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[gnuastro-commits] master 81720014 15/69: Book: adding documentation of
From: |
Mohammad Akhlaghi |
Subject: |
[gnuastro-commits] master 81720014 15/69: Book: adding documentation of 'psf-model-flux-factor' script |
Date: |
Wed, 26 Jan 2022 12:39:10 -0500 (EST) |
branch: master
commit 81720014e6d2c20deafd12598d96fe7556a78772
Author: Raul Infante-Sainz <infantesainz@gmail.com>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Book: adding documentation of 'psf-model-flux-factor' script
Until this commit, the documentation and information of this script was
missing. With this commit, the basic information and the options of this
script have been added into the book of Gnuastro. In addition to that, also
very minor corrections to the script itself have been done.
---
bin/script/psf-model-flux-factor.in | 13 +--
doc/gnuastro.texi | 163 ++++++++++++++++++++++++++++++++++--
2 files changed, 162 insertions(+), 14 deletions(-)
diff --git a/bin/script/psf-model-flux-factor.in
b/bin/script/psf-model-flux-factor.in
index fe361267..962a4f0b 100644
--- a/bin/script/psf-model-flux-factor.in
+++ b/bin/script/psf-model-flux-factor.in
@@ -45,7 +45,6 @@ tmpdir=""
corewidth=""
normradii=""
sigmaclip=""
-oversample=""
stampwidth=""
normop="median"
version=@VERSION@
@@ -95,11 +94,11 @@ $scriptname options:
-O, --mode=STR Coordinates mode ('wcs' or 'img').
-c, --center=FLT,FLT Center coordinates of the object.
-W, --stampwidth=INT Width of the stamp in pixels.
- -w, --corewidth=INT Area width of the central object in pixels for
unmasking.
-n, --normradii=INT,INT Minimum and maximum radii (in pixels)
- for computing the normalization value.
- -S, --mask=STR Segmentation image (sky = 0).
- -s, --maskhdu=STR HDU/extension of the segmentation image.
+ for computing the flux factor value.
+ -m, --mask=STR Segmentation image (sky = 0).
+ -M, --maskhdu=STR HDU/extension of the segmentation image.
+ -w, --corewidth=INT Area width of the central object in pixels for
unmasking.
-R, --rmax=FLT Maximum radius for the radial profile (in pixels).
-N, --normop=STR Operator for computing the normalization value
(mean, sigclip-mean, etc.).
@@ -109,7 +108,6 @@ $scriptname options:
-o, --output Output table with the radial profile.
-t, --tmpdir Directory to keep temporary files.
-k, --keeptmp Keep temporal/auxiliar files.
- -v, --oversample Oversample for higher resolution radial profile.
Operating mode:
-?, --help Print this help list.
@@ -247,9 +245,6 @@ do
-o|--output) output="$2"; check_v "$1"
"$output"; shift;shift;;
-o=*|--output=*) output="${1#*=}"; check_v "$1"
"$output"; shift;;
-o*) output=$(echo "$1" | sed -e's/-o//'); check_v "$1"
"$output"; shift;;
- -v|--oversample) oversample="$2"; check_v
"$1" "$oversample"; shift;shift;;
- -v=*|--oversample=*) oversample="${1#*=}"; check_v
"$1" "$oversample"; shift;;
- -v*) oversample=$(echo "$1" | sed -e's/-v//'); check_v
"$1" "$oversample"; shift;;
# Non-operating options.
-q|--quiet) quiet="--quiet"; shift;;
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index ab1c9a53..980b9958 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -659,6 +659,7 @@ PSF construction and correction
* Invoking astscript-psf-create-make-stamp:: How to call
astscript-psf-create-make-stamp
* Invoking astscript-psf-create-junction:: How to call
astscript-psf-create-junction
+* Invoking astscript-psf-model-flux-factor:: How to call
astscript-psf-model-flux-factor
Library
@@ -23132,7 +23133,7 @@ It can be either a FITS table, or plain-text table
(determined from your given f
@itemx --center=FLT[,FLT[,...]]
The central position of the radial profile.
This option is used for placing the center of the profiles.
-This parameter is used in @ref{Crop} to center an crop the region.
+This parameter is used in @ref{Crop} to center and crop the region.
The positions along each dimension must be separated by a comma (@key{,}) and
fractions are also acceptable.
The number of values given to this option must be the same as the dimensions
of the input dataset.
The units of the coordinates are read based on the value to the
@option{--mode} option, see below.
@@ -23427,7 +23428,7 @@ This script merges two different PSFs at a given radius
and some other parameter
Once the PSF has been constructed by the procedure above (or any other
methodology), it can be used for modeling the stars: the scattered light.
The absolute flux of a PSF has no sense.
To model a star with a PSF it is necessary to scale the PSF up or down in
order to put it at the same level of flux than the star.
-To do that, we have the script @file{astscript-psf-model-flux-factor.in}.
+To do that, we have the script @file{astscript-psf-model-flux-factor}.
It is in charge of computing the flux factor by which it is necessary to
multiply the PSF in order to put it at the same level than a given star.
Once the flux factor has been computed, it is possible put the PSF at the same
sky position and with the same flux level than the star.
@@ -23441,6 +23442,7 @@ For more on installed scripts please see (see
@ref{Installed scripts}).
@menu
*Invoking astscript-psf-create-make-stamp:: How to call
astscript-psf-create-make-stamp
*Invoking astscript-psf-create-junction:: How to call
astscript-psf-create-junction
+*Invoking astscript-psf-model-flux-factor:: How to call
astscript-psf-model-flux-factor
@end menu
@@ -23475,7 +23477,7 @@ $ astscript-psf-create-make-stamp image.fits --mode=img
\
## Each stamp will have 150 pixels of width, and the normalization
## will be computed within the ring of 20-30 pixels.
$ asttable catalog.fits | while read -r ra dec mag; do \
- astscript-psf-create-make-stamp.in image.fits \
+ astscript-psf-create-make-stamp image.fits \
--mode=wcs \
--stampwidth=150 \
--center=$ra,$dec \
@@ -23506,7 +23508,7 @@ This option thus accepts only two values: @option{img}
or @option{wcs}.
@itemx --center=FLT[,FLT[,...]]
The central position of the object.
This option is used for placing the center of the stamp.
-This parameter is used in @ref{Crop} to center an crop the image.
+This parameter is used in @ref{Crop} to center and crop the image.
The positions along each dimension must be separated by a comma (@key{,}).
The number of values given to this option must be the same as the dimensions
of the input dataset.
The units of the coordinates are read based on the value to the
@option{--mode} option, see above.
@@ -23662,7 +23664,7 @@ Radius (in pixels) at which the junction of the images
is done.
@itemx --fluxfactor=FLT
Factor by which the core (@option{--core}) is multiplied.
This factor is necessary to put the two different parts of the PSF at the same
flux level.
-A convenient way of obtaining this value is by using the script
@file{astscript-model-flux-factor}, see @ref{TBD}.
+A convenient way of obtaining this value is by using the script
@file{astscript-model-flux-factor}, see @ref{Invoking
astscript-psf-model-flux-factor}.
@item -Q FLT
@itemx --axisratio=FLT
@@ -23693,6 +23695,157 @@ This option is useful for debugging.
+@node Invoking astscript-psf-model-flux-factor
+@subsection Invoking astscript-psf-model-flux-factor
+This installed script will consider an object within the input image and it
will obtain the radial profile of that object.
+In the same way, it will compute the radial profile of a given PSF image.
+Then, by comparing the two radial profiles in the same region, it will
calculate the factor by which it is necessary to multiply the PSF image in
order to scale it at the same level of flux than the object.
+
+The computation of this flux factor is commonly used when joining two
different parts of the same PSF, see @ref{Invoking
astscript-psf-create-junction}.
+Also when modeling a star in order to subtract it using the PSF, see
@ref{Invoking astscript-psf-model-scattered-light}.
+
+This script can be used with the following general template:
+
+@example
+$ astscript-psf-model-flux-factor [OPTION...] FITS-file
+@end example
+
+@noindent
+Examples:
+
+@example
+## Compute the flux factor by which it is necessary to multiply
+## the PSF (psf.fits) to put it at the same level than the object
+## in the pixel position (x,y)=(53,69). Use the ring between
+## the radii 20 and 30 pixels for computing that flux factor.
+$ astscript-psf-model-flux-factor image.fits --mode=img \
+ --center=53,69 --normradii=20,30 --psf=psf.fits
+
+## Consider that in image.fits are some stars that are going to
+## be considered for obtaining the flux factors. If catalog.fits
+## is a catalog containing the centers (in WCS), then this loop will
+## compute these flux factors, one for each star in the catalog.
+$ asttable catalog.fits | while read -r ra dec mag; do \
+ astscript-psf-model-flux-factor image.fits \
+ --mode=wcs \
+ --psf=psf.fits \
+ --center=$ra,$dec \
+ --normradii=20,30 \
+ --output=fluxfactor-"$ra"-"$dec".txt; done
+
+@end example
+
+The input is an image from which the star is considered.
+The output will be the flux factor: the value by which the PSF image
(@option{--psf}) has to be multiplied to put it at the same level than the
object specified (@option{--center}), within the ring of pixels specified by
the option @option{--normradii}.
+More options are available with the goal of obtaining a good flux factor value.
+A full description of each option is given below.
+
+
+@table @option
+
+@item -h STR
+@itemx --hdu=STR
+The HDU/extension of the input image to use.
+
+@item -p STR
+@itemx --psf=STR
+Filename of the PSF image.
+The PSF is assumed to be centered in this image.
+
+@item -P STR
+@itemx --psfhdu=STR
+The HDU/extension of the PSF image.
+
+@item -O STR
+@itemx --mode=STR
+Interpret the center position of the object (values given to
@option{--center}) in image or WCS coordinates.
+This option thus accepts only two values: @option{img} or @option{wcs}.
+
+@item -c FLT[,FLT[,...]]
+@itemx --center=FLT[,FLT[,...]]
+The central position of the object.
+This parameter is used in @ref{Crop} to center and crop the image.
+The positions along each dimension must be separated by a comma (@key{,}).
+The number of values given to this option must be the same as the dimensions
of the input dataset.
+The units of the coordinates are read based on the value to the
@option{--mode} option, see above.
+
+@item -W INT
+@itemx --stampwidth=INT
+Size (width) of the image stamp in pixels.
+This is an intermediate product computed internally by the script.
+By default, the size of the stamp is automatically set to be as small as
possible (i.e., two times the external radius of the ring specified by
@option{--rnorm}) to make the computation fast.
+As a consequence, this option is only relevant for checking and testing that
everything is fine.
+
+@item -n INT[,INT[,...]]
+@itemx --normradii=INT[,INT[,...]]
+Region around the central position in which the flux factor is computed.
+The option takes two values separated by a comma (@key{,}).
+The first value is the inner radius, the second is the outer radius.
+These two radius define a ring of pixels around the center that is used for
obtaining the flux factor value.
+
+@item -m STR
+@itemx --mask=STR
+Filename of the segmentation image.
+It is possible use a segmentation image to mask all the objects that are not
the central object.
+The segmentation image specified by this option must have the same dimensions
than the input image.
+Non object pixels must have pixel values equal to zero, these pixels are not
masked on the final stamp.
+Object pixels must have pixel values different from zero, these pixels are
masked with NaN values on the final stamp.
+In order to not mask the central object (in case it is identified in the
segmentation image as an object), a region around the center is considered from
the segmentation image.
+The size of that region can be specified by the option @option{--corewidth},
see below.
+As a consequence, all pixels with values equal to the central one in the
segmentation image are not masked in the final stamp image.
+Internally, all of these pixels are converted to zero values so they are not
masked.
+
+@item -M STR
+@itemx --maskhdu=STR
+The HDU/extension of the segmentation image (@option{--mask}).
+
+@item -w INT
+@itemx --corewidth=INT
+Width of the region that is used to compute the central object over the
segmentation image @option{--mask}, with the goal of not masking it.
+If a segmentation image is provided, then it is necessary to not mask the
central object.
+To do that, a central region is considered in order to compute the values of
the central object on the segmentation image.
+Once it has been identified, that pixels are not masked.
+With this option, it is possible to control the size of the central region for
computing the central object values.
+
+@item -R FLT
+@itemx --rmax=FLT
+Maximum radius (in pixels) for computing the radial profile.
+By default, the radial profile will be computed up to a radial distance equal
to the maximum radius that fits into the stamp image.
+As a consequence, this option is only relevant for checking and testing that
everything is fine.
+
+@item -N STR
+@itemx --normop=STR
+The operator for measuring the values within the ring defined by the option
@option{--normradii}.
+The operator given to this option will be directly passed to the radial
profile script @file{astscript-radial-profile}, see @ref{Generate radial
profile}.
+As a consequence, all MakeCatalog measurements (median, mean, sigclip-mean,
sigclip-number, etc.) can be used here.
+For a full list of MakeCatalog's measurements, please run
@command{astmkcatalog --help}.
+In the same way, this operator is used to compute the final flux factor value.
+This calculation is done by dividing the two radial profiles (object and PSF)
and then taking the averaged value using this operator.
+
+@item -s FLT,FLT
+@itemx --sigmaclip=FLT,FLT
+Sigma clipping parameters: only relevant if sigma-clipping operators are
requested by @option{--normop}.
+For more on sigma-clipping, see @ref{Sigma clipping}.
+
+@item -t STR
+@itemx --tmpdir=STR
+Several intermediate files are necessary to obtain the flux factor value.
+All of these temporal files are saved into a temporal directory.
+With this option, you can directly specify this directory.
+By default (when this option isn't called), it will be built in the running
directory and given an input-based name.
+If the directory doesn't exist at run-time, this script will create it.
+Once all temporal files are not necessary, this directory is removed.
+You can disable the deletion of the temporary directory with the
@option{--keeptmp} option, see below.
+
+@item -k
+@itemx --keeptmp
+Don't delete the temporary directory (see description of @option{--tmpdir}
above).
+This option is useful for debugging.
+For example, to check that the intermediate images have the desired center,
they are properly masked, etc.
+@end table
+
+
+
- [gnuastro-commits] master 57b27b9e 12/69: PSF scripts: correcting several bugs and homogenizing the notation, (continued)
- [gnuastro-commits] master 57b27b9e 12/69: PSF scripts: correcting several bugs and homogenizing the notation, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master b14fdf1d 04/69: PSF stamp: fixing wrong directory of this script, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 4c5fe969 17/69: Book: fully working example on how to construct and correct the PSF, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master ccae240f 29/69: PSF stamp: bug in --rmax option introduced in previous commit fixed, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master de1b645b 20/69: PSF stamp: computing radial profile up to the minimum possible value, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 194b49d1 59/69: PSF select-stars: change the name of the two varibales., Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 781f0f33 39/69: PSF scripts: checking that the input file actually exists, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 0a6625ab 61/69: Book: explain about two new option in the psf-create-select-stars, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 6901ec82 49/69: PSF select-stars: check the image and catalog have a overlap area or not, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master f9b7edfa 10/69: PSF stamp: removing the option --oversample as it is not enabled, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 81720014 15/69: Book: adding documentation of 'psf-model-flux-factor' script,
Mohammad Akhlaghi <=
- [gnuastro-commits] master 9ca784e4 27/69: PSF select stars: if the image has not stars in `--min` and `--max` range, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master f1cfd384 25/69: PSF select stars: remove --input add --output and --catalog, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master bf8792c2 52/69: Book: For selecting stars some mandatory options did not mention, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master f3619dd5 57/69: Book: edits in the PSF scripts, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master ce020710 41/69: Book: new section for the tutorial on how to construct and extended PSF, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 9ab3dd28 51/69: PSF stamp: new option to set a mask sky pixel value: maskskyval, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 31f0373a 05/69: PSF model: new script for putting a PSF image into a sky position, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 0ea23b70 69/69: Book: PSF tutorial now with instruction to build first inner region, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 00f2ab56 63/69: PSF select-stars: simplifying some parts and language corrections, Mohammad Akhlaghi, 2022/01/26
- [gnuastro-commits] master 6638c671 53/69: Book: correct the definition of option --minaxisratio, Mohammad Akhlaghi, 2022/01/26