in the checklist at the start of @ref{Invoking
astscript-fits-view}.
As you hover your mouse over the image, notice how the ``Value'' and
positional fields on the top of the ds9 window get updated.
@@ -2178,7 +2179,7 @@ Press the ``up'' key on your keyboard (possibly multiple
times) to see your prev
@cartouche
@noindent
-@strong{Your locale does not use `.' as decimal separator:} on systems that do
not use an English language environment, dates, numbers and etc can be printed
in different formats (for example, `0.5' can be written as `0,5': with a comma).
+@strong{Your locale does not use `.' as decimal separator:} on systems that do
not use an English language environment, the dates, numbers, etc., can be
printed in different formats (for example, `0.5' can be written as `0,5': with
a comma).
With the @code{LC_NUMERIC} line at the start of the script below, we are
ensuring a unified format in the output of @command{seq}.
For more, please see @ref{Numeric locale}.
@end cartouche
@@ -2463,7 +2464,7 @@ $ rm myprogram* z-vs-tandist*
@subsection Option management and configuration files
In the previous section (@ref{Cosmological coverage and visualizing tables}),
when you ran CosmicCalculator, you only specified the redshfit with
@option{-z2} option.
You did not specify the cosmological parameters that are necessary for the
calculations!
-Parameters like the Hubble constant (@mymath{H_0}), the matter density, etc.
+Parameters like the Hubble constant (@mymath{H_0}) and the matter density.
In spite of this, CosmicCalculator done its processing and printed results.
None of Gnuastro's programs keep a default value internally within their code
(they are all set by the user)!
@@ -3180,7 +3181,7 @@ 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 all images and this can be done easily with MakeCatalog.
In fact this is one of the reasons that NoiseChisel or Segment do not generate
a catalog like most other detection/segmentation software.
-This gives you the freedom of selecting the pixels for measurement in any way
you like (from other filters, other software, manually, and etc).
+This gives you the freedom of selecting the pixels for measurement in any way
you like (from other filters, other software, manually, etc.).
Fortunately in these images, the Point spread function (PSF) is very similar,
allowing us to use a single labeled image output for all filters@footnote{When
the PSFs between two images differ largely, you would have to PSF-match the
images before using the same pixels for measurements.}.
The F160W image is deeper, thus providing better detection/segmentation, and
redder, thus observing smaller/older stars and representing more of the mass in
the galaxies.
@@ -3501,7 +3502,7 @@ Column meta-data (including a name) are not just limited
to FITS tables and can
Table also has tools to limit the displayed rows.
for example, with the first command below only rows with a magnitude in the
range of 29 to 30 will be shown.
With the second command, you can further limit the displayed rows to rows with
an S/N larger than 10 (a range between 10 to infinity).
-You can further sort the output rows, only show the top (or bottom) N rows and
etc, for more see @ref{Table}.
+You can further sort the output rows, only show the top (or bottom) N rows,
etc., see @ref{Table} for more.
@example
$ asttable cat/xdf-f160w.fits -hCLUMPS --range=MAGNITUDE,28:29
@@ -3772,7 +3773,7 @@ $ astscript-fits-view cmd.fits --ds9scale=minmax \
--ds9extra="-grid yes -grid type publication"
@end example
-If you are happy with the grid and coloring and etc, you can also use ds9 to
save this as a JPEG image to directly use in your documents/slides with these
extra DS9 options (DS9 will write the image to @file{cmd-2d.jpeg} and quit
immediately afterwards):
+If you are happy with the grid and coloring and the rest, you can also use ds9
to save this as a JPEG image to directly use in your documents/slides with
these extra DS9 options (DS9 will write the image to @file{cmd-2d.jpeg} and
quit immediately afterwards):
@example
$ astscript-fits-view cmd.fits --ds9scale=minmax \
@@ -3783,7 +3784,7 @@ $ astscript-fits-view cmd.fits --ds9scale=minmax \
@cindex PGFPlots (@LaTeX{} package)
This is good for a fast progress update.
But for your paper or more official report, you want to show something with
higher quality.
-For that, you can use the PGFPlots package in @LaTeX{} to add axes in the same
font as your text, sharp grids and many other elegant/powerful features (like
over-plotting interesting points, lines and etc).
+For that, you can use the PGFPlots package in @LaTeX{} to add axes in the same
font as your text, sharp grids and many other elegant/powerful features (like
over-plotting interesting points and lines).
But to load the 2D histogram into PGFPlots first you need to convert the FITS
image into a more standard format, for example, PDF.
We will use Gnuastro's @ref{ConvertType} for this, and use the
@code{sls-inverse} color map (which will map the pixels with a value of zero to
white):
@@ -3928,7 +3929,7 @@ $ astfits matched.fits
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 extension are the matched rows of the respective input table:
those in the first HDU come from the first input and those in the second HDU
come from the second.
-However, their order may be different from the input tables because the rows
match: the first row in the first HDU matches with the first row in the second
HDU, and etc.
+However, their order may be different from the input tables because the rows
match: the first row in the first HDU matches with the first row in the second
HDU, etc.
You can also see which objects did not match with the @option{--notmatched},
like below.
Note how each extension of now has a different number of rows.
@@ -4070,7 +4071,7 @@ You can build very complex workflows with Make, for
example, see @url{https://ar
@subsection FITS images in a publication
In the previous section (@ref{Reddest clumps cutouts and parallelization}), we
visually inspected the positions of the reddest objects using DS9.
-That is very good for an interactive inspection of the objects: you can
zoom-in and out, you can do measurements and etc.
+That is very good for an interactive inspection of the objects: you can
zoom-in and out, you can do measurements, etc.
Once the experimentation phase of your project is complete, you want to show
these objects over the whole image in a report, paper or slides.
One solution is to use DS9 itself!
@@ -6382,7 +6383,7 @@ $ asttable outer/67510-6-10.fits \
First let's have a look at all the masked postage stamps of the cropped stars.
Once they all open, feel free to zoom-in, they are all matched and locked.
-It is always good to check the different stamps to ensure the quality and
possible two dimensional features that are difficult to detect from the radial
profiles (i.e., ghosts, internal reflections, etc.).
+It is always good to check the different stamps to ensure the quality and
possible two dimensional features that are difficult to detect from the radial
profiles (such as ghosts and internal reflections).
@example
$ astscript-fits-view finding-normradii/cropped-masked*.fits
@@ -7046,7 +7047,7 @@ $ astmkprof -P
[[[ ... Truncated lines ... ]]]
# Output:
- type float32 # Type of output: e.g., int16, float32, etc...
+ type float32 # Type of output: e.g., int16, float32, etc.
mergedsize 1000,1000 # Number of pixels along first FITS axis.
oversample 5 # Scale of oversampling (>0 and odd).
@@ -7866,12 +7867,12 @@ Since it is a run-time dependency, it can be installed
at any later time (after
@subsection Bootstrapping dependencies
Bootstrapping is only necessary if you have decided to obtain the full version
controlled history of Gnuastro, see @ref{Version controlled source} and
@ref{Bootstrapping}.
-Using the version controlled source enables you to always be up to date with
the most recent development work of Gnuastro (bug fixes, new functionalities,
improved algorithms, etc).
+Using the version controlled source enables you to always be up to date with
the most recent development work of Gnuastro (bug fixes, new functionalities,
improved algorithms, etc.).
If you have downloaded a tarball (see @ref{Downloading the source}), then you
can ignore this subsection.
To successfully run the bootstrapping process, there are some additional
dependencies to those discussed in the previous subsections.
These are low level tools that are used by a large collection of Unix-like
operating systems programs, therefore they are most probably already available
in your system.
-If they are not already installed, you should be able to easily find them in
any GNU/Linux distribution package management system (@command{apt-get},
@command{yum}, @command{pacman}, etc).
+If they are not already installed, you should be able to easily find them in
any GNU/Linux distribution package management system (@command{apt-get},
@command{yum}, @command{pacman}, etc.).
The short names in parenthesis in @command{typewriter} font after the package
name can be used to search for them in your package manager.
For the GNU Portability Library, GNU Autoconf Archive and @TeX{} Live, it is
recommended to use the instructions here, not your operating system's package
manager.
@@ -8076,7 +8077,7 @@ For better archivability and compression ratios,
Gnuastro's recommended tarball
Therefore, the package manager commands below also contain Lzip.
@table @asis
-@item @command{apt-get} (Debian-based OSs: Debian, Ubuntu, Linux Mint, etc)
+@item @command{apt-get} (Debian-based OSs: Debian, Ubuntu, Linux Mint, etc.)
@cindex Debian
@cindex Ubuntu
@cindex Linux Mint
@@ -8120,7 +8121,7 @@ Gnuastro is
@url{https://tracker.debian.org/pkg/gnuastro,packaged} in Debian (an
Just make sure it is the most recent version.
@item @command{dnf}
-@itemx @command{yum} (Red Hat-based OSs: Red Hat, Fedora, CentOS, Scientific
Linux, etc)
+@itemx @command{yum} (Red Hat-based OSs: Red Hat, Fedora, CentOS, Scientific
Linux, etc.)
@cindex RHEL
@cindex Fedora
@cindex CentOS
@@ -11618,7 +11619,7 @@ $ seq 0.5 1
@end example
@noindent
-With the simple command below, you can check your current locale environment
variables for specifying the formats of various things like date, time,
monetary, telephone, numbers and etc.
+With the simple command below, you can check your current locale environment
variables for specifying the formats of various things like date, time,
monetary, telephone, numbers, etc.
You can change any of these, by simply giving different values to the
respective variable like above.
For a more complete explanation on each variable, see
@url{https://www.baeldung.com/linux/locale-environment-variables}.
@@ -12423,7 +12424,7 @@ This option can also interpret the older FITS date
format (@code{DD/MM/YYThh:mm:
In this case (following the GNU C Library), this option will make the
following assumption: values 68 to 99 correspond to the years 1969 to 1999, and
values 0 to 68 as the years 2000 to 2068.
This is a very useful option for operations on the FITS date values, for
example, sorting FITS files by their dates, or finding the time difference
between two FITS files.
-The advantage of working with the Unix epoch time is that you do not have to
worry about calendar details (for example, the number of days in different
months, or leap years, etc).
+The advantage of working with the Unix epoch time is that you do not have to
worry about calendar details (for example, the number of days in different
months, or leap years).
@item --wcscoordsys=STR
@cindex Galactic coordinate system
@@ -12922,7 +12923,7 @@ Thick line that has a fixed tangential size (for
example, in kilo parsecs) at th
@item
Contours over the image to show radio/X-ray emission, over an optical image
for example.
@item
-Text or arrows or etc, over certain parts of the image.
+Text, arrows, etc., over certain parts of the image.
@end itemize
@cindex PGFPlots
@@ -12942,7 +12943,7 @@ Therefore the full script (except for the data download
step) is available in @r
@cindex TiKZ
@cindex Matplotlib
PGFPlots uses the same @LaTeX{} graphic engine that typesets your paper/slide.
-Therefore when you build your plots and figures using PGFPlots (and its
underlying package
PGF/TiKZ@footnote{@url{http://mirrors.ctan.org/graphics/pgf/base/doc/pgfmanual.pdf}})
your plots will blend beautifully within your text: same fonts, same colors,
same line properties and etc.
+Therefore when you build your plots and figures using PGFPlots (and its
underlying package
PGF/TiKZ@footnote{@url{http://mirrors.ctan.org/graphics/pgf/base/doc/pgfmanual.pdf}})
your plots will blend beautifully within your text: same fonts, same colors,
same line properties, etc.
Since most papers (and presentation slides@footnote{To build slides, @LaTeX{}
has packages like Beamer, see
@url{http://mirrors.ctan.org/macros/latex/contrib/beamer/doc/beameruserguide.pdf}})
are made with @LaTeX{}, PGFPlots is therefore the best tool for those who use
@LaTeX{} to create documents.
PGFPlots also does not need any extra dependencies beyond a basic/minimal
@TeX{}-live installation, so it is much more reliable than tools like
Matplotlib in Python that have hundreds of fast-evolving
dependencies@footnote{See Figure 1 of Alliez et al. 2020 at
@url{https://arxiv.org/pdf/1905.11123.pdf}}.
@@ -13607,7 +13608,7 @@ Note that this behavior is ideal for gray-scale images,
if you want a color imag
@subsubsection Drawing with vector graphics
With the options described in this section, you can draw marks over your
to-be-published images (for example, in PDF).
-Each mark can be highly customized so they can have different shapes, colors,
linewidths, text, text size and etc.
+Each mark can be highly customized so they can have different shapes, colors,
linewidths, text, text size, etc.
The properties of the marks should be stored in a table that is given to the
@option{--marks} option described below.
A fully working demo on adding marks is provided in @ref{Marking objects for
publication}.
@@ -13668,7 +13669,7 @@ $ astconvertt image.fits --output=image.pdf \
--markcoords=RA,DEC
@end example
-You can highly customize each mark with different columns in @file{marks.fits}
using the @option{--mark*} options below (for example, using different colors,
different shapes, different sizes, text and etc on each mark).
+You can highly customize each mark with different columns in @file{marks.fits}
using the @option{--mark*} options below (for example, using different colors,
different shapes, different sizes, text, and the rest on each mark).
@item --markshdu=STR/INT
The HDU (or extension) name or number of the table containing mark properties
(file given to @option{--marks}).
@@ -13695,7 +13696,7 @@ The column name(s), or number(s), containing the shapes
of each mark (in table g
The shapes can either be identified by their name, or their numerical
identifier.
If identifying them by name in a plain-text table, you need to define a string
column (see @ref{Gnuastro text table format}).
The full list of names is shown below, with their numerical identifier in
parenthesis afterwards.
-For each shape, you can also specify properties like the size, line width,
rotation, color and etc.
+For each shape, you can also specify properties such as the size, line width,
rotation, and color.
See the description of the relevant @option{--mark*} option below.
@table @code
@@ -13884,7 +13885,7 @@ If you are not already familiar with the shape of each
font, please use @option{
@section Table
Tables are the high-level products of processing on low-leveler data like
images or spectra.
-for example, in Gnuastro, MakeCatalog will process the pixels over an object
and produce a catalog (or table) with the properties of each object like
magnitudes, positions and etc (see @ref{MakeCatalog}).
+for example, in Gnuastro, MakeCatalog will process the pixels over an object
and produce a catalog (or table) with the properties of each object such as
magnitudes and positions (see @ref{MakeCatalog}).
Each one of these properties is a column in its output catalog (or table) and
for each input object, we have a row.
When there are only a small number of objects (rows) and not too many
properties (columns), then a simple plain text file is mainly enough to store,
transfer, or even use the produced data.
@@ -13902,7 +13903,7 @@ So while the FITS table standards are very beneficial
for the tools that recogni
This creates limitations for their generic use.
Table is Gnuastro's solution to this problem.
-Table has a large set of operations that you can directly do on any recognized
table (like selecting certain rows, doing arithmetic on the columns and etc).
+Table has a large set of operations that you can directly do on any recognized
table (such as selecting certain rows and doing arithmetic on the columns).
For operations that Table does not do internally, FITS tables (ASCII or
binary) are directly accessible to the users of Unix-like operating systems (in
particular those working the command-line or shell, see @ref{Command-line
interface}).
With Table, a FITS table (in binary or ASCII formats) is only one command away
from AWK (or any other tool you want to use).
Just like a plain text file that you read with the @command{cat} command.
@@ -14431,7 +14432,7 @@ By default all the columns of the given file will be
appended, if you only want
Note that the columns given to @option{--catcolumns} must be present in all
the given files (if this option is called more than once with more than one
file).
If the file given to this option is a FITS file, it is necessary to also
define the corresponding HDU/extension with @option{--catcolumnhdu}.
-Also note that no operation (for example, row selection, arithmetic or etc) is
applied to the table given to this option.
+Also note that no operation (such as row selection and arithmetic) is applied
to the table given to this option.
If the appended columns have a name, and their name is already present in the
table before adding those columns, the column names of each file will be
appended with a @code{-N}, where @code{N} is a counter starting from 1 for each
appended table.
Just note that in the FITS standard (and thus in Gnuastro), column names are
not case-sensitive.
@@ -14667,7 +14668,7 @@ Therefore this option cannot be called with
@option{--head}, @option{--tail}, or
@cindex Random row selection
@cindex Row selection, by random
Select @code{INT} rows from the input table by random (assuming a uniform
distribution).
-This option is applied @emph{after} the value-based selection options (like
@option{--sort}, @option{--range}, @option{--polygon} and etc).
+This option is applied @emph{after} the value-based selection options (such as
@option{--sort}, @option{--range}, and @option{--polygon}).
On the other hand, only the row counters are randomly selected, this option
does not change the order.
Therefore, if @option{--rowrandom} is called together with @option{--sort},
the returned rows are still sorted.
This option cannot be called with @option{--head}, @option{--tail}, or
@option{--rowrange}.
@@ -14805,7 +14806,7 @@ $ astfits query-output.fits -h0
With the full command used to download the dataset, you only need a minimal
knowledge of ADQL to do lower-level customizations on your downloaded dataset.
You can simply copy that command and change the parts of the query string you
want: ADQL is very powerful!
-for example, you can ask the server to do mathematical operations on the
columns and apply selections after those operations, or combine/match multiple
datasets and etc.
+For example, you can ask the server to do mathematical operations on the
columns and apply selections after those operations, or combine/match multiple
datasets.
We will try to add high-level interfaces for such capabilities, but generally,
do not limit yourself to the high-level operations (that cannot cover
everything!).
@menu
@@ -15412,7 +15413,7 @@ Please see the description of this option in
@ref{Invoking astcrop} for its synt
@noindent
@strong{CAUTION:} In WCS mode, the image has to be aligned with the celestial
coordinates, such that the first FITS axis is parallel (opposite direction) to
the Right Ascension (RA) and the second FITS axis is parallel to the
declination.
If these conditions are not met for an image, Crop will warn you and abort.
-You can use Warp's @option{--align} option to align the input image with these
coordinates, see @ref{Warp}.
+You can use Warp to align the input image to standard celestial corrdinates,
see @ref{Warp}.
@end cartouche
@end table
@@ -16116,7 +16117,7 @@ $ astarithmetic 125.0 10 +
@end example
For this particular command, the fix above will be as fast as the
@code{uint16} solution.
-This is because there are only two numbers, and the overhead of Arithmetic
(reading configuration files, and etc) dominates the running time.
+This is because there are only two numbers, and the overhead of Arithmetic
(reading configuration files, etc.) dominates the running time.
However, for large datasets, the @code{uint16} solution will be faster (as you
saw above), Arithmetic will consume less RAM while running, and the output will
consume less storage in your system (all major benefits)!
It is possible to do internal checks in Gnuastro and catch integer overflows
and correct them internally.
@@ -16154,8 +16155,8 @@ Reading NaN as a floating point number in Gnuastro is
not case-sensitive.
@end cartouche
@menu
-* Basic mathematical operators:: for example, +, -, /, log, pow, and etc.
-* Trigonometric and hyperbolic operators:: sin, cos, atan, asinh, and etc
+* Basic mathematical operators:: For example, +, -, /, log, and pow.
+* Trigonometric and hyperbolic operators:: sin, cos, atan, asinh, etc.
* Constants:: Physical and Mathematical constants.
* Unit conversion operators:: Various unit conversions necessary.
* Statistical operators:: Statistics of a single dataset (for example,
mean).
@@ -17374,7 +17375,7 @@ Astronomical images are usually stored as an array
multi-byte pixels with differ
for example, images from CCDs are usually in the unsigned 16-bit integer type
(each pixel takes 16 bits, or 2 bytes, of memory) and fully reduced deep images
have a 32-bit floating point type (each pixel takes 32 bits or 4 bytes).
On the other hand, during the data reduction, we need to preserve a lot of
meta-data about some pixels.
-For example, if a cosmic ray had hit the pixel during the exposure, or if the
pixel was saturated, or is known to have a problem, or if the optical
vignetting is too strong on it, and etc.
+For example, if a cosmic ray had hit the pixel during the exposure, or if the
pixel was saturated, or is known to have a problem, or if the optical
vignetting is too strong on it.
A crude solution is to make a new image when checking for each one of these
things and make a binary image where we flag (set to 1) pixels that satisfy any
of these conditions above, and set the rest to zero.
However, processing pipelines sometimes need more than 20 flags to store
important per-pixel meta-data, and recall that the smallest numeric data type
is one byte (or 8 bits, that can store up to 256 different values), while we
only need two values for each flag!
This is a major waste of storage space!
@@ -19460,7 +19461,7 @@ To find the overlap area of the output pixel over the
input pixels, we need to d
Usually, it is sufficient to define a pixel with a four-vertice polygon.
However, when a non-linear distortion (for example, @code{SIP} or @code{TPV})
is present and the distortion is significant over an output pixel's size
(usually far from the reference point), the shadow of the output pixel on the
input grid can be curved.
To account for such cases (which can only happen when correcting for
non-linear distortions), Warp has the @option{--edgesampling} option to sample
the output pixel over more vertices.
-For more, see the description of this option in @ref{Align pixels with WCS and
remove distortions}.
+For more, see the description of this option in @ref{Align pixels with WCS
account for distortions}.
@node Invoking astwarp, , Resampling, Warp
@subsection Invoking Warp
@@ -19492,6 +19493,10 @@ $ astwarp d.fits $grid --output=D.fits
$ astarithmetic A.fits B.fits C.fits D.fits 4 5 0.2 sigclip-mean \
-g1 --output=stack.fits
+## Warp a previously created mock image to the same pixel grid as the
+## real image (including any distortions).
+$ astwarp mock.fits --gridfile=real.fits
+
## Rotate and then scale input image:
$ astwarp --rotate=37.92 --scale=0.8 image.fits
@@ -19518,7 +19523,10 @@ Just note that the file size will also be double!
For more on the precision of various types, see @ref{Numeric data types}.
By default (if no linear operation is requested), Warp will align the pixel
grid of the input image to the WCS coordinates it contains.
-This operation and the the options that govern it are described in @ref{Align
pixels with WCS and remove distortions}.
+This operation and the the options that govern it are described in @ref{Align
pixels with WCS account for distortions}.
+You can Warp an input image to the same pixel grid as a reference FITS file
using the @option{--wcsfile} option.
+In this case, the output image will take all the information needed from the
reference WCS file and HDU/extension specified with @option{--wcshdu}, thus it
will discard any other resampling options given.
+
If you need any custom linear warping (independent of the WCS, see @ref{Linear
warping basics}), you need to call the respective operation manually.
These are described in @ref{Linear warps to be called explicitly}.
Please note that you may not use both linear and non-linear modes
simultaneously.
@@ -19543,12 +19551,12 @@ As a result, with @option{--coveredfrac=0}, the sum
of the pixels in the input a
@end table
@menu
-* Align pixels with WCS and remove distortions:: Default operation.
-* Linear warps to be called explicitly:: Other waprs.
+* Align pixels with WCS account for distortions:: Default operation.
+* Linear warps to be called explicitly:: Other warps.
@end menu
-@node Align pixels with WCS and remove distortions, Linear warps to be called
explicitly, Invoking astwarp, Invoking astwarp
-@subsubsection Align pixels with WCS and remove distortions
+@node Align pixels with WCS account for distortions, Linear warps to be called
explicitly, Invoking astwarp, Invoking astwarp
+@subsubsection Align pixels with WCS account for distortions
@cindex Resampling
@cindex WCS distortion
@@ -19560,6 +19568,16 @@ When none of the linear warps@footnote{For linear
warps, see @ref{Linear warps t
In the process, any possibly existing distortion is also removed (such as
@code{TPV} and @code{SIP}).
Usually, the WCS axes are the Right Ascension and Declination in equatorial
coordinates.
The output image's pixel grid is highly customizable through the options in
this section.
+To learn about Warp's strategy to build the new pixel grid, see
@ref{Resampling}.
+For strong distortions (that produce strong curvatures), you can fine-tune the
area-based resampling with @option{--edgesampling}, as described below.
+
+On the other hand, sometimes you need to Warp an input image to the exact same
grid of an already available reference FITS image with an existing WCS.
+If that image is already aligned, finding its center, number of pixels and
pixel scale can be annoying (and just increase the complexity of your script).
+On the other hand, if that image is not aligned (for example, has a certain
rotation in the sky, and has a different distortion), there are too many WCS
parameters to set (some are not yet available explicitly in the options here)!
+For such scenarios, Warp has the @option{--gridfile} option.
+When @option{--gridfile} is called, the options below that are used to define
the output's WCS will be ignored (these options: @option{--center},
@option{--widthinpix}, @option{--cdelt}, @option{--ctype}).
+In this case, the output's WCS and pixel grid will exactly match the image
given to @option{--gridfile} (including any rotation, pixel scale, or
distortion or projection).
+See the description of @option{--gridfile} below for more.
@table @option
@item -c FLT,FLT
@@ -19567,7 +19585,7 @@ The output image's pixel grid is highly customizable
through the options in this
@cindex CRVALi
@cindex Aligning an image
WCS coordinates of the center of the central pixel of the output image.
-If @option{--center} isn't given, the output will have have the same central
WCS coordinate as the input.
+When @option{--center} or @option{--gridfile} aren't given, the output will
have have the same central WCS coordinate as the input.
Usually, the WCS coordinates are Right Ascension and Declination (when the
first three characters of @code{CTYPE1} and @code{CTYPE2} are respectively
@code{RA-} and @code{DEC}).
For more on the @code{CTYPEi} keyword values, see @code{--ctype}.
@@ -19575,7 +19593,7 @@ For more on the @code{CTYPEi} keyword values, see
@code{--ctype}.
@item -w INT,INT
@itemx --widthinpix=INT,INT
Pixel width and height of the output image.
-When @option{--widthinpix} isn't given, Warp will calculate the necessary size
of the output pixel grid to fully contain the input image.
+When @option{--widthinpix} or @option{--gridfile} aren't given, Warp will
calculate the necessary size of the output pixel grid to fully contain the
input image.
This option should be given two @emph{odd} integers that are greater than 1,
so that the output image can have a @emph{central} pixel.
Recall that through the @option{--center} option, you specify the WCS
coordinate of the center of the central pixel.
@@ -19589,7 +19607,7 @@ If any of the given values are even, Warp will
automatically add a single pixel
Coordinate deltas or increments (@code{CDELTi} in the FITS standard), or the
pixel scale in both dimensions.
If a single value is given, it will be used for both axes.
In this way, the output's pixels will be squares on the sky at the reference
point (as is usually expected!).
-When this option isn't given, Warp will read the input's pixel scale and
choose the larger of @code{CDELT1} or @code{CDELT2} so the output pixels are
square.
+When @option{--cdelt} or @option{--gridfile} aren't given, Warp will read the
input's pixel scale and choose the larger of @code{CDELT1} or @code{CDELT2} so
the output pixels are square.
Usually (when dealing with RA and Dec, and the @code{CUNITi}s have a value of
@code{deg}), the units of the given values are degrees/pixel.
Warp allows you to easily convert from @emph{arcsec} to @emph{degrees} by
simply appending a @code{/3600} to the value.
@@ -19602,7 +19620,9 @@ For example, for an output image of pixel scale
@code{0.27} arcsec/pixel, you ca
@cindex Resampling
The coordinate types of the output (@code{CTYPE1} and @code{CTYPE2} keywords
in the FITS standard), separated by a comma.
By default the value to this option is `@code{RA---TAN,DEC--TAN}'.
-Therefore if you don't call this option, the output WCS coordinates will be
Right Ascension and Declination, while the output's pojection will be
@url{https://en.wikipedia.org/wiki/Gnomonic_projection,Gnomonic}, also known as
Tantential (TAN).
+However, if @option{--gridfile} is given, this option is ignored.
+
+If you don't call @option{--ctype} or @option{--gridfile}, the output WCS
coordinates will be Right Ascension and Declination, while the output's
pojection will be
@url{https://en.wikipedia.org/wiki/Gnomonic_projection,Gnomonic}, also known as
Tantential (TAN).
This combination is the most common in extragalactic imaging surveys.
For other coordinates and projections in your output use other values, as
described below.
@@ -19709,7 +19729,49 @@ HEALPix
HEALPix polar, aka "butterfly"
@end table
+@item -G
+@itemx --gridfile
+FITS filename containing the final pixel grid and WCS for the output image.
+The HDU/extension containing should be specified with @option{--gridhdu} or
its short option @option{-H}.
+The HDU should contain a WCS, otherwise, Warp will abort with a crash.
+When this option is used, Warp will read the respective WCS and the size of
the image to resample the input.
+Since this WCS of this HDU contains everything needed to construct the WCS the
options above will be ignored when @option{--gridfile} is called:
@option{--cdelt}, @option{--center}, and @option{--widthinpix}.
+
+In the example below, let's use this option to put the image of M51 in one
survey (J-PLUS) into the pixel grid of another survey (SDSS) containing M51.
+The J-PLUS field of view is very large (almost @mymath{1.5\times1.5}
deg@mymath{^2}, in @mymath{9500\times9500} pixels), while the field of view of
SDSS in each filter is small (almost @mymath{0.3\times0.25} deg@mymath{^2} in
@mymath{2048\times1489} pixels).
+With the first two commands, we'll first download the two images, then we'll
extract the portion of the J-PLUS image that overlaps with the SDSS image and
align it exactly to SDSS's pixel grid.
+Note that these are the two images that were used in two of Gnuastro's
tutorials: @ref{Building the extended PSF} and @ref{Detecting large extended
targets}.
+
+@example
+## Download the J-PLUS DR2 image of M51 in the r filter.
+$ jplusbase="http://archive.cefca.es/catalogues/vo/siap";
+$ wget $jplusbase/jplus-dr2/get_fits?id=67510 \
+ -O jplus.fits.fz
+## Download the SDSS image in r filter and decompress it
+## (Bzip2 is not a standard FITS compression algorithm).
+$ sdssbase=https://dr12.sdss.org/sas/dr12/boss/photoObj/frames
+$ wget $sdssbase/301/3716/6/frame-r-003716-6-0117.fits.bz2 \
+ -O sdss.fits.bz2
+$ bunzip2 sdss.fits.bz2
+
+## Warp and crop the J-PLUS image so the output exactly
+## matches the SDSS pixel gid.
+$ astwarp jplus.fits.fz --gridfile=sdss.fits --gridhdu=0 \
+ --output=jplus-on-sdss.fits
+
+## View the two images side-by-side:
+$ astscript-fits-view sdss.fits jplus-on-sdss.fits
+@end example
+
+As the example above shows, this option can therefore be very useful when
comparing images from multiple surveys.
+But there are other very interesting use cases also.
+For example, when you are making a mock dataset and need to add distortion to
the image so it matches the distortion of your camera.
+Through @option{--gridhdu}, you can easily insert that distortion over the
mock image and put the mock image in the pixel grid of an exposure.
+
+@item -H
+@itemx --gridhdu
+The HDU/extension of the reference WCS file specified with option
@option{--wcsfile} or its short version @option{-H} (see the description of
@option{--wcsfile} for more).
@item --edgesampling=INT
Number of extra samplings along the edge of a pixel.
@@ -19726,14 +19788,13 @@ Since the polygon clipping will happen for every
output pixel, a higher value to
-
-@node Linear warps to be called explicitly, , Align pixels with WCS and
remove distortions, Invoking astwarp
+@node Linear warps to be called explicitly, , Align pixels with WCS account
for distortions, Invoking astwarp
@subsubsection Linear warps to be called explicitly
-Linear warps include operations like rotation, scaling, sheer and etc.
+Linear warps include operations like rotation, scaling, sheer, etc.
For an introduction, see @ref{Linear warping basics}.
These are warps that don't depend on the WCS of the image and should be
expliclitly requested.
-To align the input pixel coordinates with the WCS coordinates, see @ref{Align
pixels with WCS and remove distortions}.
+To align the input pixel coordinates with the WCS coordinates, see @ref{Align
pixels with WCS account for distortions}.
While they will correct any existing WCS based on the warp, they can also
operate on images without any WCS.
For example, you have a mock image that doesn't (yet!) have its mock WCS, and
it has been created on an over-sampled grid and convolved with an over-sampled
PSF.
@@ -20130,7 +20191,7 @@ $ ds9 cmd-2d-hist.fits -cmap sls -zoom to fit -grid yes
\
-grid type publication
@end example
-If you are happy with the grid and coloring and etc, you can also use ds9 to
save this as a JPEG image to directly use in your documents/slides with these
extra DS9 options (DS9 will write the image to @file{cmd-2d.jpeg} and quit
immediately afterwards):
+If you are happy with the grid, coloring and the rest, you can also use ds9 to
save this as a JPEG image to directly use in your documents/slides with these
extra DS9 options (DS9 will write the image to @file{cmd-2d.jpeg} and quit
immediately afterwards):
@example
$ ds9 cmd-2d-hist.fits -cmap sls -zoom 4 -grid yes \
@@ -20140,7 +20201,7 @@ $ ds9 cmd-2d-hist.fits -cmap sls -zoom 4 -grid yes \
@cindex PGFPlots (@LaTeX{} package)
This is good for a fast progress update.
But for your paper or more official report, you want to show something with
higher quality.
-For that, you can use the PGFPlots package in @LaTeX{} to add axes in the same
font as your text, sharp grids and many other elegant/powerful features (like
over-plotting interesting points, lines and etc).
+For that, you can use the PGFPlots package in @LaTeX{} to add axes in the same
font as your text, sharp grids and many other elegant/powerful features (like
over-plotting interesting points and lines).
But to load the 2D histogram into PGFPlots first you need to convert the FITS
image into a more standard format, for example, PDF.
We will use Gnuastro's @ref{ConvertType} for this, and use the
@code{sls-inverse} color map (which will map the pixels with a value of zero to
white):
@@ -21528,7 +21589,7 @@ The file will have two extensions for each step (one
for the Sky and one for the
@cindex Segmentation
Once instrumental signatures are removed from the raw data (image) in the
initial reduction process (see @ref{Data manipulation}).
You are naturally eager to start answering the scientific questions that
motivated the data collection in the first place.
-However, the raw dataset/image is just an array of values/pixels, that is all!
These raw values cannot directly be used to answer your scientific questions:
for example, ``how many galaxies are there in the image?'', ``What is their
brightness?'' and etc.
+However, the raw dataset/image is just an array of values/pixels, that is all!
These raw values cannot directly be used to answer your scientific questions:
for example, ``how many galaxies are there in the image?'' and ``What is their
brightness?''.
The first high-level step your analysis will therefore be to classify, or
label, the dataset elements (pixels) into two classes:
1) Noise, where random effects are the major contributor to the value, and
@@ -21801,7 +21862,7 @@ option.
@item --convolved=FITS
Use this file as the convolved image and do not do convolution (ignore
@option{--kernel}).
NoiseChisel will just check the size of the given dataset is the same as the
input's size.
-If a wrong image (with the same size) is given to this option, the results
(errors, bugs, etc) are unpredictable.
+If a wrong image (with the same size) is given to this option, the results
(errors, bugs, etc.) are unpredictable.
So please use this option with care and in a highly controlled environment,
for example, in the scenario discussed below.
In almost all situations, as the input gets larger, the single most CPU (and
time) consuming step in NoiseChisel (and other programs that need a convolved
image) is convolution.
@@ -22859,7 +22920,7 @@ For those who feel MakeCatalog's existing
measurements/columns are not enough an
@menu
* Detection and catalog production:: Discussing why/how to treat these
separately
-* Brightness flux magnitude:: More on Magnitudes, surface brightness and etc.
+* Brightness flux magnitude:: More on Magnitudes, surface brightness, etc.
* Quantifying measurement limits:: For comparing different catalogs.
* Measuring elliptical parameters:: Estimating elliptical parameters.
* Adding new columns to MakeCatalog:: How to add new columns.
@@ -26621,7 +26682,7 @@ $ astcosmiccal -l0.7 -m0.3 -z2.1
$ astcosmiccal --obsline=lyalpha,4000 --listlinesatz
@end example
-The input parameters (for example, current matter density, etc) can be given
as command-line options or in the configuration files, see @ref{Configuration
files}.
+The input parameters (current matter density, etc.) can be given as
command-line options or in the configuration files, see @ref{Configuration
files}.
For a definition of the different parameters, please see the sections prior to
this.
If no redshift is given, CosmicCalculator will just print its input parameters
and abort.
For a full list of the input options, please see @ref{CosmicCalculator input
options}.
@@ -26637,7 +26698,7 @@ CosmicCalculator also has features to help in such
situations, please see @ref{C
@menu
* CosmicCalculator input options:: Options to specify input conditions.
-* CosmicCalculator basic cosmology calculations:: Like distance modulus,
distances and etc.
+* CosmicCalculator basic cosmology calculations:: Such as distance modulus
and distances.
* CosmicCalculator spectral line calculations:: How they get affected by
redshift.
@end menu
@@ -27478,7 +27539,7 @@ The latter case can be useful when you want to ignore
part of the 2D shape (for
You can visually see the shape of the region used by running this script with
@option{--keeptmp} and viewing the @file{values.fits} and @file{apertures.fits}
files of the temporary directory with a FITS image viewer like @ref{SAO DS9}.
You can use @ref{Viewing FITS file contents with DS9 or TOPCAT} to open them
together in one instance of DS9, with both frames matched and locked (for easy
comparison in case you want to zoom-in or out).
-for example, see the commands below (based on your target object, just change
the image name, center, position angle and etc):
+For example, see the commands below (based on your target object, just change
the image name, center, position angle, etc.):
@example
## Generate the radial profile
@@ -27497,7 +27558,7 @@ $ astscript-fits-view radial-tmp/values.fits \
@itemx --measure=STR
The operator for measuring the values over each radial distance.
The values given to this option will be directly passed to @ref{MakeCatalog}.
-As a consequence, all MakeCatalog measurements like the magnitude, magnitude
error, median, mean, signal-to-noise ratio (S/N), std, surface brightness,
sigclip-mean, sigclip-number, etc. can be used here.
+As a consequence, all MakeCatalog measurements like the magnitude, magnitude
error, median, mean, signal-to-noise ratio (S/N), std, surface brightness,
sigclip-mean, and sigclip-number can be used here.
For a full list of MakeCatalog's measurements, please run
@command{astmkcatalog --help}.
Multiple values can be given to this option, each separated by a comma.
This option can also be called multiple times.
@@ -27893,7 +27954,7 @@ The point spread function (PSF) describes how the light
of a point-like source i
Since the light of all astrophysical sources undergoes all these effects,
characterizing the PSF is key in astronomical analysis (for small and large
objects).
Consequently, having a good characterization of the PSF is fundamental to any
analysis.
-In some situations@footnote{An example scenario where a parametric PSF may be
enough: you are only interested in very small, high redshift objects that only
extended a handful of pixels.} a parametric (analytical) model is sufficient
for the PSF (Gaussian, Moffat, etc., see @ref{PSF}).
+In some situations@footnote{An example scenario where a parametric PSF may be
enough: you are only interested in very small, high redshift objects that only
extended a handful of pixels.} a parametric (analytical) model is sufficient
for the PSF (such as Gaussian or Moffat, see @ref{PSF}).
However, once you are interested in objects that are larger than a handful of
pixels, it is almost impossible to find an analytic function to adequately
characterize the PSF.
Therefore, it is necessary to obtain an empirical (non-parametric) and
extended PSF.
In this section we describe a set of installed scrips in Gnuastro that will
let you construct the non-parametric PSF using point-like sources.
@@ -28895,7 +28956,7 @@ If you are already familiar with these concepts, please
skip this section and go
@cindex Modularity
In theory, a full operating system (or any software) can be written as one
function.
Such a software would not need any headers or linking (that are discussed in
the subsections below).
-However, writing that single function and maintaining it (adding new features,
fixing bugs, documentation, etc) would be a programmer or scientist's worst
nightmare! Furthermore, all the hard work that went into creating it cannot be
reused in other software: every other programmer or scientist would have to
re-invent the wheel.
+However, writing that single function and maintaining it (adding new features,
fixing bugs, documentation, etc.) would be a programmer or scientist's worst
nightmare! Furthermore, all the hard work that went into creating it cannot be
reused in other software: every other programmer or scientist would have to
re-invent the wheel.
The ultimate purpose behind libraries (which come with headers and have to be
linked) is to address this problem and increase modularity: ``the degree to
which a system's components may be separated and recombined'' (from Wikipedia).
The more modular the source code of a program or library, the easier
maintaining it will be, and all the hard work that went into creating it can be
reused for a wider range of problems.
@@ -30851,7 +30912,7 @@ simplify the allocation (and later cleaning) of several
@code{gal_data_t}s
that are related.
For example, each column in a table is usually represented by one
-@code{gal_data_t} (so it has its own name, data type, units, etc). A
+@code{gal_data_t} (so it has its own name, data type, units, etc.). A
table (with many columns) can be seen as an array of @code{gal_data_t}s
(when the number of columns is known a-priori). The functions below are
defined to create a cleared array of data structures and to free them when
@@ -31410,7 +31471,7 @@ in the same order that they are stored. Each integer is
printed on one
line. This function is mainly good for checking/debugging your program. For
program outputs, it is best to make your own implementation with a better,
more user-friendly format. for example, the following code snippet. You can
-also modify it to print all values in one line, etc, depending on the
+also modify it to print all values in one line, etc., depending on the
context of your program.
@example
@@ -31515,7 +31576,7 @@ the same order that they are stored. Each integer is
printed on one
line. This function is mainly good for checking/debugging your program. For
program outputs, it is best to make your own implementation with a better,
more user-friendly format. For example, the following code snippet. You can
-also modify it to print all values in one line, etc, depending on the
+also modify it to print all values in one line, etc., depending on the
context of your program.
@example
@@ -31604,7 +31665,7 @@ the same order that they are stored. Each floating
point number is printed
on one line. This function is mainly good for checking/debugging your
program. For program outputs, it is best to make your own implementation with
a better, more user-friendly format. For example, in the following code
-snippet. You can also modify it to print all values in one line, etc,
+snippet. You can also modify it to print all values in one line, etc.,
depending on the context of your program.
@example
@@ -31694,9 +31755,9 @@ Return a pointer to the last node in @code{list}.
Print the values within each node of @code{*list} on the standard output in
the same order that they are stored. Each floating point number is printed
on one line. This function is mainly good for checking/debugging your
-program. For program outputs, it s best to make your own implementation with
+program. For program outputs, it is best to make your own implementation with
a better, more user-friendly format. For example, in the following code
-snippet. You can also modify it to print all values in one line, etc,
+snippet. You can also modify it to print all values in one line, etc.,
depending on the context of your program.
@example
@@ -32620,7 +32681,7 @@ So to avoid leaking memory, if a sub-second string is
requested, it must be free
When a sub-second string does not exist (and it is requested), then a value of
@code{NULL} and NaN will be written in @code{*subsecstr} and @code{*subsec}
respectively.
This is a very useful function for operations on the FITS date values, for
example, sorting FITS files by their dates, or finding the time difference
between two FITS files.
-The advantage of working with the Unix epoch time is that you do not have to
worry about calendar details (for example, the number of days in different
months, or leap years, etc).
+The advantage of working with the Unix epoch time is that you do not have to
worry about calendar details (such as the number of days in different months or
leap years).
@end deftypefun
@deftypefun void gal_fits_key_read_from_ptr (fitsfile @code{*fptr}, gal_data_t
@code{*keysll}, int @code{readcomment}, int @code{readunit})
@@ -33438,7 +33499,7 @@ However you still need to be cautious in the following
scenarios below.
Many users or operating systems may still use an older version.
@item
The @code{wcsprm} structure of WCSLIB is not thread-safe: you can't use the
same pointer on multiple threads.
-for example, if you use @code{gal_wcs_img_to_world} simultaneously on multiple
threads, you shouldn't pass the same @code{wcsprm} structure pointer.
+For example, if you use @code{gal_wcs_img_to_world} simultaneously on multiple
threads, you shouldn't pass the same @code{wcsprm} structure pointer.
You can use @code{gal_wcs_copy} to keep and use separate copies the main
structure within each thread, and later free the copies with
@code{gal_wcs_free}.
@end itemize
@@ -35419,7 +35480,7 @@ have any type), see above for the definition of
permutation.
@cindex Coordinate matching
Matching is often necessary when two measurements of the same points have been
done using different instruments (or hardware), different software or different
configurations of the same software.
In other words, you have two catalogs or tables, and each has N columns
containing the N-dimensional ``coordinate'' values of each point.
-Each table can have other columns too, for example, one can have brightness
measurements in one filter, and another can have morphology measurements or etc.
+Each table can have other columns too, for example, one can have brightness
measurements in one filter, and another can have morphology measurements.
The matching functions here will use the coordinate columns of the two tables
to find a permutation for each, and the total number of matched rows
(@mymath{N_{match}}).
This will enable you to match by the positions if you like.
@@ -35459,7 +35520,7 @@ When the aperture is an ellipse, distances between the
points are also calculate
@strong{Output permutations ignore internal sorting}: the output permutations
will correspond to the initial inputs.
Therefore, even when @code{inplace!=0} (and this function re-arranges the
inputs in place), the output permutation will correspond to original (possibly
non-sorted) inputs. The reason for this is that you rarely want to permute the
actual positional columns after the match.
-Usually, you also have other columns (for example, the brightness, morphology
and etc) and you want to find how they differ between the objects that match.
+Usually, you also have other columns (such as the brightness and morphology)
and you want to find how they differ between the objects that match.
Once you have the permutations, they can be applied to those other columns
(see @ref{Permutations}) and the higher-level processing can continue.
So if you do not need the coordinate columns for the rest of your analysis, it
is better to set @code{inplace=1}.
@@ -36505,7 +36566,7 @@ tile/value will be associated to each clump based on
its flux-weighted
(only positive values) center.
The main output is an internally allocated, 1-dimensional array with one
-value per label. The array information (length, type, etc) will be
+value per label. The array information (length, type, etc.) will be
written into the @code{sig} generic data container. Therefore
@code{sig->array} must be @code{NULL} when this function is called. After
this function, the details of the array (number of elements, type and size,
@@ -36875,7 +36936,7 @@ Gnuastro's Warp program uses the following functions
for its default mode (when
Through the following functions, you can directly access those features in
your own custom programs.
The linear warping operations of the Warp program aren't yet brought into the
library.
If you need them please get in touch with us at @code{bug-gnuastro@@gnu.org}.
-For a demo please refer to @ref{Library demo - resampling an image to a new
grid}.
+For usage examples of this library, please see @ref{Library demo - Warp to
another image} or @ref{Library demo - Warp to new grid}.
You are free to provide any valid WCS keywords to the functions defined in
this library using the @code{gal_warp_wcsalign_t} data type.
This might be used to align the input image to the standard WCS grid,
potentially changing the pixel scale, removing any valid WCS non-linear
distortion available, and projecting to any valid WCS projection type.
@@ -36886,22 +36947,25 @@ The main data container for inputs, output and
internal variables to simplify th
Due to the large number of input variables, this structure makes it easy to
call the main functions.
Similar to @code{gal_data_t}, the @code{gal_warp_wcsalign_t} is a structure
@code{typedef}'d as a new type, see @ref{Library data container}.
Please note that this structure has elements that are @emph{allocated}
dynamically and must be freed after usage.
-@code{gal_warp_wcsalign_free} only frees the internal variables, so you are
responsible for freeing your own inputs (like @code{cdelt}, @code{input} and
etc) and the output.
+@code{gal_warp_wcsalign_free} only frees the internal variables, so you are
responsible for freeing your own inputs (@code{cdelt}, @code{input}, etc.) and
the output.
The internal variables are cached here to cut cpu-intensive computations.
+To prevent from using uninitialized variables, we recommend using the helper
function @code{gal_warp_wcsalign_template} to get a clean structure before
setting your own variables.
The structure and each of its elements are defined below:
@example
typedef struct
@{
- /* Arguments given (and later freed) by the caller. */
- gal_data_t *ctype;
- gal_data_t *cdelt;
+ /* Arguments given (and later freed) by the caller. If 'twcs' is
+ given, then the "WCS To build" elements will be ignored. */
gal_data_t *input;
- gal_data_t *widthinpix;
- gal_data_t *center;
size_t numthreads;
double coveredfrac;
size_t edgesampling;
+ gal_data_t *widthinpix;
+ struct wcsprm *twcs; /* WCS Predefined. */
+ gal_data_t *ctype; /* WCS To build. */
+ gal_data_t *cdelt; /* WCS To build. */
+ gal_data_t *center; /* WCS To build. */
/* Output (must be freed by caller) */
gal_data_t *output;
@@ -36917,31 +36981,9 @@ typedef struct
@end example
@table @code
-@item gal_data_t *ctype
-The output's projection type.
-The dataset has to have the type @code{GAL_TYPE_STRING}, containing exactly
two strings.
-Both strings will be directly passed to WCSLIB and should conform to the FITS
standard's @code{CTYPEi} keywords, see the description of @option{--ctype} in
@ref{Align pixels with WCS and remove distortions}.
-For example, @code{"RA---TAN"} and @code{"DEC--TAN"}, or @code{"RA---HPX"} and
@code{"DEC--HPX"}.
-
-@item gal_data_t *cdelt
-Output pixel scale (size of pixel in the WCS units: value to @code{CUNITi}
keywords in FITS, usually degrees).
-The dataset should have a type of @code{GAL_TYPE_FLOAT64} and contain exactly
two values.
-Hint: to convert arcsec to degrees, just divide by 3600.
-
@item gal_data_t *input
The input dataset.
-This dataset must contain both the image array of type
@code{GAL_TYPE_FLOAT64}, and @code{input->wcs} should not be @code{NULL} for
the WCS-aligning operations to work, see @ref{Library demo - resampling an
image to a new grid}.
-
-@item gal_data_t *widthinpix
-Output image size (width and height) in number of pixels.
-If a @code{NULL} pointer is passed, the WCS-aligning operations will estimate
the output image size internally such that it contains the full input.
-This dataset should have a type of @code{GAL_TYPE_SIZE_T} and contain exactly
two @emph{odd} values.
-This ensures that the center of the central pixel lies at the requested
central coordinate (note that an image with an even number of pixels doesn't
have a ``central'' pixel!
-
-@item gal_data_t *center
-WCS coordinate of the center of the central pixel of the output.
-The units depend on the WCS, for example, if the @code{CUNITi} keywords are
@code{deg}, it is in degrees.
-This dataset should have a type of @code{GAL_TYPE_FLOAT64} and contain exactly
two values.
+This dataset must contain both the image array of type
@code{GAL_TYPE_FLOAT64}, and @code{input->wcs} should not be @code{NULL} for
the WCS-aligning operations to work, see @ref{Library demo - Warp to new grid}.
@item size_t numthreads
Number of threads to use during the WCS aligning operations.
@@ -36958,10 +37000,53 @@ For more, see the description of
@option{--coveredfrac} in @ref{Invoking astwarp
Set the number of extra vertices along each edge of the output pixel's polygon
to account for potential curvature due to projection or distortion.
A value of @code{0} is usually enough for this (so the pixel is only defined
by a four vertice polygon.
Greater values increase memory usage and program execution time.
-For more, plese see the description of @option{--edgesampling} in @ref{Align
pixels with WCS and remove distortions}.
+For more, plese see the description of @option{--edgesampling} in @ref{Align
pixels with WCS account for distortions}.
+
+@item gal_data_t *widthinpix
+Output image size (width and height) in number of pixels.
+If a @code{NULL} pointer is passed, the WCS-aligning operations will estimate
the output image size internally such that it contains the full input.
+This dataset should have a type of @code{GAL_TYPE_SIZE_T} and contain exactly
two @emph{odd} values.
+This ensures that the center of the central pixel lies at the requested
central coordinate (note that an image with an even number of pixels doesn't
have a ``central'' pixel!
+
+@item struct wcsprm *twcs
+The target grid WCS which must follow the standard WCSLIB structure.
+You can read it from a file using @code{gal_wcs_read} or create an entirely
new one with @code{gal_wcs_create} and later free it with @code{gal_wcs_free},
see @ref{World Coordinate System}.
+If this element is given, the @code{ctype}, @code{cdelt} and @code{center}
elements (which are used to construct a WCS internally) are ignored.
+
+Please note that the @code{wcsprm} structure doesn't contain the image size.
+To set the final image size, you should use @option{widthinpix}.
+
+@item gal_data_t *ctype
+The output's projection type.
+The dataset has to have the type @code{GAL_TYPE_STRING}, containing exactly
two strings.
+Both strings will be directly passed to WCSLIB and should conform to the FITS
standard's @code{CTYPEi} keywords, see the description of @option{--ctype} in
@ref{Align pixels with WCS account for distortions}.
+For example, @code{"RA---TAN"} and @code{"DEC--TAN"}, or @code{"RA---HPX"} and
@code{"DEC--HPX"}.
+
+@item gal_data_t *cdelt
+Output pixel scale (size of pixel in the WCS units: value to @code{CUNITi}
keywords in FITS, usually degrees).
+The dataset should have a type of @code{GAL_TYPE_FLOAT64} and contain exactly
two values.
+Hint: to convert arcsec to degrees, just divide by 3600.
+
+@item gal_data_t *center
+WCS coordinate of the center of the central pixel of the output.
+The units depend on the WCS, for example, if the @code{CUNITi} keywords are
@code{deg}, it is in degrees.
+This dataset should have a type of @code{GAL_TYPE_FLOAT64} and contain exactly
two values.
+
@end table
@end deftp
+@deftypefun gal_warp_wcsalign_t gal_warp_wcsalign_template (void)
+A high-level helper function that returns a clean @code{gal_warp_wcsalign_t}
struct with all values initialized
+This function returns a copy of a statically allocated structure. So you don't
need to free the returned structure.
+
+The Warp library decides on the program flow based on this struct.
+Uninitialized pointers can point to random space in RAM which can create
segmentation faults, or even worse, produce unnoticed side-effects.
+It is therefore good practice to manually set unused pointers to @code{NULL}
and give blank values to numbers
+Since there are many variables and pointers in @code{gal_warp_wcsalign_t}, it
is easy to forget @emph{initializing} them.
+With that said, we recommend using this function to minimize human error.
+
+
+@end deftypefun
@deftypefun void gal_warp_wcsalign (gal_warp_wcsalign_t *wa)
A high-level function to align the input dataset's pixels to its WCS
coordinates and write the result in @code{wa->output}.
@@ -37474,7 +37559,7 @@ The last one (@code{INVALID}) is for sanity checks (for
example, to know if the
@cindex SAO DS9 region file
@cindex Region file (SAO DS9)
Returns an allocated generic data container (@code{gal_data_t}, with an array
of @code{GAL_TYPE_FLOAT64}) containing the vertices of a polygon within the SAO
DS9 region file given by @code{*filename}.
-Since SAO DS9 region files are 2 dimensional, if there are @mymath{N} vertices
in the SAO DS9 region file, the returned dataset will have @mymath{2\times N}
elements (first two elements belonging to first vertice, and etc).
+Since SAO DS9 region files are 2 dimensional, if there are @mymath{N} vertices
in the SAO DS9 region file, the returned dataset will have @mymath{2\times N}
elements (first two elements belonging to first vertice, etc.).
The mode to interpret the vertice coordinates is also read from the SAO DS9
region file and written into the @code{status} attribute of the output
@code{gal_data_t}.
The coordinate mode can be one of the @code{GAL_DS9_COORD_MODE_*} macros,
mentioned above.
@@ -37518,7 +37603,8 @@ use those that are generated by Gnuastro after
@command{make check} in the
* Library demo - inspecting neighbors:: Inspect the neighbors of a pixel.
* Library demo - multi-threaded operation:: Doing an operation on threads.
* Library demo - reading and writing table columns:: Simple Column I/O.
-* Library demo - resampling an image to a new grid::
+* Library demo - Warp to another image:: Output pixel grid and WCS from
another image.
+* Library demo - Warp to new grid:: Define a new pixel grid and WCS to
resample the input.
@end menu
@node Library demo - reading a image, Library demo - inspecting neighbors,
Library demo programs, Library demo programs
@@ -37766,7 +37852,7 @@ main(void)
-@node Library demo - reading and writing table columns, Library demo -
resampling an image to a new grid, Library demo - multi-threaded operation,
Library demo programs
+@node Library demo - reading and writing table columns, Library demo - Warp to
another image, Library demo - multi-threaded operation, Library demo programs
@subsection Library demo - reading and writing table columns
Tables are some of the most common inputs to, and outputs of programs. This
@@ -37905,14 +37991,119 @@ main(void)
-@node Library demo - resampling an image to a new grid, , Library demo -
reading and writing table columns, Library demo programs
-@subsection Library demo - resampling an image to a new grid
-Gnuastro's warp library allows you to resample an image from a grid to another
entirely using the WCSLIB.
-You may use it to remove non-linear distortions from an image, change pixel
scale, projection type, or just align the image to get it ready for
@emph{stacking} several images.
-Here you can find an example program that demonstrates the usage of the
respective functions in @ref{Warp library}.
+@node Library demo - Warp to another image, Library demo - Warp to new grid,
Library demo - reading and writing table columns, Library demo programs
+@subsection Library demo - Warp to another image
+Gnuastro's warp library (that you can access by including
@file{gnuastro/warp.h}) allows you to resample an image from a grid to another
entirely using the WCSLIB (while acconting for distortions if necessary; see
@ref{Warp library}).
+The Warp library uses a pixel-mixing or area-based resampling approach which
is fully described in @ref{Resampling}.
+The most generic uses cases for this library are already available in the
@ref{Invoking astwarp} program.
+For a related demo (where the output grid and WCS are constructed from
scratch), see @ref{Library demo - Warp to new grid}.
-To compile the program, put the code below in a plain-text file (let's assume
its called @file{align.c}) and use @ref{BuildProgram} with this command:
`@command{astbuildprog align.c}'.
+In the example below, we are warping the @code{input.fits} file to the same
pixel grid and WCS as @code{reference.fits} image (assuming it is in hdu
@code{0}).
+Feel free to change these names to your own test file names.
+This can be useful when you have a complex grid and WCS containing various
keywords such as non-linear distortion coefficients, etc.
+For example datasets, see the description of the @option{--gridfile} option in
@ref{Align pixels with WCS account for distortions}.
+
+To compile the demonstration program below, copy and paste the contents in a
plain-text file (let's assume you named it @file{align-to-img.c}) and use
@ref{BuildProgram} with this command: `@command{astbuildprog align-to-img.c}'.
+Please note that the demo program does not perform many sanity checks to avoid
making it too complex and to highlight this particular feature in the library.
+For a robust method write programs with all the necessary sanity checks, see
Gnuastro's Warp source code, see @ref{Program source}.
+
+@example
+@verbatim
+#include <stdio.h>
+#include <stdlib.h>
+
+#include <gnuastro/wcs.h> /* contains gnuastro's fits.h */
+#include <gnuastro/warp.h> /* contains gnuastro's data.h */
+#include <gnuastro/array.h> /* contains gnuastro's type.h */
+
+int
+main(void)
+{
+ /* Input file's name and HDU. */
+ char *filename="input.fits", *hdu="1";
+
+ /* Reference file's name and HDU. */
+ char *gridfile="reference.fits", *gridhdu="0";
+
+ /* Output file name. */
+ char *outname="align-to-img.fits";
+
+ /* Low-level variables needed to read the reference file's size. */
+ int nwcs;
+ size_t ndim, *dsize;
+
+ /* Initialize the 'wa' struct with empty values and NULL pointers. */
+ gal_warp_wcsalign_t wa=gal_warp_wcsalign_template();
+
+ /* Read the input image and its WCS. */
+ wa.input=gal_array_read_one_ch_to_type(filename, hdu, NULL,
+ GAL_TYPE_FLOAT64, -1, 0);
+ wa.input->wcs=gal_wcs_read(filename, hdu, 0, 0, 0, &wa.input->nwcs);
+
+ /* Prepare the warp input structure, use all threads available. */
+ wa.coveredfrac=1; wa.edgesampling=0; wa.numthreads=0;
+
+ /* Set the target grid to be the same as wcsref.fits file on hdu 0. */
+ wa.twcs=gal_wcs_read(gridfile, gridhdu, 0, 0, 0, &nwcs);
+ if(wa.twcs==NULL)
+ {
+ fprintf(stderr, "%s (hdu %s): no WCS! Can't continue\n",
+ gridfile, gridhdu);
+ exit(EXIT_FAILURE);
+ }
+
+ /* Read the output image size (from the reference image). Note that
+ 'dsize' will be freed while freeing 'widthinpix'). */
+ dsize=gal_fits_img_info_dim(gridfile, gridhdu, &ndim);
+
+ /* Convert the 'dsize' to a 'gal_data_t' so the library can use it. */
+ wa.widthinpix=gal_data_alloc(dsize, GAL_TYPE_SIZE_T, 1, &ndim,
+ NULL, 1, -1, 0, NULL, NULL, NULL);
+
+ /* Do the warp, then convert the output to a 32-bit float (the default
+ float64 is too much for observational data and just wastes
+ storage!). But if you are warping mock data before adding noise
+ (where you do have float64 level precision), remove the type
+ conversion line. */
+ gal_warp_wcsalign(&wa);
+ wa.output=gal_data_copy_to_new_type_free(wa.output, GAL_TYPE_FLOAT32);
+
+ /* WARNING: make sure there is no file with same name as 'out.fits'
+ or the result will be appended to its final HDU. */
+ gal_fits_img_write(wa.output, outname, NULL, "warp-demo");
+
+ /* Clean up. */
+ gal_data_free(wa.input);
+ gal_data_free(wa.output);
+ gal_data_free(wa.widthinpix);
+
+ /* Give control back to the operating system. */
+ return EXIT_SUCCESS;
+}
+@end verbatim
+@end example
+
+
+
+
+@node Library demo - Warp to new grid, , Library demo - Warp to another
image, Library demo programs
+@subsection Library demo - Warp to new grid
+Gnuastro's warp library (that you can access by including
@file{gnuastro/warp.h}) allows you to resample an image from a grid to another
entirely using the WCSLIB (while acconting for distortions if necessary; see
@ref{Warp library}).
+The Warp library uses a pixel-mixing or area-based resampling approach which
is fully described in @ref{Resampling}.
+The most generic uses cases for this library are already available in the
@ref{Invoking astwarp} program.
+For a related demo (where the output grid and WCS are imported from another
file), see @ref{Library demo - Warp to another image}.
+
+In the example below, we'll assume you have the SDSS image downloaded in
@ref{Downloading and validating input data}.
+After downloading the image as described there, you will have @file{r.fits} in
your current directory.
+We will therefore use @file{r.fits} as the input to the rest program here.
+The image is not aligned to the celestial coordinates, so we will align the
pixel and WCS coordinates, but set the center of the pixel grid to be at
(RA,Dec) of (202.4173735,47.3374525).
+We also give it a @code{TAN} projection with a pixel scale of 0.27 arcsecs, a
defined center pixel.
+However, we'll let the Warp library measure the proper output image size that
will contain the aligned image.
+
+To compile the demonstration program below, copy and paste the contents in a
plain-text file (let's assume you named it @file{align-to-new.c}) and use
@ref{BuildProgram} with this command: `@command{astbuildprog align-to-new.c}'.
+Please note that the demo program does not perform many sanity checks to avoid
making it too complex and to highlight this particular feature in the library.
+For a robust method write programs with all the necessary sanity checks, see
Gnuastro's Warp source code, see @ref{Program source}.
@example
@verbatim
@@ -37927,14 +38118,14 @@ int
main(void)
{
/* Input file's name and HDU. */
- char *filename="input.fits", *hdu="1";
+ char *filename="r.fits", *hdu="0";
/* Output file name. */
- char *outname="output.fits";
+ char *outname="align-to-new.fits";
/* RA/Dec of the center of the central pixel of output. Please
change the center based on your input. */
- double center[]={52.55401335, -28.74252337};
+ double center[]={202.4173735, 47.3374525};
/* Coordinate and Projection algorithms of output. */
char *ctype[2]={"RA---TAN", "DEC--TAN"};
@@ -37944,55 +38135,57 @@ main(void)
/* For intermediate steps. */
size_t two=2;
- gal_warp_wcsalign_t nl;
+
+ /* Initialize the 'wa' struct with empty values and NULL pointers. */
+ gal_warp_wcsalign_t wa=gal_warp_wcsalign_template();
/* Set the width (and height!) of the output in pixels (as a 1D and
2 element 'gal_data_t'). When it is NULL, the library will
calculate the appropriate width to fully fit the input image
after alignment. */
- nl.widthinpix=NULL;
+ wa.widthinpix=NULL;
/* Set the number of threads to use. If the value is '0', the
library will estimate the maximum available threads at
run-time on the host operating system. */
- nl.numthreads=0;
+ wa.numthreads=0;
/* Read the input image and its WCS. */
- nl.input=gal_array_read_one_ch_to_type(filename, hdu, NULL,
+ wa.input=gal_array_read_one_ch_to_type(filename, hdu, NULL,
GAL_TYPE_FLOAT64, -1, 0);
- nl.input->wcs=gal_wcs_read(filename, hdu, 0, 0, 0, &nl.input->nwcs);
+ wa.input->wcs=gal_wcs_read(filename, hdu, 0, 0, 0, &wa.input->nwcs);
/* Prepare the warp input structure. */
- nl.coveredfrac=1; nl.edgesampling=0;
- nl.ctype=gal_data_alloc(ctype, GAL_TYPE_STRING, 1, &two, NULL, 1,
+ wa.coveredfrac=1; wa.edgesampling=0;
+ wa.ctype=gal_data_alloc(ctype, GAL_TYPE_STRING, 1, &two, NULL, 1,
-1, 0, NULL, NULL, NULL);
- nl.cdelt=gal_data_alloc(cdelt, GAL_TYPE_FLOAT64, 1, &two, NULL, 1,
+ wa.cdelt=gal_data_alloc(cdelt, GAL_TYPE_FLOAT64, 1, &two, NULL, 1,
-1, 0, NULL, NULL, NULL);
- nl.center=gal_data_alloc(center, GAL_TYPE_FLOAT64, 1, &two, NULL, 1,
+ wa.center=gal_data_alloc(center, GAL_TYPE_FLOAT64, 1, &two, NULL, 1,
-1, 0, NULL, NULL, NULL);
/* Do the warp, then convert it to a 32-bit float. */
- gal_warp_wcsalign(&nl);
- nl.output=gal_data_copy_to_new_type_free(nl.output, GAL_TYPE_FLOAT32);
+ gal_warp_wcsalign(&wa);
+ wa.output=gal_data_copy_to_new_type_free(wa.output, GAL_TYPE_FLOAT32);
/* WARNING: make sure there is no file with same name as 'out.fits'
or the result will be appended to its final HDU. */
- gal_fits_img_write(nl.output, outname, NULL, "warp-demo");
+ gal_fits_img_write(wa.output, outname, NULL, "warp-demo");
/* Remove the pointers to arrays that we didn't allocate (and thus,
should not be freed by 'gal_data_free' below). */
- nl.cdelt->array=nl.center->array=nl.ctype->array=NULL;
+ wa.cdelt->array=wa.center->array=wa.ctype->array=NULL;
- /* Clean up and return. */
- gal_data_free(nl.cdelt); gal_data_free(nl.ctype);
- gal_data_free(nl.input); gal_data_free(nl.output);
- gal_data_free(nl.center); gal_data_free(nl.widthinpix);
+ /* Clean up. */
+ gal_data_free(wa.cdelt); gal_data_free(wa.ctype);
+ gal_data_free(wa.input); gal_data_free(wa.output);
+ gal_data_free(wa.center); gal_data_free(wa.widthinpix);
/* Give control back to the operating system. */
return EXIT_SUCCESS;
@@ -38382,7 +38575,7 @@ As much as order does not matter when you include the
header of each group,
sort them by length, as described above.
@item
-All function names, variables, etc should be in lower case. Macros and
+All function names, variables, etc., should be in lower case. Macros and
constant global @code{enum}s should be in upper case.
@item
@@ -39111,7 +39304,7 @@ bar bAr foo
Nicely done!
Just note that the strings are sorted alphabetically, not in the original
order.
-Also, an arbitrary number of space characters are printed between them (based
on the number of suggestions and terminal size and etc).
+Also, an arbitrary number of space characters are printed between them (based
on the number of suggestions and terminal size, etc.).
Now, if you type @samp{f} and press @key{[TAB]}, bash will automatically
figure out that you wanted @code{foo} and it be completed right away:
@example
@@ -39694,7 +39887,7 @@ the development of Gnuastro, so please adhere to the
following guidelines.
The body should be very descriptive. Start the commit message body by
explaining what changes your commit makes from a user's perspective (added,
changed, or removed options, or arguments to programs or libraries, or
-modified algorithms, or new installation step, etc).
+modified algorithms, or new installation step, etc.).
@item
@cindex Mailing list: gnuastro-commits
@@ -39779,7 +39972,7 @@ As described in `Pro Git', there are two methods for
you to contribute to Gnuast
@item
You can send commit patches by email as fully explained in `Pro Git'.
This is good for your first few contributions.
-Just note that raw patches (containing only the diff) do not have any
meta-data (author name, date, etc).
+Just note that raw patches (containing only the diff) do not have any
meta-data (author name, date, etc.).
Therefore they will not allow us to fully acknowledge your contributions as an
author in Gnuastro: in the @file{AUTHORS} file and at the start of the PDF book.
These author lists are created automatically from the version controlled
source.
@@ -39788,7 +39981,7 @@ See Pro Git's
@url{https://git-scm.com/book/en/v2/Distributed-Git-Contributing-t
If you would like to get more heavily involved in Gnuastro's development, then
you can try the next solution.
@item
-You can have your own forked copy of Gnuastro on any hosting site you like
(Codeberg, Gitlab, GitHub, BitBucket, etc) and inform us when your changes are
ready so we merge them in Gnuastro.
+You can have your own forked copy of Gnuastro on any hosting site you like
(Codeberg, Gitlab, GitHub, BitBucket, etc.) and inform us when your changes are
ready so we merge them in Gnuastro.
This is more suited for people who commonly contribute to the code (see
@ref{Forking tutorial}).
@end enumerate
@@ -39954,7 +40147,7 @@ It uses a technique to detect very faint and diffuse,
irregularly shaped signal
@item Statistics
(@file{aststatistics}, see @ref{Statistics}) Statistical calculations on the
input dataset (column in a table, image or datacube).
-This includes man operations like generating histogram, sigma clipping, least
squares fitting and etc.
+This includes man operations such as generating histogram, sigma clipping, and
least squares fitting.
@item Table
(@file{asttable}, @ref{Table}) Convert FITS binary and ASCII tables into other
such tables, print them on the command-line, save them in a plain text file, do
arithmetic on the columns or get the FITS table information.
@@ -39980,7 +40173,7 @@ They can be run just like a program and behave very
similarly (with minor differ
@item astscript-radial-profile
(See @ref{Generate radial profile}) Calculate the radial profile of an object
within an image.
-The object can be at any location in the image, using various measures
(median, sigma-clipped mean and etc), and the radial distance can also be
measured on any general ellipse.
+The object can be at any location in the image, using various measures
(median, sigma-clipped mean, etc.), and the radial distance can also be
measured on any general ellipse.
@item astscript-sort-by-night
(See @ref{Sort FITS files by night}) Given a list of FITS files, and a HDU and
keyword name (for a date), this script separates the files in the same night
(possibly over two calendar days).
diff --git a/lib/gnuastro/warp.h b/lib/gnuastro/warp.h
index e736b1f5..0ca9742a 100644
--- a/lib/gnuastro/warp.h
+++ b/lib/gnuastro/warp.h
@@ -52,15 +52,17 @@ __BEGIN_C_DECLS /* From C++ preparations */
typedef struct
{
- /* Arguments given (and later freed) by the caller. */
- gal_data_t *ctype; /* Type of the coordinates. */
- gal_data_t *cdelt; /* Pixel scale of the output image. */
- gal_data_t *input; /* Pointer to input data structure. */
- gal_data_t *center; /* Center of the image in RA and Dec. */
- gal_data_t *widthinpix; /* Output image width and height in pixels. */
+ /* Arguments given (and later freed) by the caller. Note that if 'twcs'
+ is given, then the "WCS-Build" elements will be ignored. */
+ gal_data_t *input; /* Pointer to input image. */
size_t numthreads; /* Number of threads to use. */
double coveredfrac; /* Acceptable fraction of output covered. */
size_t edgesampling; /* Order of samplings along each pixel edge. */
+ gal_data_t *widthinpix; /* Output image width and height in pixels. */
+ struct wcsprm *twcs; /* WCS-Predefined: the wcsprm. */
+ gal_data_t *ctype; /* WCS-Build: Type of the coordinates. */
+ gal_data_t *cdelt; /* WCS-Build: Pixel scale of the output. */
+ gal_data_t *center; /* WCS-Build: Center of output in RA and Dec.*/
/* Output (must be freed by caller) */
gal_data_t *output; /* Pointer to output data structure. */
@@ -78,12 +80,17 @@ typedef struct
-/* Create the empty output WCS-ready image */
+/* Return an empty set of the wcsalign data structure. */
+gal_warp_wcsalign_t
+gal_warp_wcsalign_template();
+
+
+/* Create the empty output WCS-ready image. */
void
gal_warp_wcsalign_init(gal_warp_wcsalign_t *wa);
-/* Fill nonlinear output by pixel */
+/* Fill nonlinear output by pixel. */
void
gal_warp_wcsalign_onpix(gal_warp_wcsalign_t *wa, size_t ind);
@@ -93,12 +100,13 @@ gal_warp_wcsalign_onthread(void *inparam);
/* Spin-off the threads and finalize the output 'gal_data_t' image in
- 'nl->output' */
+ 'wa->output'. */
void
gal_warp_wcsalign(gal_warp_wcsalign_t *wa);
-/* Clean up the entire struct */
+/* Clean up ONLY the internal variables. Caller must 'free' their own
+ inputs as well as the output (e.g. the input image). */
void
gal_warp_wcsalign_free(gal_warp_wcsalign_t *wa);
diff --git a/lib/warp.c b/lib/warp.c
index b77714d9..52d5a1ae 100644
--- a/lib/warp.c
+++ b/lib/warp.c
@@ -119,7 +119,7 @@ warp_alloc_perimeter(gal_data_t *input)
/* Create a base image with WCS consisting of the basic geometry
keywords */
static void
-warp_wcsalign_init_output(gal_warp_wcsalign_t *wa)
+warp_wcsalign_init_output_from_params(gal_warp_wcsalign_t *wa)
{
/* Low level variables */
size_t i, nkcoords, *osize;
@@ -553,7 +553,25 @@ warp_wcsalign_check_2d(gal_data_t *in, uint8_t type, const
char *func,
+/* Create the output image using the WCS struct from the given 'gridfile'
+ and 'gridhdu'. */
static void
+warp_wcsalign_init_output_from_wcs(gal_warp_wcsalign_t *wa,
+ const char *func)
+{
+ size_t *dsize=wa->widthinpix->array;
+
+ /* Create the output image dataset with the target WCS given. */
+ wa->output=gal_data_alloc(NULL, GAL_TYPE_FLOAT64, 2, dsize, wa->twcs,
+ 0, wa->input->minmapsize, wa->input->quietmmap,
+ "Aligned", NULL, NULL);
+}
+
+
+
+
+
+static void *
warp_wcsalign_init_params(gal_warp_wcsalign_t *wa, const char *func)
{
size_t *tmp=NULL;
@@ -570,28 +588,6 @@ warp_wcsalign_init_params(gal_warp_wcsalign_t *wa, const
char *func)
"'gal_data_copy_to_new_type_free' for the conversion", func,
gal_type_name(wa->input->type, 1));
- /* Check the 2D inputs. */
- warp_wcsalign_check_2d(wa->ctype, GAL_TYPE_STRING, func, "ctype",
- "Any pair of valid WCSLIB ctype is "
- "allowed, e.g. 'RA---TAN, DEC--TAN'");
- warp_wcsalign_check_2d(wa->cdelt, GAL_TYPE_FLOAT64, func, "cdelt",
- "This is the pixel scale in degrees");
- warp_wcsalign_check_2d(wa->center, GAL_TYPE_FLOAT64, func, "center",
- "This is the output image center in degrees");
-
- /* check 'widthinpix', it can be null for automatic detection */
- if(wa->widthinpix)
- {
- warp_wcsalign_check_2d(wa->widthinpix, GAL_TYPE_SIZE_T, func,
- "widthinpix", "This is the output "
- "image size");
- tmp=wa->widthinpix->array;
- if(tmp[0]%2==0 || tmp[1]%2==0)
- error(EXIT_FAILURE, 0, "%s: 'widthinpix' takes exactly 2 ODD "
- "values, detected EVEN value in %zux%zu", func, tmp[0],
- tmp[1]);
- }
-
/* Check 'coveredfrac'. */
if(isnan( wa->coveredfrac ))
error(EXIT_FAILURE, 0, "%s: no 'coveredfrac' specified. This is the "
@@ -623,6 +619,52 @@ warp_wcsalign_init_params(gal_warp_wcsalign_t *wa, const
char *func)
wa->nhor=GAL_BLANK_SIZE_T;
wa->ncrn=GAL_BLANK_SIZE_T;
wa->gcrn=GAL_BLANK_SIZE_T;
+
+ /* If a target WCS is given ignore other variables and initialize the
+ output image. */
+ if(wa->twcs)
+ {
+ /* Check the widthinpix element. */
+ warp_wcsalign_check_2d(wa->widthinpix, GAL_TYPE_SIZE_T, func,
+ "widthinpix", "This is the output image "
+ "size in pixels");
+ warp_wcsalign_init_output_from_wcs(wa, func);
+
+ /* Warp will ignore the following parameters, warn the user if
+ detected any. */
+ if(wa->cdelt || wa->center || wa->ctype)
+ error(EXIT_SUCCESS, 0, "%s: WARNING: target WCS is already "
+ "defined with 'gridfile' and 'gridhdu', ignoring extra "
+ "non-linear parameter(s) given", func);
+ return NULL;
+ }
+
+ /* No 'gridfile' given, Warp must create the output WCS using given
+ parameters. Proceed with checking the 2D input parameters. */
+ warp_wcsalign_check_2d(wa->ctype, GAL_TYPE_STRING, func, "ctype",
+ "Any pair of valid WCSLIB ctype is "
+ "allowed, e.g. 'RA---TAN, DEC--TAN'");
+ warp_wcsalign_check_2d(wa->cdelt, GAL_TYPE_FLOAT64, func, "cdelt",
+ "This is the pixel scale in degrees");
+ warp_wcsalign_check_2d(wa->center, GAL_TYPE_FLOAT64, func, "center",
+ "This is the output image center in degrees");
+
+ /* Check 'widthinpix', it can be null for automatic detection */
+ if(wa->widthinpix)
+ {
+ warp_wcsalign_check_2d(wa->widthinpix, GAL_TYPE_SIZE_T, func,
+ "widthinpix", "This is the output "
+ "image size");
+ tmp=wa->widthinpix->array;
+ if(tmp[0]%2==0 || tmp[1]%2==0)
+ error(EXIT_FAILURE, 0, "%s: 'widthinpix' takes exactly 2 ODD "
+ "values, detected EVEN value in %zux%zu", func, tmp[0],
+ tmp[1]);
+ }
+
+ /* Initialize the output image for further processing. */
+ warp_wcsalign_init_output_from_params(wa);
+ return NULL;
}
@@ -767,11 +809,9 @@ gal_warp_wcsalign_init(gal_warp_wcsalign_t *wa)
gal_data_t *input=wa ? wa->input : NULL;
size_t es = wa ? wa->edgesampling : GAL_BLANK_SIZE_T;
- /* Run a sanity check on the input parameters */
+ /* Run a sanity check on the input parameters and initialize the output
+ image. */
warp_wcsalign_init_params(wa, __func__);
-
- /* Create the output image */
- warp_wcsalign_init_output(wa);
os0=wa->output->dsize[0];
os1=wa->output->dsize[1];
gcrn=1+os1*(es+1);
@@ -941,6 +981,39 @@ gal_warp_wcsalign_onthread(void *inparam)
+/* Helper function that returns an empty set of the wcsalign data structure
+ to prevent using uninitialized variables without warnings. Please note
+ if you are not using this template to set 'gal_warp_wcsalign_t' values,
+ you MUST pass NULL to unused pointers at least. */
+gal_warp_wcsalign_t
+gal_warp_wcsalign_template()
+{
+ gal_warp_wcsalign_t wa;
+
+ wa.twcs=NULL;
+ wa.cdelt=NULL;
+ wa.ctype=NULL;
+ wa.input=NULL;
+ wa.center=NULL;
+ wa.output=NULL;
+ wa.vertices=NULL;
+ wa.widthinpix=NULL;
+ wa.isccw=GAL_BLANK_INT;
+ wa.v0=GAL_BLANK_SIZE_T;
+ wa.gcrn=GAL_BLANK_SIZE_T;
+ wa.ncrn=GAL_BLANK_SIZE_T;
+ wa.nhor=GAL_BLANK_SIZE_T;
+ wa.numthreads=GAL_BLANK_SIZE_T;
+ wa.coveredfrac=GAL_BLANK_FLOAT64;
+ wa.edgesampling=GAL_BLANK_SIZE_T;
+
+ return wa;
+}
+
+
+
+
+
/* Clean up the internally allocated variables from the 'wa' struct. */
void
gal_warp_wcsalign_free(gal_warp_wcsalign_t *wa)
@@ -953,18 +1026,18 @@ gal_warp_wcsalign_free(gal_warp_wcsalign_t *wa)
-/* Finalize the output 'gal_data_t' image in 'nl->output' */
+/* Finalize the output 'gal_data_t' image in 'wa->output' */
void
-gal_warp_wcsalign(gal_warp_wcsalign_t *nl)
+gal_warp_wcsalign(gal_warp_wcsalign_t *wa)
{
/* Calculate and allocate the output image size and WCS */
- gal_warp_wcsalign_init(nl);
+ gal_warp_wcsalign_init(wa);
/* Fill the output image */
- gal_threads_spin_off(gal_warp_wcsalign_onthread, nl, nl->output->size,
- nl->numthreads, nl->input->minmapsize,
- nl->input->quietmmap);
+ gal_threads_spin_off(gal_warp_wcsalign_onthread, wa, wa->output->size,
+ wa->numthreads, wa->input->minmapsize,
+ wa->input->quietmmap);
/* Clean up the internally allocated variables */
- gal_warp_wcsalign_free(nl);
+ gal_warp_wcsalign_free(wa);
}
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- [gnuastro-commits] master 9af5d8ad: Warp: new --gridfile option to warp one image to grid of another,
Mohammad Akhlaghi <=