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[gnuastro-commits] master 8e5ab9e 28/32: astscript-radial-profile: simpl
|
From: |
Mohammad Akhlaghi |
|
Subject: |
[gnuastro-commits] master 8e5ab9e 28/32: astscript-radial-profile: simplifying the script |
|
Date: |
Wed, 24 Feb 2021 22:36:20 -0500 (EST) |
branch: master
commit 8e5ab9e26a0b456cfc96d2c4fefbb208f44a0c5f
Author: Raul Infante-Sainz <infantesainz@gmail.com>
Commit: Raul Infante-Sainz <infantesainz@gmail.com>
astscript-radial-profile: simplifying the script
Until this commit, the radial profile script evolved in the direction of
having more and more options within it. However, this goes in the
opposite direction of the minimalistic and modularity principle. Tasks
such as the binning of the radial profile, the modification of the
columns of the final output, or the detection of signal to measure high
level values do not have to be computed in this script. The aim of this
script is clear: compute measurements over radial apertures of a given
object from a specific image.
With this commit, all of these not extrictly necessary tasks have been
removed from the script. Now, it only computes the radial profile
values. In addition to this, many other modifications have been done.
The most important one is the use of long-name variable inside the code.
This allows much faster identification of bugs/problems and the solution
of them. For example, instead of using the variable `x' for the x center
of the object, along with the entire script, now the `xcenter' variable
name is used. The same happen with the rest of variables.
---
bin/script/radial-profile.in | 426 +++++++++++--------------------------------
1 file changed, 111 insertions(+), 315 deletions(-)
diff --git a/bin/script/radial-profile.in b/bin/script/radial-profile.in
index f1f878d..2cc361e 100644
--- a/bin/script/radial-profile.in
+++ b/bin/script/radial-profile.in
@@ -4,7 +4,7 @@
# under `print_help' (below) for more.
#
# Original author:
-# Copyright (C) 2020 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2020-2021 Raul Infante-Sainz <infantesainz@gmail.com>
# Contributing author(s):
# Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
# Copyright (C) 2020 Zahra Sharbaf <zahra.sharbaf2@gmail.com>
@@ -33,26 +33,17 @@ set -e
# Default option values (can be changed with options on the command-line).
hdu=1
-rmax=max
-mode=img
-x=center
-y=center
-m=median
-s='3,0.2'
-Q=1
-p=0
-b=1
-w=1
-k=1
-X="1 x"
-Y="1 x"
-Z="1 x"
-i="radius"
-j="v"
-l="S/N"
+rmax="max"
+mode="img"
+qratio=1
+pangle=0
+xcenter="center"
+ycenter="center"
+measure="--mean"
+sigmaclip="3,0.2"
quiet=0
-prefix=./
tmpdir=""
+keeptmp=0
output="default"
version=@VERSION@
scriptname=@SCRIPT_NAME@
@@ -99,19 +90,11 @@ $scriptname options:
-R, --rmax=FLT Maximum radius for the radial profile (in pixels).
-Q, --qratio=FLT Axis ratio for ellipse profiles (A/B).
-p, --pangle=FLT Position angle for ellipse profiles.
- -m, --measure=STR Operator for measuring the value (mean, median,
etc.).
- -s, --sigmaclip=FLT,FLT Parameters for sigma clipping measure operator.
- -b, --binning=INT Size of the bin for averaging group of pixels.
- -a, --cprofiles=STR Configuration file for astmkprof.
- -c, --ccatalog=STR Configuration file for astmkcatalog.
- -X, --xarith=STR Operation for the first column of radial profile.
- -Y, --yarith=STR Operation for the second column of the radial
profile.
- -i, --iname=STR Name of first column of radial profile (radius).
- -j, --jname=STR Name of second column of radial profile (measured
value).
- -l, --lname=STR Name of third column of radial profile (S/N).
+ -m, --measure=STR Operators for measuring the value (mean, median,
etc.).
+ -s, --sigmaclip=FLT,FLT Parameters for sigma clipping measure operators.
Output:
- -k, --keeptemp Keep temporal/auxiliar files.
+ -k, --keeptmp Keep temporal/auxiliar files.
-o, --output Output table with the radial profile.
Operating mode:
@@ -137,7 +120,7 @@ EOF
print_version() {
cat <<EOF
$scriptname (GNU Astronomy Utilities) $version
-Copyright (C) 2020, Free Software Foundation, Inc.
+Copyright (C) 2020-2021, 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.
@@ -200,65 +183,37 @@ 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|--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;;
- -s|--sigmaclip) s="$2"; check_v "$1"
"$s"; shift;shift;;
- -s=*|--sigmaclip=*) s="${1#*=}"; check_v "$1"
"$s"; shift;;
- -s*) s=$(echo "$1" | sed -e's/-s//'); check_v "$1"
"$s"; shift;;
- -b|--binning) b="$2"; check_v "$1" "$b";
shift;shift;;
- -b=*|--binning=*) b="${1#*=}"; check_v "$1" "$b";
shift;;
- -b*) b=$(echo "$1" | sed -e's/-b//'); check_v "$1" "$b";
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;;
- -X|--xarith) X="$2"; check_v "$1" "$X";
shift;shift;;
- -X=*|--xarith=*) X="${1#*=}"; check_v "$1" "$X";
shift;;
- -X*) X=$(echo "$1" | sed -e's/-X//'); check_v "$1" "$X";
shift;;
- -Y|--yarith) Y="$2"; check_v "$1" "$Y";
shift;shift;;
- -Y=*|--yarith=*) Y="${1#*=}"; check_v "$1" "$Y";
shift;;
- -Y*) Y=$(echo "$1" | sed -e's/-Y//'); check_v "$1" "$Y";
shift;;
- -Z|--zarith) Z="$2"; check_v "$1" "$Z";
shift;shift;;
- -Z=*|--zarith=*) Z="${1#*=}"; check_v "$1" "$Z";
shift;;
- -Z*) Z=$(echo "$1" | sed -e's/-Z//'); check_v "$1" "$Z";
shift;;
- -i|--iname) i="$2"; check_v "$1" "$i";
shift;shift;;
- -i=*|--iname=*) i="${1#*=}"; check_v "$1" "$i";
shift;;
- -i*) i=$(echo "$1" | sed -e's/-i//'); check_v "$1" "$i";
shift;;
- -j|--jname) j="$2"; check_v "$1" "$j";
shift;shift;;
- -j=*|--jname=*) j="${1#*=}"; check_v "$1" "$j";
shift;;
- -j*) j=$(echo "$1" | sed -e's/-j//'); check_v "$1" "$j";
shift;;
- -l|--lname) l="$2"; check_v "$1" "$k";
shift;shift;;
- -l=*|--lname=*) l="${1#*=}"; check_v "$1" "$k";
shift;;
- -l*) l=$(echo "$1" | sed -e's/-l//'); check_v "$1" "$k";
shift;;
-
+ -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) xcenter="$2"; check_v
"$1" "$xcenter"; shift;shift;;
+ -x=*|--xcenter=*) xcenter="${1#*=}"; check_v
"$1" "$xcenter"; shift;;
+ -x*) xcenter=$(echo "$1" | sed -e's/-x//'); check_v
"$1" "$xcenter"; shift;;
+ -y|--ycenter) ycenter="$2"; check_v
"$1" "$ycenter"; shift;shift;;
+ -y=*|--ycenter=*) ycenter="${1#*=}"; check_v
"$1" "$ycenter"; shift;;
+ -y*) ycenter=$(echo "$1" | sed -e's/-y//'); check_v
"$1" "$ycenter"; 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) qratio="$2"; check_v
"$1" "$qratio"; shift;shift;;
+ -Q=*|--qratio=*) qratio="${1#*=}"; check_v
"$1" "$qratio"; shift;;
+ -Q*) qratio=$(echo "$1" | sed -e's/-Q//'); check_v
"$1" "$qratio"; shift;;
+ -p|--pangle) pangle="$2"; check_v
"$1" "$pangle"; shift;shift;;
+ -p=*|--pangle=*) pangle="${1#*=}"; check_v
"$1" "$pangle"; shift;;
+ -p*) pangle=$(echo "$1" | sed -e's/-p//'); check_v
"$1" "$pangle"; shift;;
+ -m|--measure) measure="$2"; check_v
"$1" "$measure"; shift;shift;;
+ -m=*|--measure=*) measure="${1#*=}"; check_v
"$1" "$measure"; shift;;
+ -m*) measure=$(echo "$1" | sed -e's/-m//'); check_v
"$1" "$measure"; shift;;
+ -s|--sigmaclip) sigmaclip="$2"; check_v
"$1" "$sigmaclip"; shift;shift;;
+ -s=*|--sigmaclip=*) sigmaclip="${1#*=}"; check_v
"$1" "$sigmaclip"; shift;;
+ -s*) sigmaclip=$(echo "$1" | sed -e's/-s//'); check_v
"$1" "$sigmaclip"; shift;;
# Output parameters
- -k|--keeptemp) k=0; shift;;
- -k*|--keeptemp=*) on_off_option_error --keeptemp -k;;
+ -k|--keeptmp) keeptmp=1; shift;;
+ -k*|--keeptmp=*) on_off_option_error --keeptmp -k;;
--tmpdir) tmpdir="$2"; check_v "$1"
"$tmpdir"; shift;shift;;
--tmpdir=*) tmpdir="${1#*=}"; check_v "$1"
"$tmpdir"; shift;;
-o|--output) output="$2"; check_v "$1"
"$output"; shift;shift;;
@@ -299,13 +254,13 @@ fi
# If one of X or Y are given the other also needs to be given.
-if [ "z$x" = zcenter ]; then
- if ! [ "z$y" = zcenter ]; then
+if [ "z$xcenter" = zcenter ]; then
+ if ! [ "z$ycenter" = zcenter ]; then
echo "Center position's Y axis value is given, but not X!"
exit 1
fi
else
- if [ "z$y" = zcenter ]; then
+ if [ "z$ycenter" = zcenter ]; then
echo "Center position's X axis value is given, but not Y!"
exit 1
fi
@@ -318,16 +273,16 @@ fi
# Convert center to image coordinates if necessary
# ------------------------------------------------
#
-# If the user gave the central position, and has said its in WCS, then
-# convert them to image mode so we can safely assume image coordianates
-# from now on.
-if ! [ "z$x" = zcenter ]; then
+# If the user provides specific coordinates in WCS (--mode=wcs), then convert
+# them to image mode so we can safely assume image coordianates from now on. To
+# do that, WCS information from the input header image is used.
+if ! [ "z$xcenter" = zcenter ]; then
if [ $mode = wcs ]; then
- xy=$(echo "$x $y" \
+ xy=$(echo "$xcenter $ycenter" \
| asttable -c'arith $1 $2 wcstoimg' \
--wcsfile=$inputs --wcshdu=$hdu)
- x=$(echo $xy | awk '{print $1}');
- y=$(echo $xy | awk '{print $2}');
+ xcenter=$(echo $xy | awk '{print $1}');
+ ycenter=$(echo $xy | awk '{print $2}');
fi
fi
@@ -335,37 +290,36 @@ fi
-
# Set default central position
# ----------------------------
#
-# If the user don't set the x and y coordinates to be "center" (The
+# If the user does not set the x and y coordinates to be `center' (the
# coordinates of the object), then compute the center of the image for
-# constructing the profiles.
+# constructing the profiles. Here, we are assuming that the object is already
+# centered on the input image.
#
# In the FITS standard, pixels are counted from 1, and the integers are in
# the center of the pixel. So after dividing the pixel size of the image by
-# 2, we should add it with 0.5 to be the "center" of the image.
-if [ "z$x" = zcenter ]; then
- x=$(astfits $inputs --hdu=$hdu | awk '/^NAXIS1/{print $3/2+0.5}')
- y=$(astfits $inputs --hdu=$hdu | awk '/^NAXIS2/{print $3/2+0.5}')
+# 2, we should add it with 0.5 to be the `center' of the image.
+if [ "z$xcenter" = zcenter ]; then
+ xcenter=$(astfits $inputs --hdu=$hdu | awk '/^NAXIS1/{print $3/2+0.5}')
+ ycenter=$(astfits $inputs --hdu=$hdu | awk '/^NAXIS2/{print $3/2+0.5}')
fi
-
# Calculate the maximum radius
# ----------------------------
#
-# If the user set the rmax parameter to "max", then compute the maximum
+# If the user set the --rmax parameter to `max', then compute the maximum
# radius possible on the image.
#
-# If the user hasn't given any maximum radius, we give the most reliable
+# If the user has not given any maximum radius, we give the most reliable
# maximum radius (where the full circumference will be within the
# image). If the radius goes outside the image, then the measurements and
-# calculations can be biased, so when the user hasn't provided any maximum
+# calculations can be biased, so when the user has not provided any maximum
# radius, we should only confine ourselves to a radius where the results
# are reliable.
#
@@ -380,7 +334,7 @@ fi
if [ "z$rmax" = zmax ]; then
rmax=$(astfits $inputs --hdu=$hdu \
| awk '/^NAXIS1/{X=$3} /^NAXIS2/{Y=$3} \
- END{ x='$x'; y='$y'; \
+ END{ x='$xcenter'; y='$ycenter'; \
printf("%s\n%s\n%s\n%s", x, y, X-x, Y-y); }' \
| aststatistics --minimum )
fi
@@ -389,19 +343,24 @@ fi
-# Define the final output file
-# ----------------------------
+# Define the final output file and temporal directory
+# ---------------------------------------------------
#
# Here, it is defined the final output file containing the radial profile.
# If the user has defined a specific path/name for the output, it will be
-# used for saving the output file. If the user do not specify a output name,
+# used for saving the output file. If the user does not specify a output name,
# then a default value containing the center and mode will be generated.
bname_prefix=$(basename $inputs | sed 's/\.fits/ /' | awk '{print $1}')
-defaultname=$(pwd)/"$bname_prefix"_radial_profile_$mode"_$x"_"$y"
+defaultname=$(pwd)/"$bname_prefix"_rprofile_$mode"_$xcenter"_"$ycenter"
+if [ z$output = zdefault ]; then output="$defaultname.fits"; fi
+
+# Construct the temporal directory. There, necessary temporal files will be
+# kept during the execution of the script. If the user wants to keep this
+# directory (--keeptmp option), it will not be deleted.
if [ z$tmpdir = z ]; then tmpdir=$defaultname
else tmpdir=$(realpath $tmpdir); fi
if ! [ -d $tmpdir ]; then mkdir $tmpdir; fi
-if [ z$output = zdefault ]; then output="$defaultname.fits"; fi
+
@@ -410,28 +369,24 @@ if [ z$output = zdefault ]; then
output="$defaultname.fits"; fi
# Crop image
# ----------
#
-# Crop the input image around the desired point so we can continue
-# processing only on those pixels (we don't need the other pixels).
+# Crop the input image around the desired point so we can continue processing
+# only on those pixels (we do not need the other pixels).
#
-# Crop's output always has the range of pixels from the original image used
-# in the 'ICF1PIX' keyword value. So to find the new center (important if
-# it has sub-pixel positions), we can simply get the first and third value
-# of that string, and convert to the cropped coordinate system. Note that
-# because FITS pixel couting starts from 1, we need to subtract '1'.
+# The crop's output always has the range of pixels from the original image used
+# in the `ICF1PIX' keyword value. So, to find the new center (important if it
+# is sub-pixel precission), we can simply get the first and third value of that
+# string, and convert to the cropped coordinate system. Note that because FITS
+# pixel couting starts from 1, we need to subtract `1'.
crop=$tmpdir/crop.fits
cropwidth=$(echo $rmax | awk '{print $1*2+1}')
-astcrop $inputs --hdu=$hdu --center=$x,$y --mode=img \
+astcrop $inputs --hdu=$hdu --center=$xcenter,$ycenter --mode=img \
--width=$cropwidth --output=$crop
dxy=$(astfits $crop -h1 \
| grep ICF1PIX \
| sed -e"s/'/ /g" -e's/\:/ /g' -e's/,/ /' \
| awk '{print $3-1, $5-1}')
-echo "x:$x"
-echo "y:$y"
-echo "cropwidth: $cropwidth"
-echo "dxy: $dxy"
-x=$(echo "$x $cropwidth $dxy" | awk '{if($1>int($2/2)) print $1-$3; else print
int($2/2)+$1-int($1)}')
-y=$(echo "$y $cropwidth $dxy" | awk '{if($1>int($2/2)) print $1-$4; else print
int($2/2)+$1-int($1)}')
+xcenter=$(echo "$xcenter $cropwidth $dxy" | awk '{if($1>int($2/2)) print
$1-$3; else print int($2/2)+$1-int($1)}')
+ycenter=$(echo "$ycenter $cropwidth $dxy" | awk '{if($1>int($2/2)) print
$1-$4; else print int($2/2)+$1-int($1)}')
@@ -440,190 +395,36 @@ y=$(echo "$y $cropwidth $dxy" | awk '{if($1>int($2/2))
print $1-$4; else print i
# Generate the apertures image
# ----------------------------
#
-# The apertures image is genrated using MakeProfiles with the parameters
-# previously specified in the ascii file.
+# The apertures image is generated using MakeProfiles with the parameters
+# specified in the echo statement:
+
+# rmax -- maximum radius value (in pixels)
+# xcenter -- X center position (in pixels).
+# ycenter -- Y center position (in pixels).
+# 7 -- type of the profiles (radial distance).
+# 1 -- the Sersic or Moffat index.
+# pangle -- position angle.
+# qratio -- axis ratio.
+# rmax -- magnitude of the profile within the truncation radius (rmax).
+# 1 -- Truncation in radius unit.
apertures=$tmpdir/apertures.fits
-echo "x:$x"
-echo "y:$y"
-echo "$rmax $x $y 7 $rmax 1 $p $Q $rmax 1" \
- | astmkprof --background=$crop --backhdu=1 --mforflatpix \
- --mode=$mode --clearcanvas --type=int16 \
- --circumwidth=$w --replace --output=$apertures \
- --config=$a
-
-
-
-
-# Obtain the radial profile
-# -------------------------
-#
-# The radial profile is obtained using Catalog. In practice, what is done is
-# to obtain a catalogue using the segmentation image previously generated
-# (the elliptical apertures) and the original input image for computing the
-# values.
-if [ $b = 1 ]; then
- fprofile=$tmpdir/catalog-apertures.fits
- astmkcatalog $apertures -h1 --valuesfile=$crop --valueshdu=1 \
- --ids --$m --config=$c -o$fprofile
-else
- # Detection signal
- #
- # If the user set the default value of binning variable($b) except 1,
- # we need to have signal to noise ratio column to obtain radial
- # profile. To obtain signal to noise ratio for each radial profile; at
- # first we have to detect signal of noise.
- detection=$(echo $output | sed -e"s|.fits|_detected.fits|g")
- astnoisechisel $crop -o$detection
-
-
-
-
-
- # Obtain the radial profile
- # -------------------------
- #
- # The radial profile is obtained using Catalog. In practice, what is
- # done is to obtain a catalogue using the segmentation image previously
- # generated (the elliptical apertures) and the original input image for
- # computing the values. Also using of SKY_STD extinction of noisechisel
- # output for computing signal to noise ratio.
- fprofile=$tmpdir/catalog-apertures.fits
- astmkcatalog $apertures -h1 --valuesfile=$crop --valueshdu=$hdu \
- --instd=$detection --stdhdu=SKY_STD --ids --$m --sn \
- --config=$c -o$fprofile
-fi
-
-
-
-
-
-# Binning data
-# ------------
-#
-# In order to increase the signal-to-noise ratio of the radial profile, it
-# is possible to bin the data. It is done in any case, if the user set the
-# default value of binning variable($b) except 1, because the binning will
-# be equal to 1 so the output binned will be the same as the input. To do
-# the binning of the data, a small Awk script is used.Because of the
-# behavior of signal to noise ratio isn't linear. We used the different
-# way to do binning the S/N column. Since the Awk script will print the
-# columns as float values, it is necessary to change the headers. To do
-# that, Sed is used to replace all ocurrences of i32 to f32.
-bprofile=$tmpdir/catalog-apertures-binned.fits
-if [ $b != 1 ]; then
-
- asttable $fprofile \
- | awk -v b=$b '/^#/{print} BEGIN { N = b }
{ for (i = 1; i <= 2; i++) sum[i] += $i}
- { for (i = 3; i == 3; i++) sum[i] += $i ** 2}
- {if (i != 3)
- {
- N = b
- }
- else
- {
- N = b ** 0.5
- }
- }
- NR % N == 0 { for (i = 1; i <= NF; i++)
- {
- printf("%.6f%s",sum[i]/N, ( i == NF) ? "\n" : " ")
- sum[i] = 0
- }
- }' | asttable -o$bprofile
-else
- cp $fprofile $bprofile
-fi
+echo "$rmax $xcenter $ycenter 7 $rmax 1 $pangle $qratio $rmax 1" \
+ | astmkprof --background=$crop --backhdu=1 --mforflatpix \
+ --mode=img --clearcanvas --type=int16 \
+ --circumwidth=1 --replace --output=$apertures
-# Modify the radial profile
+# Obtain the radial profile
# -------------------------
#
-# The user may want to operate the different columns of the radial profile
-# to obtain them in different units. For example, it is common to use radial
-# distances in arcec or arcmin in astronomical images. If this is the case,
-# the user will specify the operation to transform the radius in pixels to
-# arcsecs with the --X option. The same happen with the measured column
-# (--Y). They are strings that will be used in the Table program for operate
-# appropiately the different columns. But before this, the necessary
-# metadata information is saved in a temporal file.
-
-# The metadata consists in the column names and comment about the
-# modification by the operation. First column is the radius in pixels, the
-# name of this column is set by the parameter --i (set to radius by
-# default). Second column is the measured values, the name of this column
-# is set by the parameter --j (set to v by default). Third column is the
-# S/N values, the name of this column is set by the parameter --l (set to
-# S/N by default). If the user does not give a name for the second column,
-# the output name will be the combination of the default and the operator
-# used for measuring in the apertures. For example, if the user choose the
-# mean to make the measure (--measure or -m) and do not specify any name
-# for the output column (--jname or -j), the output column name will be:
-# vmean. The reason of adding the character v to the operator is because it
-# may happen that in later step, the user will use the column value with
-# the Table program. If this is the case, the program will crash because it
-# will mix the name of the operator with the name of the column.
-#
-# Column names
-xcolname=$i
-ycolname=$j
-zcolname=$l
-if [ z$j = zv ]; then
- ycolname=$j$m
-fi
-
-aprofile=$tmpdir/catalog-arith.txt
-echo "# Column 1: $xcolname [modified,f32,] Binned $b and arith $X" > $aprofile
-echo "# Column 2: $ycolname [modified,f32,] Binned $b and arith $Y" >>
$aprofile
-#
-if [ $b != 1 ]; then
- echo "# Column 3: $zcolname [modified,f32,] Binned $b and arith $Z" >>
$aprofile
-
- # Make the appropiate operation over the two columns of the radial profile
- # and add it to the temporal file with the meta-data.
- asttable $bprofile \
- -c'arith $1 '"$X" \
- -c'arith $2 '"$Y" \
- -c'arith $3 '"$Z" >> $aprofile
-else
- # Make the appropiate operation over the two columns of the radial profile
- # and add it to the temporal file with the meta-data.
- asttable $bprofile \
- -c'arith $1 '"$X" \
- -c'arith $2 '"$Y" >> $aprofile
-fi
-
-
-
-
-
-# Finally, read the temporal file with the metadata information as well as
-# the radial profile values, and save it as a fits table using Table.
-cat $aprofile | asttable -o$output
-
-
-
-
-
-# Calculate the Half-Light Radii
-# ------------------------------
-#
-# This parameter can calulate for that time the user set the default value
-# of binning variable($b) except 1.
-#
-# The half-light or 'effective' radius as the radius within which half of
-# the object's luminosity is contained.
-if [ $b != 1 ]; then
- halfoflight=$(asttable $output | awk 'NR>=3{if(max<$2){max=$2}}END{print
max/2}')
- radius=$(asttable $output \
- | awk '{if('$(echo
$halfoflight)'<=$2){line=$1;light=$2}}END{print line}')
- echo "Half-Light-Radii: $radius pixels from the center of the object"
-fi
-
-
-
+# The radial profile is obtained using Catalog. In practice, what is done is to
+# obtain a catalogue using the segmentation image previously generated (the
+# elliptical apertures) and the original input image for measuring the values.
+astmkcatalog $apertures -h1 --valuesfile=$crop --valueshdu=1 \
+ --ids $measure --sigmaclip=$sigmaclip --output=$output
@@ -632,14 +433,9 @@ fi
# Remove temporal files
# ---------------------
#
-# If the user has specified this option, temporal files will be removed.
-k=0
-if [ $k = 1 ]; then
- rm $crop \
- $aprofile \
- $bprofile \
- $fprofile \
- $detection \
- $apertures
- rm -df $tmpdir
+# If the user does not specify to keep the temporal files with the option
+# `--keeptmp', then remove the whole directory.
+if [ $keeptmp = 0 ]; then
+ rm -rf $tmpdir
fi
+
- [gnuastro-commits] master 8089ea3 27/32: astscript-radial-profile: Samaeh's changes included, conflicts fixed, (continued)
- [gnuastro-commits] master 8089ea3 27/32: astscript-radial-profile: Samaeh's changes included, conflicts fixed, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 04a8bec 29/32: Book: simplifying documentation of astscript-radial-profile, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 362819c 30/32: astscript-radial-profile: fixed bug when creating the temporal directory, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master c9647b5 31/32: Imported work on the radial profile script, minor conflict fixed, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 1072b2b 02/32: astscript-radial-profile: added the option -b for binning the data, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 87f5383 23/32: astscript-radial-profile: minor corrections of previous commits, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master e41c2e4 24/32: astscript-radial-profile: sigma clip parameters for measurements added, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 337e46d 18/32: The half-light radii, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 2df5a22 19/32: Signal to noise ratio for each radius, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 846fc39 25/32: Radial profile script modifications, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 8e5ab9e 28/32: astscript-radial-profile: simplifying the script,
Mohammad Akhlaghi <=