[gnuastro-commits] master 4e019cb 05/32: astscript-radial-profile: fixing some bugs and modifying metadata

[Mohammad Akhlaghi]

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.