[gnuastro-commits] master 863abd7 01/32: astscript-radial-profile: adding script for making radial profiles

[Mohammad Akhlaghi]

branch: master
commit 863abd7f89568b6382d408cc377de9cf0a4f1308
Author: Raul Infante-Sainz <infantesainz@gmail.com>
Commit: Raul Infante-Sainz <infantesainz@gmail.com>

    astscript-radial-profile: adding script for making radial profiles
    
    With this commit, I am adding a script for making radial profiles. This
    is the very early version of this script, and because of that, a lot of
    information (specially for the book) is missing and has to be added.
    However, I am commiting this work to be safe and not loose information.
    
    Basically, this script takes an input image and compute the radial
    profiles over defined apertures. To do that, the apertures are defined
    with `astmkprof' setting the center of the apertures (WCS o IMG
    mode) as well as the ellipticity and the position angle. In the same
    way, the minimum and maximum radius have to be selected (otherwise it
    will take the maximum possible value for the radius). Once the apertures
    are defined, it uses `astmkcatalog' for obtaining the wanted measure
    (tipically mean, median, brightness, etc.) over the defined apertures.
    
    So, at the end, the result is a table with two columns, first one is the
    radial distance from the center, and the other column is the measured
    parameter over the aperture.
---
 bin/script/radial-profile.in | 335 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 335 insertions(+)

diff --git a/bin/script/radial-profile.in b/bin/script/radial-profile.in
new file mode 100644
index 0000000..4c4a75a
--- /dev/null
+++ b/bin/script/radial-profile.in
@@ -0,0 +1,335 @@
+#!/bin/sh
+
+# Obtain averaged radial profiles, run with `--help', or see description
+# under `print_help' (below) for more.
+#
+# Original author:
+#   Copyright (C) 2020   Raul Infante-Sainz <infantesainz@gmail.com>
+# Contributing author(s):
+#   Copyright (C) 2020   Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020, Free Software Foundation, Inc.
+#
+# Gnuastro is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option)
+# any later version.
+#
+# Gnuastro is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with Gnuastro. If not, see <http://www.gnu.org/licenses/>.
+
+
+# Exit the script in the case of failure
+set -e
+
+
+
+
+
+# Default option values (can be changed with options on the
+# command-line).
+hdu=1
+rmin=1
+rmax=10
+mode=img
+x=center
+y=center
+m=median
+Q=0
+p=0
+w=1
+k=1
+quiet=0
+prefix=./
+version=0.11
+scriptname=astscript-radial-profile
+
+# Axis ratio
+# Position angle
+# Circum width
+
+
+
+
+
+# Output of `--usage' and `--help':
+print_usage() {
+    cat <<EOF
+$scriptname: run with '--help' for list of options
+EOF
+}
+
+print_help() {
+    cat <<EOF
+Usage: $scriptname [OPTION] FITS-files
+
+This script is part of GNU Astronomy Utilities $version.
+
+This script will consider the input image for constructing the radial
+profile around a given center with elliptical apertures.
+
+For more information, please run any of the following commands. In
+particular the first contains a very comprehensive explanation of this
+script's invocation: expected input(s), output(s), and a full description
+of all the options.
+
+     Inputs/Outputs and options:           $ info $scriptname
+     Full Gnuastro manual/book:            $ info gnuastro
+
+If you couldn't find your answer in the manual, you can get direct help from
+experienced Gnuastro users and developers. For more information, please run:
+
+     $ info help-gnuastro
+
+$scriptname options:
+ Input:
+  -h, --hdu=STR           HDU/extension of all input FITS files.
+  -O, --mode=STR          Coordinate mode `img' or `wcs'.
+  -x, --xcenter=FLT       Coordinate of the center along the first axis.
+  -y, --ycenter=FLT       Coordinate of the center along the second axis.
+  -r, --rmin=FLT          Minimum radius for the radial profiles (in pixels).
+  -R, --rmax=FLT          Maximum radius for the radial profiles (in pixels).
+  -Q, --qratio=FLT        Axis ratio for ellipse apertures (A/B).
+  -p, --pangle=FLT        Position angle for ellipse apertures.
+  -m, --measure=STR       Operator for measuring the parameter (mean, median, 
etc.).
+  -a, --cprofiles=STR     Configuration file for astmkprof.
+  -c, --ccatalog=STR      Configuration file for astmkcatalog.
+
+ Output:
+  -k, --keeptemp          Keep temporal/auxiliar files.
+  -k, --keeptemp          Keep temporal/auxiliar files.
+
+ Operating mode:
+  -h, --help              Print this help list.
+      --cite              BibTeX citation for this program.
+  -q, --quiet             Don't print the list.
+  -V, --version           Print program version.
+
+Mandatory or optional arguments to long options are also mandatory or optional
+for any corresponding short options.
+
+GNU Astronomy Utilities home page: http://www.gnu.org/software/gnuastro/
+
+Report bugs to bug-gnuastro@gnu.org.
+EOF
+}
+
+
+
+
+
+# Output of `--version':
+print_version() {
+    cat <<EOF
+$scriptname (GNU Astronomy Utilities) $version
+Copyright (C) 2020, Free Software Foundation, Inc.
+License GPLv3+: GNU General public license version 3 or later.
+This is free software: you are free to change and redistribute it.
+There is NO WARRANTY, to the extent permitted by law.
+
+Written/developed by Raul Infante-Sainz
+EOF
+}
+
+
+
+
+
+# Functions to check option values and complain if necessary.
+on_off_option_error() {
+    if [ "x$2" = x ]; then
+        echo "$scriptname: '$1' doesn't take any values."
+    else
+        echo "$scriptname: '$1' (or '$2') doesn't take any values."
+    fi
+    exit 1
+}
+
+check_v() {
+    if [ x"$2" = x ]; then
+        echo "$scriptname: option '$1' requires an argument."
+        echo "Try '$scriptname --help' for more information."
+        exit 1;
+    fi
+}
+
+
+
+
+
+# Separate command-line arguments from options. Then put the option
+# value into the respective variable.
+#
+# OPTIONS WITH A VALUE:
+#
+#   Each option has three lines because we want to all common formats: for
+#   long option names: `--longname value' and `--longname=value'. For short
+#   option names we want `-l value', `-l=value' and `-lvalue' (where `-l'
+#   is the short version of the hypothetical `--longname' option).
+#
+#   The first case (with a space between the name and value) is two
+#   command-line arguments. So, we'll need to shift it two times. The
+#   latter two cases are a single command-line argument, so we just need to
+#   "shift" the counter by one. IMPORTANT NOTE: the ORDER OF THE LATTER TWO
+#   cases matters: `-h*' should be checked only when we are sure that its
+#   not `-h=*').
+#
+# OPTIONS WITH NO VALUE (ON-OFF OPTIONS)
+#
+#   For these, we just want the two forms of `--longname' or `-l'. Nothing
+#   else. So if an equal sign is given we should definitely crash and also,
+#   if a value is appended to the short format it should crash. So in the
+#   second test for these (`-l*') will account for both the case where we
+#   have an equal sign and where we don't.
+while [ $# -gt 0 ]
+do
+    case "$1" in
+        # Input parameters.
+        -h|--hdu)         hdu="$2";                           check_v "$1" 
"$hdu";  shift;shift;;
+        -h=*|--hdu=*)     hdu="${1#*=}";                      check_v "$1" 
"$hdu";  shift;;
+        -h*)              hdu=$(echo "$1"  | sed -e's/-h//'); check_v "$1" 
"$hdu";  shift;;
+        -O|--mode)        mode="$2";                           check_v "$1" 
"$mode";  shift;shift;;
+        -O=*|--mode=*)    mode="${1#*=}";                      check_v "$1" 
"$mode";  shift;;
+        -O*)              mode=$(echo "$1"  | sed -e's/-O//'); check_v "$1" 
"$mode";  shift;;
+        -x|--xcenter)     x="$2";                           check_v "$1" "$x"; 
 shift;shift;;
+        -x=*|--xcenter=*) x="${1#*=}";                      check_v "$1" "$x"; 
 shift;;
+        -x*)              x=$(echo "$1"  | sed -e's/-x//'); check_v "$1" "$x"; 
 shift;;
+        -y|--ycenter)     y="$2";                           check_v "$1" "$y"; 
 shift;shift;;
+        -y=*|--ycenter=*) y="${1#*=}";                      check_v "$1" "$y"; 
 shift;;
+        -y*)              y=$(echo "$1"  | sed -e's/-y//'); check_v "$1" "$y"; 
 shift;;
+        -r|--rmin)        rmin="$2";                           check_v "$1" 
"$rmin";  shift;shift;;
+        -r=*|--rmin=*)    rmin="${1#*=}";                      check_v "$1" 
"$rmin";  shift;;
+        -r*)              rmin=$(echo "$1"  | sed -e's/-r//'); check_v "$1" 
"$rmin";  shift;;
+        -R|--rmax)        rmax="$2";                           check_v "$1" 
"$rmax";  shift;shift;;
+        -R=*|--rmax=*)    rmax="${1#*=}";                      check_v "$1" 
"$rmax";  shift;;
+        -R*)              rmax=$(echo "$1"  | sed -e's/-R//'); check_v "$1" 
"$rmax";  shift;;
+        -Q|--qratio)      Q="$2";                           check_v "$1" "$Q"; 
 shift;shift;;
+        -Q=*|--qratio=*)  Q="${1#*=}";                      check_v "$1" "$Q"; 
 shift;;
+        -Q*)              Q=$(echo "$1"  | sed -e's/-q//'); check_v "$1" "$Q"; 
 shift;;
+        -p|--pangle)      p="$2";                           check_v "$1" "$p"; 
 shift;shift;;
+        -p=*|--pangle=*)  p="${1#*=}";                      check_v "$1" "$p"; 
 shift;;
+        -p*)              p=$(echo "$1"  | sed -e's/-p//'); check_v "$1" "$p"; 
 shift;;
+        -m|--measure)     m="$2";                           check_v "$1" "$m"; 
 shift;shift;;
+        -m=*|--measure=*) m="${1#*=}";                      check_v "$1" "$m"; 
 shift;;
+        -m*)              m=$(echo "$1"  | sed -e's/-m//'); check_v "$1" "$m"; 
 shift;;
+        -a|--caper)       a="$2";                           check_v "$1" "$a"; 
 shift;shift;;
+        -a=*|--caper=*)   a="${1#*=}";                      check_v "$1" "$a"; 
 shift;;
+        -a*)              a=$(echo "$1"  | sed -e's/-a//'); check_v "$1" "$a"; 
 shift;;
+        -c|--ccat)        c="$2";                           check_v "$1" "$c"; 
 shift;shift;;
+        -c=*|--ccat=*)    c="${1#*=}";                      check_v "$1" "$c"; 
 shift;;
+        -c*)              c=$(echo "$1"  | sed -e's/-c//'); check_v "$1" "$c"; 
 shift;;
+
+        # Output parameters
+        -k|--keeptemp)    k=0; shift;;
+        -k*|--keeptemp=*) on_off_option_error --keeptemp -k;;
+        -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;;
+
+        # Non-operating options.
+        -q|--quiet)       quiet=1; shift;;
+        -q*|--quiet=*)    on_off_option_error --quiet -q;;
+        -?|--help)        print_help; exit 0;;
+        -'?'*|--help=*)   on_off_option_error --help -?;;
+        -V|--version)     print_version; exit 0;;
+        -V*|--version=*)  on_off_option_error --version -V;;
+        --cite)           astfits --cite; exit 0;;
+        --cite=*)         on_off_option_error --cite;;
+
+        # Unrecognized option:
+        -*) echo "$scriptname: unknown option '$1'"; exit 1;;
+
+        # Not an option (not starting with a `-'): assumed to be input FITS
+        # file name.
+        *) inputs="$1 $inputs"; shift;;
+    esac
+done
+
+
+
+
+
+# Basic sanity checks on arguments.
+if [ x"$inputs" = x ]; then
+    echo "$scriptname: no input FITS files."
+    echo "Run with '--help' for more information on how to run."
+    exit 1
+fi
+
+
+
+
+# If the user set the x and y coordinates to be "centre", then compute the
+# centre of the image for constructing the profiles.
+if [ "z$x" = zcenter ] && [ "z$y" = zcenter ]; then
+  xpix=$(astfits $inputs --hdu=$hdu | grep NAXIS1 | awk '{print $3}')
+  x=$(echo "$(seq $xpix)" | aststatistics --median)
+  ypix=$(astfits $inputs --hdu=$hdu | grep NAXIS2 | awk '{print $3}')
+  y=$(echo "$(seq $ypix)" | aststatistics --median)
+fi
+
+
+
+
+# If the user set the rmax parameter to "max", then compute the maximum
+# radius possible on the image. Assuming that the object is in one corner of
+# the image, this radius is given by the diagonal of the image
+if [ "x$rmax" = xmax ]; then
+  xpix=$(astfits $inputs --hdu=$hdu | grep NAXIS1 | awk '{print $3}')
+  ypix=$(astfits $inputs --hdu=$hdu | grep NAXIS2 | awk '{print $3}')
+  rmax=$(astarithmetic "$xpix"f 2f pow "$ypix"f 2f pow + sqrt --quiet)
+fi
+
+
+
+
+
+# Generate the apertures
+aperturestxt=$(echo $output | sed -e"s|.fits|-apertures.txt|g")
+echo "$rmax $x $y 7 $rmax 1 $p $Q $rmax 1" > $aperturestxt
+
+
+
+
+
+# Generate the profiles
+aperturesfits=$(echo $output | sed -e"s|.fits|-apertures.fits|g")
+astmkprof $aperturestxt --background=$inputs --backhdu=$hdu \
+          --mforflatpix --mode=$mode --clearcanvas --type=int16 \
+          --circumwidth=$w --replace --output=$aperturesfits \
+          --config=$a
+
+
+
+
+
+# Construct the catalogue <-> Radial profile
+fprofiles=$(echo $output | sed -e"s|.fits|-profile_"$mode"_$x-$y.fits|g")
+astmkcatalog $aperturesfits -h1 --valuesfile=$inputs -o$output \
+             --ids --$m --config=$c
+
+
+
+
+# Remove temporal files if the user has specified this option
+if [ $k = 1 ]; then
+  rm $aperturestxt $aperturesfits
+fi
+
+
+
+
+
+#zp=$(astfits $inputs -h$hdu | grep -w ZP | awk '{print $3}')
+#pscale=0.389
+#muprofile=$(echo $inputs | sed -e"s|.fits|-sbprofile_"$mode"_$x-$y.fits|g")
+#asttable $fprofiles \
+#         -c"arith OBJ_ID $pscale x" \
+#         -c"arith MEDIAN log10 -2.5 x $zp + $pscale log10 5 x +" \
+#         -o$output
+
+