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[gnuastro-commits] master 4e019cb 05/32: astscript-radial-profile: fixin
From: |
Mohammad Akhlaghi |
Subject: |
[gnuastro-commits] master 4e019cb 05/32: astscript-radial-profile: fixing some bugs and modifying metadata |
Date: |
Wed, 24 Feb 2021 22:36:15 -0500 (EST) |
branch: master
commit 4e019cb6bb756b4af6bc7b6e496b4908ce081451
Author: Raul Infante-Sainz <infantesainz@gmail.com>
Commit: Raul Infante-Sainz <infantesainz@gmail.com>
astscript-radial-profile: fixing some bugs and modifying metadata
Until this commit, the radial profile script was some bugs that I found
once I started to check it from scratch. For example, the axis ratio
(`-Q' or `--qratio') was set to 0 as default value, however, it cannot
be zero! The default value should be 1. Another important bug fixed is
the generation of an output radial profile even if the user do not
specify the name with the `-o' or `--output' options.
With this commit, these bugs have been fixes. In addition to this, the
temporal files generated for obtaining the final radial profile have
been also modified to have better names. The metadata information
included in the final radial now contains the operations that have been
done in order to obtain both columns. So, it is kept the binning and the
final arithmetic operation as comments.
---
bin/script/radial-profile.in | 46 ++++++++++++++++++++++++++++++--------------
1 file changed, 32 insertions(+), 14 deletions(-)
diff --git a/bin/script/radial-profile.in b/bin/script/radial-profile.in
index ae6d480..19c3e16 100644
--- a/bin/script/radial-profile.in
+++ b/bin/script/radial-profile.in
@@ -38,7 +38,7 @@ mode=img
x=center
y=center
m=median
-Q=0
+Q=1
p=0
b=1
w=1
@@ -48,6 +48,7 @@ Y="1 x"
quiet=0
prefix=./
version=0.11
+output="default"
scriptname=astscript-radial-profile
@@ -98,10 +99,11 @@ $scriptname options:
-a, --cprofiles=STR Configuration file for astmkprof.
-c, --ccatalog=STR Configuration file for astmkcatalog.
-X, --xarith=STR Operation for the first column of radial profile.
- -Y, --yarith=STR Operaton for the second column of the radial profile.
+ -Y, --yarith=STR Operation for the second column of the radial
profile.
Output:
-k, --keeptemp Keep temporal/auxiliar files.
+ -o, --output Output table with the radial profile.
Operating mode:
-h, --help Print this help list.
@@ -295,7 +297,7 @@ fi
# If the user set the rmax parameter to "max", then compute the maximum
# radius possible on the image. Assuming that the object is in one corner of
# the image, this radius is given by the diagonal of the image
-if [ "x$rmax" = xmax ]; then
+if [ "z$rmax" = zmax ]; then
xpix=$(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)
@@ -305,12 +307,29 @@ fi
+# Define the final output file
+# ----------------------------
+#
+# 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,
+# then a default value containing the center and mode will be generated.
+if [ z$output = zdefault ]; then
+ bname_ext=$(basename $inputs)
+ bname=$(echo $bname_ext | sed
-e"s|.fits|_radial_profile_"$mode"_$x-$y.fits|g")
+ output=$prefix$bname
+fi
+
+
+
+
+
# Generate the aperture parameters
# --------------------------------
#
# Here, an ascii file is generated with the parameters that will be feed
# into MakeProfiles in order to construct the apertures image.
-aperturestxt=$(echo $output | sed -e"s|.fits|-apertures.txt|g")
+aperturestxt=$(echo $output | sed -e"s|.fits|_apertures.txt|g")
echo "$rmax $x $y 7 $rmax 1 $p $Q $rmax 1" > $aperturestxt
@@ -322,7 +341,7 @@ echo "$rmax $x $y 7 $rmax 1 $p $Q $rmax 1" > $aperturestxt
#
# The apertures image is genrated using MakeProfiles with the parameters
# previously specified in the ascii file.
-aperturesfits=$(echo $output | sed -e"s|.fits|-apertures.fits|g")
+aperturesfits=$(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 \
@@ -339,9 +358,9 @@ astmkprof $aperturestxt --background=$inputs --backhdu=$hdu
\
# to obtain a catalogue using the segmentation image previously generated
# (the elliptical apertures) and the original input image for computing the
# values.
-fprofile=$(echo $output | sed -e"s|.fits|-profile_"$mode"_$x-$y.fits|g")
-astmkcatalog $aperturesfits -h1 --valuesfile=$inputs -o$fprofile \
- --ids --$m --config=$c
+fprofile=$(echo $output | sed -e"s|.fits|_catalogue.fits|g")
+astmkcatalog $aperturesfits -h1 --valuesfile=$inputs --valueshdu=$hdu \
+ --ids --$m --config=$c -o$fprofile
@@ -357,8 +376,8 @@ astmkcatalog $aperturesfits -h1 --valuesfile=$inputs
-o$fprofile \
# small Awk script is used. Since the Awk script will print the columns as
# float values, it is necessary to change the headers. To do that, Sed is
# used to replace all ocurrences of i32 to f32.
-bprofile=$(echo $output | sed -e"s|.fits|-binned-profile_"$mode"_$x-$y.fits|g")
-asttable $fprofile --colinfoinstdout \
+bprofile=$(echo $output | sed -e"s|.fits|_binned.fits|g")
+asttable $fprofile \
| awk -v b=$b '/^#/{print} \
BEGIN { N = b }
{ for (i = 1; i <= NF; i++) sum[i] += $i }
@@ -368,7 +387,6 @@ asttable $fprofile --colinfoinstdout \
sum[i] = 0
}
}' \
- | sed -e"s/i32/f32/g" \
| asttable -o$bprofile
@@ -389,9 +407,9 @@ asttable $fprofile --colinfoinstdout \
# the column names (radius and $m), column units (modified), column type
# (float32), and comment (here it is said how the columns have been
# modified.
-aprofile=$(echo $output | sed -e"s|.fits|-arith-profile_"$mode"_$x-$y.fits|g")
-echo "# Column 1: radius [modified,f32,] Modified with $X" > $aprofile
-echo "# Column 2: $m [modified,f32,] Modified with $Y" >> $aprofile
+aprofile=$(echo $output | sed -e"s|.fits|_arith.fits|g")
+echo "# Column 1: radius [modified,f32,] Binned $b and modified with arith $X"
> $aprofile
+echo "# Column 2: $m [modified,f32,] Binned $b and modified with arith $Y" >>
$aprofile
# Make the appropiate operation over the two columns of the radial profile
# and add it to the temporal file with the meta-data.
- [gnuastro-commits] master updated (ea59208 -> 4294506), Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 863abd7 01/32: astscript-radial-profile: adding script for making radial profiles, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 7eac053 03/32: astscript-radial-profile: improving comments and information, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 4e019cb 05/32: astscript-radial-profile: fixing some bugs and modifying metadata,
Mohammad Akhlaghi <=
- [gnuastro-commits] master dd4f925 06/32: astscript-radial-profile: adding documentation to the GNUASTRO book, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 5e84045 04/32: astscript-radial-profile: allowing to manipulate the final profile, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 82f8176 08/32: astscript-radial-profile: adding usage example to GNUASTRO book, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 0634f04 14/32: Book: describing remaining options of radial profile script, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 2f2970f 09/32: Adding Vim .swp temporal files to .gitignore, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 3fcd49a 10/32: astscript-radial-profile: setting name and version from the compilation, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master ebab496 15/32: Book: changed the place of radial profile script documentation, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 6400ca4 16/32: Some minor correction in description, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master 4f3d70d 20/32: Binning data in some case, Mohammad Akhlaghi, 2021/02/24
- [gnuastro-commits] master b36c21f 17/32: astscript-radial-profile: modification to use $ instead of c in Table, Mohammad Akhlaghi, 2021/02/24