[gnuastro-commits] master cad6503d 11/11: psf-scale-factor: minor stylistic polishing

[Mohammad Akhlaghi]

branch: master
commit cad6503d44fc8cffd413116dfc866769e24010af
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    psf-scale-factor: minor stylistic polishing
    
    Until now, there were some TABs within parts of this script, and some of
    the pipes were not broken into a second line. Also within the
    documentation, the two '@itemx's should be '@item'.
    
    With this commit, to unify the format of the script code with the rest of
    the scripts, they have been corrected; and the '@item's have also been
    fixed.
---
 bin/script/psf-scale-factor.sh | 112 +++++++++++++++++++++++------------------
 doc/gnuastro.texi              |   4 +-
 2 files changed, 64 insertions(+), 52 deletions(-)

diff --git a/bin/script/psf-scale-factor.sh b/bin/script/psf-scale-factor.sh
index 37c23891..ca6b5ee0 100755
--- a/bin/script/psf-scale-factor.sh
+++ b/bin/script/psf-scale-factor.sh
@@ -374,9 +374,10 @@ $scriptname: no center coordinates provided. You can 
specify the object's centra
 EOF
     exit 1
 else
-    ncenter=$(echo $center | awk 'BEGIN{FS=","} \
-                                  {for(i=1;i<=NF;++i) c+=$i!=""} \
-                                  END{print c}')
+    ncenter=$(echo $center \
+                  | awk 'BEGIN{FS=","} \
+                         {for(i=1;i<=NF;++i) c+=$i!=""} \
+                         END{print c}')
     if [ x$ncenter != x2 ]; then
         cat <<EOF
 $scriptname: '--center' (or '-c') only takes two values, but $ncenter were 
given in '$center'
@@ -387,9 +388,10 @@ fi
 
 # If x-shifts is provided.
 if [ x"$xshifts" != x ]; then
-    nxshifts=$(echo $xshifts | awk 'BEGIN{FS=","} \
-                                   {for(i=1;i<=NF;++i) c+=$i!=""} \
-                                   END{print c}')
+    nxshifts=$(echo $xshifts \
+                   | awk 'BEGIN{FS=","} \
+                          {for(i=1;i<=NF;++i) c+=$i!=""} \
+                          END{print c}')
     if [ x$nxshifts != x3 ]; then
         cat <<EOF
 $scriptname: '--xshifts' (or '-x') takes three values (xmin,xstep,xmax), but 
$nxshifts were given in '$xshifts'
@@ -397,7 +399,9 @@ EOF
         exit 1
     fi
     xstep=""
-    xstep=$(echo $xshifts | awk 'BEGIN{FS=","} {if ($2 <= 0.0) print "xstep <= 
0.0"}')
+    xstep=$(echo $xshifts \
+                | awk 'BEGIN{FS=","} \
+                       {if ($2 <= 0.0) print "xstep <= 0.0"}')
     if [ x"$xstep" != x ]; then
         cat <<EOF
 $scriptname: the 'xstep' from the option --xshifts=xmin,xstep,xmax (or '-x') 
is equal or lower than zero ($xshifts), but it has to be a value above zero
@@ -412,9 +416,10 @@ fi
 
 # If y-shifts is provided.
 if [ x"$yshifts" != x ]; then
-    nyshifts=$(echo $yshifts | awk 'BEGIN{FS=","} \
-                                   {for(i=1;i<=NF;++i) c+=$i!=""} \
-                                   END{print c}')
+    nyshifts=$(echo $yshifts \
+                   | awk 'BEGIN{FS=","} \
+                          {for(i=1;i<=NF;++i) c+=$i!=""} \
+                          END{print c}')
     if [ x$nyshifts != x3 ]; then
         cat <<EOF
 $scriptname: '--yshifts' (or '-x') takes three values (xmin,xstep,xmax), but 
$nyshifts were given in '$yshifts'
@@ -422,7 +427,9 @@ EOF
         exit 1
     fi
     xstep=""
-    xstep=$(echo $yshifts | awk 'BEGIN{FS=","} {if ($2 <= 0.0) print "ystep <= 
0.0"}')
+    xstep=$(echo $yshifts \
+                | awk 'BEGIN{FS=","} \
+                       {if ($2 <= 0.0) print "ystep <= 0.0"}')
     if [ x"$xstep" != x ]; then
         cat <<EOF
 $scriptname: the 'ystep' from the option --yshifts=xmin,ystep,xmax (or '-y') 
is equal or lower than zero ($yshifts), but it has to be a value above zero
@@ -492,6 +499,7 @@ objectid="$xcoord"_"$ycoord"
 
 
 
+
 # Define a temporary directory and the final output file
 # ------------------------------------------------------
 #
@@ -562,22 +570,23 @@ if [ "$mode" = wcs ]; then
     cdelt2=$(astfits $inputs --hdu=$hdu --pixelscale --quiet | awk '{print 
$2}')
 
 else
-    # In principle, the PSF does not have WCS information. Here, fake WCS info
-    # is included in order to use warp and center/re-size the PSF to the same
-    # size than the warped image. Fake WCS is constructed as follow: reference
-    # pixel is the center pixel. This pixel is assigned to be RA, Dec = 180.0,
-    # 0.0 deg. Pixel scale is set to 1.0 arcsec/pixel in both axis.
+    # In principle, the PSF does not have WCS information. Here, fake WCS
+    # info is included in order to use warp and center/re-size the PSF to
+    # the same size than the warped image. The fake WCS is constructed as
+    # follows: reference pixel is the center pixel. This pixel is assigned
+    # to be RA, Dec = 180.0, 0.0 deg. Pixel scale is set to 1.0
+    # arcsec/pixel in both axis.
     crval1=180.0
     crval2=0.0
     cdelt1=1.0
     cdelt2=1.0
+
     # For the IMAGE: center coordinates in wcs and img
+    fake_wcs=$tmpdir/fake-wcs-$objectid.fits
     naxis1=$(astfits $inputs --hdu=$hdu --keyval NAXIS1 --quiet)
     naxis2=$(astfits $inputs --hdu=$hdu --keyval NAXIS2 --quiet)
     center1=$(echo $naxis1 | awk '{print $1/2}')
     center2=$(echo $naxis2 | awk '{print $1/2}')
-
-    fake_wcs=$tmpdir/fake-wcs-$objectid.fits
     echo "1 $center1 $center2 1 1 1 1 1 1 1" \
         | astmkprof --oversample=1 \
                     --type=uint8 \
@@ -695,16 +704,16 @@ for xs in $(seq $xshiftswcs); do
     for ys in $(seq $yshiftswcs); do
 
         # Compute the shifts in WCS
-       xspix=$(astarithmetic $xs $xpscale / --quiet \
+        xspix=$(astarithmetic $xs $xpscale / --quiet \
                               | awk '{printf "%.10f\n", $1}')
-       yspix=$(astarithmetic $ys $ypscale / --quiet \
+        yspix=$(astarithmetic $ys $ypscale / --quiet \
                               | awk '{printf "%.10f\n", $1}')
 
         # New shifted center in WCS
         xcwcs_shift=$(astarithmetic $xcwcs $xs + --quiet)
         ycwcs_shift=$(astarithmetic $ycwcs $ys + --quiet)
 
-       # To ease the filename reading, put the offsets in pixels
+        #To ease the filename reading, put the offsets in pixels
         label_shift=xs_ys_"$xspix"_"$yspix"
 
 
@@ -753,30 +762,33 @@ for xs in $(seq $xshiftswcs); do
         # Crop and unlabel the segmentation image
         # ---------------------------------------
         #
-        # If the user provides a segmentation image, treat it appropiately in 
order
-        # to mask all objects that are not the central one. If not, just 
consider
-        # that the cropped and masked image is the cropped (not masked) image. 
The
-        # process is as follow:
-        #   - Compute the central clump and object labels. This is done with 
the
-        #     option '--oneelemstdout' of Crop.
+        # If the user provides a segmentation image, treat it appropiately
+        # in order to mask all objects that are not the central one. If
+        # not, just consider that the cropped and masked image is the
+        # cropped (not masked) image. The process is as follow:
+        #   - Compute the central clump and object labels. This is done
+        #     with the option '--oneelemstdout' of Crop.
         #   - Crop the original mask image.
-        #   - Crop the original mask image to a central region (core), in 
order to
-        #     compute what is the central object id. This is necessary to 
unmask
-        #     this object.
-       #   - In the original cropped mask, convert pixels belonging to the 
central
-        #     object to zeros. By doing this, the central object becomes as 
sky.
+        #   - Crop the original mask image to a central region (core), in
+        #     order to compute what is the central object id. This is
+        #     necessary to unmask this object.
+        #   - In the original cropped mask, convert pixels belonging to the
+        #     central object to zeros. By doing this, the central object
+        #     becomes as sky.
         #   - Mask all non zero pixels in the mask image as nan values.
         if [ x"$segment" != x ]; then
+
             # Find the object and clump labels of the target.
             clab=$(astcrop $segment --hdu=CLUMPS --mode=img --width=1,1 \
                            --oneelemstdout --center=$xcimg,$ycimg --quiet)
             olab=$(astcrop $segment --hdu=OBJECTS --mode=img --width=1,1 \
                            --oneelemstdout --center=$xcimg,$ycimg --quiet)
 
-            # If for any reason, a clump or object label couldn't be 
initialized at
-            # the given coordiante, simply ignore this step. But print a 
warning so
-            # the user is informed of the situation (and that this is a bug: 
'clab'
-            # should be initialized!).
+            # If for any reason, a clump or object label couldn't be
+            # initialized at the given coordiante, simply ignore this
+            # step. But print a warning so the user is informed of the
+            # situation (and that this is a bug: 'clab' should be
+            # initialized!).
             if [ x"$clab" = x   -o   x"$olab" = x ]; then
                 if [ x"$quiet" = x ]; then
                     cat <<EOF
@@ -790,26 +802,26 @@ EOF
                     echo "$scriptname: $segment: at $center, found clump $clab 
in object $olab"
                 fi
 
-               # In order to warp the objects and clumps image, WCS
-               # information is needed. If mode is wcs, just copy the HDU.
-               # If mode is img (no wcs info), it is necessary to inject
-               # the fake WCS information in advance.
+                # In order to warp the objects and clumps image, WCS
+                # information is needed. If mode is wcs, just copy the HDU.
+                # If mode is img (no wcs info), it is necessary to inject
+                # the fake WCS information in advance.
                 clumps_wcs=$tmpdir/clumps-wcs-$objectid-$label_shift.fits
                 objects_wcs=$tmpdir/objects-wcs-$objectid-$label_shift.fits
                 if [ "$mode" = wcs ]; then
                     astfits $segment --copy CLUMPS --output $clumps_wcs
                     astfits $segment --copy OBJECTS --output $objects_wcs
                 else
-                   astarithmetic $segment --hdu CLUMPS \
+                    astarithmetic $segment --hdu CLUMPS \
                                   --wcsfile=$fake_wcs --output=$clumps_wcs
-                   astarithmetic $segment --hdu OBJECTS \
+                    astarithmetic $segment --hdu OBJECTS \
                                   --wcsfile=$fake_wcs --output=$objects_wcs
                 fi
 
-               # Crop the object and clump images. We don't use Warp
-               # because it is not able to properly account integer values
-               # images because they become float32 and thus the
-               # segmentation clumps/objects are not correct.
+                # Crop the object and clump images. We don't use Warp
+                # because it is not able to properly account integer values
+                # images because they become float32 and thus the
+                # segmentation clumps/objects are not correct.
                 croped_clp=$tmpdir/croped-clumps-$objectid-$label_shift.fits
                 croped_obj=$tmpdir/croped-objects-$objectid-$label_shift.fits
                 astcrop $clumps_wcs \
@@ -839,12 +851,12 @@ EOF
             warped_masked=$warped
         fi
 
-       # Set the used the center position for the output. If the original
-       # mode requested was IMG, the current center postion (that is in
-       # WCS) needs to be transformed to IMG.
+        # Set the used the center position for the output. If the original
+        # mode requested was IMG, the current center postion (that is in
+        # WCS) needs to be transformed to IMG.
         xc_out=$xcwcs_shift
         yc_out=$ycwcs_shift
-       if [ x"$mode" = x"img" ]; then
+        if [ x"$mode" = x"img" ]; then
             xcyc_shift=$(echo "$xcwcs_shift,$ycwcs_shift" \
                            | asttable  --column='arith $1 $2 wcs-to-img' \
                                        --wcsfile=$inputs_wcs --wcshdu=1 $quiet)
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index a4e75785..8746deb1 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -35945,14 +35945,14 @@ The result is that all objects and clumps that 
contaminate the central source ar
 Sigma clipping parameters used in the end to find the final scale factor from 
the distribution of all pixels used.
 For more on sigma-clipping, see @ref{Sigma clipping}.
 
-@itemx --xshifts=FLT,FLT,FLT
+@item --xshifts=FLT,FLT,FLT
 Shifts on the centering position provided by @option{--center} in units of 
pixels.
 The three parameters used by the program @code{seq} to create the different 
shifted positions.
 For example, @option{--xshifts=-3.0,0.4,+1.0} will shift the center position 
from -3.0 pixels to +1.0 pixels in step of 0.4 pixels, along the x direction.
 It will compute the scaling factor for all of those position, and the scale 
factor for wich the standard deviation is the smallest will be provided as the 
best center.
 The re-computed center position is also provided as part of the output.
 
-@itemx --yshifts=FLT,FLT,FLT
+@item --yshifts=FLT,FLT,FLT
 Same than the @option{--xshifts} but for the y direction.
 See above for more information.