[gnuastro-commits] master 4f206b8b 20/23: astscript-color-faint-gray: minor modifications to have better file names

[Mohammad Akhlaghi]

branch: master
commit 4f206b8bd2b26e5568af32afca4e8a5815627077
Author: Raul Infante-Sainz <infantesainz@gmail.com>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    astscript-color-faint-gray: minor modifications to have better file names
    
    Until this commit, there were some file names that were not following the
    same logic. Also some images were saved as float64 without any good reason.
    
    With this commit, these issues have been corrected. Now the file naming
    follow the same logic and some of them has been renamed to have better
    description. In order to save space, the float64 images are now saved as
    float32. A couple of text lines of the tutorial have been also corrected.
---
 bin/script/color-faint-gray.sh | 129 +++++++++++++++++++++--------------------
 doc/gnuastro.texi              |   9 +--
 2 files changed, 72 insertions(+), 66 deletions(-)

diff --git a/bin/script/color-faint-gray.sh b/bin/script/color-faint-gray.sh
index 957f4b7d..b2bc5ea1 100644
--- a/bin/script/color-faint-gray.sh
+++ b/bin/script/color-faint-gray.sh
@@ -139,22 +139,22 @@ $scriptname options:
   -G, --gamma             Gamma parameter (nonlinear, overrides bias/contrast).
 
  Color and gray parameters
-      --coloronly         No black and grayscale regions.
+      --coloronly         No grayscale regions, background in black.
       --grayval=FLT       Gray threshold (highest value to use grayscale).
       --colorval=FLT      Color threshold (lowest value to have color).
-      --graykernelfwhm=FLT Kernel FWHM for convolving the background image.
+      --graykernelfwhm=FLT  Kernel FWHM for convolving the background image.
       --colorkernelfwhm=FLT Kernel FWHM for color separation ref. image.
 
  Output:
-      --checkparams       Print distribution of values used to find params.
   -k, --keeptmp           Keep temporary/auxiliar files.
   -o, --output            Output color image name.
+      --checkparams       Print distribution of values used to find params.
 
  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.
+      --cite              BibTeX citation for this program.
 
 Mandatory or optional arguments to long options are also mandatory or optional
 for any corresponding short options.
@@ -252,12 +252,12 @@ do
         -z=*|--zeropoint=*)  aux="${1#*=}";                             
check_v "$1" "$aux"; zeropoint="$zeropoint $aux"; shift;;
         -z*)                 aux="$(echo "$1"  | sed -e's/-z//')";      
check_v "$1" "$aux"; zeropoint="$zeropoint $aux"; shift;;
 
-        -s|--stretch)       stretch="$2";                               
check_v "$1" "$stretch";  shift;shift;;
-        -s=*|--stretch=*)   stretch="${1#*=}";                          
check_v "$1" "$stretch";  shift;;
-        -s*)                stretch=$(echo "$1"  | sed -e's/-s//');     
check_v "$1" "$stretch";  shift;;
-        -Q|--qbright)       qbright="$2";                               
check_v "$1" "$qbright";  shift;shift;;
-        -Q=*|--qbright=*)   qbright="${1#*=}";                          
check_v "$1" "$qbright";  shift;;
-        -Q*)                qbright=$(echo "$1"  | sed -e's/-Q//');     
check_v "$1" "$qbright";  shift;;
+        -s|--stretch)        stretch="$2";                              
check_v "$1" "$stretch";  shift;shift;;
+        -s=*|--stretch=*)    stretch="${1#*=}";                         
check_v "$1" "$stretch";  shift;;
+        -s*)                 stretch=$(echo "$1"  | sed -e's/-s//');    
check_v "$1" "$stretch";  shift;;
+        -Q|--qbright)        qbright="$2";                              
check_v "$1" "$qbright";  shift;shift;;
+        -Q=*|--qbright=*)    qbright="${1#*=}";                         
check_v "$1" "$qbright";  shift;;
+        -Q*)                 qbright=$(echo "$1"  | sed -e's/-Q//');    
check_v "$1" "$qbright";  shift;;
 
         -G|--gamma)          gamma="$2";                                
check_v "$1" "$gamma";  shift;shift;;
         -G=*|--gamma=*)      gamma="${1#*=}";                           
check_v "$1" "$gamma";  shift;;
@@ -478,10 +478,10 @@ if [ -d $tmpdir ]; then junk=1; else mkdir $tmpdir; fi
 # If the user specify a given value below which the pixel values are
 # wanted to be zero, then put all of those pixels to zero. By default,
 # no clipping will be done (a symbolic link will be put to the input).
-rclipped="$tmpdir/r_clipped.fits"
-gclipped="$tmpdir/g_clipped.fits"
-bclipped="$tmpdir/b_clipped.fits"
-kclipped="$tmpdir/k_clipped.fits"
+rclipped="$tmpdir/R_clipped.fits"
+gclipped="$tmpdir/G_clipped.fits"
+bclipped="$tmpdir/B_clipped.fits"
+kclipped="$tmpdir/K_clipped.fits"
 
 if [ x"$rmin" = x ]; then
     ln -sf $(realpath $rimage) $rclipped
@@ -531,9 +531,9 @@ fi
 # appropiately. In addition to this, if zero points are provided, the
 # images will be transformed to have micro Jansky values, this helps makes
 # a more physically meaningful comparison between the filters.
-rscaled="$tmpdir/r_scaled.fits"
-gscaled="$tmpdir/g_scaled.fits"
-bscaled="$tmpdir/b_scaled.fits"
+rscaled="$tmpdir/R_scaled.fits"
+gscaled="$tmpdir/G_scaled.fits"
+bscaled="$tmpdir/B_scaled.fits"
 
 # Compute normalized weights
 weight_sum=$(astarithmetic $rweight $gweight $bweight 3 sum --type=f32 -q)
@@ -595,7 +595,7 @@ fi
 # The asinh transformation is done on the mean of RGB images. Here, this
 # image is obtained by stacking them using the 'mean' operator. If the
 # stacked image has exact zero pixel values, change them to nan values.
-I_RGB_stack="$tmpdir/RGB-mean.fits"
+I_RGB_stack="$tmpdir/RGB_mean.fits"
 astarithmetic $rscaled --hdu=$rhdu \
               $gscaled --hdu=$ghdu \
               $bscaled --hdu=$bhdu 3 mean \
@@ -612,12 +612,12 @@ astarithmetic $rscaled --hdu=$rhdu \
 # transformation is done over the mean of RGB images. After the
 # transformation is done, it is normalized by I_RGB. Finally, the range of
 # pixel values is linear transformed to [minvalrange - maxvalrange].
-I_RGB_asinh="$tmpdir/RGB-mean-asinh.fits"
+I_RGB_asinh="$tmpdir/RGB_mean-asinh.fits"
 astarithmetic $I_RGB_stack -h1 set-I_RGB \
               I_RGB $qbright x $stretch x set-i \
               i asinh $qbright / --output=$I_RGB_asinh $quiet
 
-I_RGB_asinh_norm="$tmpdir/RGB-mean-asinh-norm.fits"
+I_RGB_asinh_norm="$tmpdir/RGB_mean-asinh-norm.fits"
 astarithmetic $I_RGB_stack -h1 set-stack \
               $I_RGB_asinh -h1 set-asinh \
               asinh stack / --output=$I_RGB_asinh_norm $quiet
@@ -655,16 +655,16 @@ maxG=$(aststatistics $I_G --maximum -q)
 maxB=$(aststatistics $I_B --maximum -q)
 maxRGB=$(astarithmetic $maxR float64 $maxG float64 $maxB float64 3 max -q)
 
-astarithmetic $I_R $maxRGB / $maxvalrange x --output=$I_R_norm $quiet
-astarithmetic $I_G $maxRGB / $maxvalrange x --output=$I_G_norm $quiet
-astarithmetic $I_B $maxRGB / $maxvalrange x --output=$I_B_norm $quiet
+astarithmetic $I_R $maxRGB / $maxvalrange x float32 --output=$I_R_norm $quiet
+astarithmetic $I_G $maxRGB / $maxvalrange x float32 --output=$I_G_norm $quiet
+astarithmetic $I_B $maxRGB / $maxvalrange x float32 --output=$I_B_norm $quiet
 
 
 
 
 
-# Transformation to change the contrast and bias
-# ----------------------------------------------
+# Transformations to enhance the image
+# ------------------------------------
 #
 # Modify the images that are going to be used for obtaining the COLOR
 # image. There are two possible options: linear and NON-linear
@@ -681,29 +681,29 @@ astarithmetic $I_B $maxRGB / $maxvalrange x 
--output=$I_B_norm $quiet
 # maxvalrange value. So, all pixels above maxrangevalue become equal to
 # maxrangevalue.
 
-I_R_transformed="$tmpdir/R_transformed.fits"
-I_G_transformed="$tmpdir/G_transformed.fits"
-I_B_transformed="$tmpdir/B_transformed.fits"
+I_R_enhanced="$tmpdir/R_enhanced.fits"
+I_G_enhanced="$tmpdir/G_enhanced.fits"
+I_B_enhanced="$tmpdir/B_enhanced.fits"
 if [ x"$gamma" != x"1.0" ]; then
   astarithmetic $I_R_norm $maxvalrange / $gamma pow $maxvalrange x set-t \
-                t t $maxvalrange gt $maxvalrange where 
--output=$I_R_transformed $quiet
+                t t $maxvalrange gt $maxvalrange where --output=$I_R_enhanced 
$quiet
   astarithmetic $I_G_norm $maxvalrange / $gamma pow $maxvalrange x set-t \
-                t t $maxvalrange gt $maxvalrange where 
--output=$I_G_transformed $quiet
+                t t $maxvalrange gt $maxvalrange where --output=$I_G_enhanced 
$quiet
   astarithmetic $I_B_norm $maxvalrange / $gamma pow $maxvalrange x set-t \
-                t t $maxvalrange gt $maxvalrange where 
--output=$I_B_transformed $quiet
+                t t $maxvalrange gt $maxvalrange where --output=$I_B_enhanced 
$quiet
 
 elif [ x"$contrast" != x"1.0" ] || [ x$bias != x"0.0" ]; then
   astarithmetic $I_R_norm $contrast x $bias + set-t \
-                t t $maxvalrange gt $maxvalrange where 
--output=$I_R_transformed $quiet
+                t t $maxvalrange gt $maxvalrange where --output=$I_R_enhanced 
$quiet
   astarithmetic $I_G_norm $contrast x $bias + set-t \
-                t t $maxvalrange gt $maxvalrange where 
--output=$I_G_transformed $quiet
+                t t $maxvalrange gt $maxvalrange where --output=$I_G_enhanced 
$quiet
   astarithmetic $I_B_norm $contrast x $bias + set-t \
-                t t $maxvalrange gt $maxvalrange where 
--output=$I_B_transformed $quiet
+                t t $maxvalrange gt $maxvalrange where --output=$I_B_enhanced 
$quiet
 
 else
-    ln -sf $(realpath $I_R_norm) $I_R_transformed
-    ln -sf $(realpath $I_G_norm) $I_G_transformed
-    ln -sf $(realpath $I_B_norm) $I_B_transformed
+    ln -sf $(realpath $I_R_norm) $I_R_enhanced
+    ln -sf $(realpath $I_G_norm) $I_G_enhanced
+    ln -sf $(realpath $I_B_norm) $I_B_enhanced
 fi
 
 
@@ -721,9 +721,9 @@ if [ x$coloronly = x1 ]; then
     # here correspond to the gray-computed ones in order to obtain exactly the
     # same color as the gray-background image (for those pixels that are not
     # background).
-    astconvertt $I_R_transformed -h1 \
-                $I_G_transformed -h1 \
-                $I_B_transformed -h1 \
+    astconvertt $I_R_enhanced -h1 \
+                $I_G_enhanced -h1 \
+                $I_B_enhanced -h1 \
                 --output=$output $quiet
 
     # Remove images
@@ -812,7 +812,7 @@ else
                       oldmax oldmin - set-oldrange \
                       newmax newmin - set-newrange \
                       image oldmin - newrange x oldrange / newmin + \
-                      --output=$I_COLORGRAY_threshold $quiet
+                      float32 --output=$I_COLORGRAY_threshold $quiet
 
     else
         I_BACK_convolved=$kclipped
@@ -842,6 +842,10 @@ else
       grayval=$colorval
     fi
 
+
+
+
+
     # Mask images
     # -----------
     #
@@ -849,16 +853,17 @@ else
     # correspond to the regions that are represented in those colormaps.
     # At the end, for debugging and finding the best paramters pourpouses,
     # a total mask is computed.
-    GRAY_MASK="$tmpdir/gray-mask.fits"
-    COLOR_MASK="$tmpdir/color-mask.fits"
-    BLACK_MASK="$tmpdir/black-mask.fits"
-    TOTAL_MASK="$tmpdir/total-mask-2color-1black-0gray.fits"
-    astarithmetic $I_COLORGRAY_threshold set-i \
-                  i $colorval lt --output $GRAY_MASK
+    GRAY_MASK="$tmpdir/GRAY_mask.fits"
+    COLOR_MASK="$tmpdir/COLOR_mask.fits"
+    BLACK_MASK="$tmpdir/BLACK_mask.fits"
+    TOTAL_MASK="$tmpdir/TOTAL_mask-2color-1black-0gray.fits"
     astarithmetic $I_COLORGRAY_threshold set-i \
                   i $colorval gt --output $COLOR_MASK
     astarithmetic $I_COLORGRAY_threshold set-i \
-                  i $colorval lt i $grayval gt and --output $BLACK_MASK
+                  i $colorval lt i $grayval gt and \
+                  --output $BLACK_MASK
+    astarithmetic $I_COLORGRAY_threshold set-i \
+                  i $colorval lt --output $GRAY_MASK
     astarithmetic $COLOR_MASK -h1 f32 2 x set-c \
                   $BLACK_MASK -h1 f32 1 x set-b \
                   $GRAY_MASK  -h1 f32 0 x set-g \
@@ -902,7 +907,7 @@ else
                   newmax newmin - set-newrange \
                   masked oldmin - newrange x oldrange / newmin + \
                   set-transformed \
-                  transformed --output=$I_GRAY_colormasked $quiet
+                  transformed float32 --output=$I_GRAY_colormasked $quiet
 
 
 
@@ -913,11 +918,11 @@ else
     #
     # Put the black pixels equal to zero. By doing this, those pixels will
     # be set to pure black color in the final image.
-    I_GRAY_colormasked_clipped="$tmpdir/GRAY_colormasked_clipped.fits"
+    I_GRAY_colormasked_zeroblack="$tmpdir/GRAY_colormasked_zeroblack.fits"
     astarithmetic $I_GRAY_colormasked -h1 set-i \
                   $BLACK_MASK         -h1 set-b \
-                  i b 0.0 where \
-                  --output=$I_GRAY_colormasked_clipped
+                  i b 0.0 where float32 \
+                  --output=$I_GRAY_colormasked_zeroblack
 
 
 
@@ -930,14 +935,14 @@ else
     # than the gray-threshold with the pixels of the reference image. This is
     # done for each input image (band).  Output images end with -gray.fits,
     # generated into the for loop.
-    I_R_transformed_gray="$tmpdir/R_transformed_gray.fits"
-    I_G_transformed_gray="$tmpdir/G_transformed_gray.fits"
-    I_B_transformed_gray="$tmpdir/B_transformed_gray.fits"
-    for f in $I_R_transformed $I_G_transformed $I_B_transformed; do
-      outputname=$(echo "$f" | sed -e's/.fits/_gray.fits/')
+    I_R_black_gray="$tmpdir/R_black_gray.fits"
+    I_G_black_gray="$tmpdir/G_black_gray.fits"
+    I_B_black_gray="$tmpdir/B_black_gray.fits"
+    for f in $I_R_enhanced $I_G_enhanced $I_B_enhanced; do
+      outputname=$(echo "$f" | sed -e's/_enhanced.fits/_black_gray.fits/')
       astarithmetic $f \
-                    $I_GRAY_colormasked_clipped isblank not \
-                    $I_GRAY_colormasked_clipped \
+                    $I_GRAY_colormasked_zeroblack isblank not \
+                    $I_GRAY_colormasked_zeroblack \
                     where -g1 --output=$outputname $quiet;
     done
 
@@ -951,9 +956,9 @@ else
     # Once all the previous treatment has been done for each image, then
     # combine all with Convert program to obtain the colored image (with the
     # low S/N regions in gray).
-    astconvertt $I_R_transformed_gray -h1 \
-                $I_G_transformed_gray -h1 \
-                $I_B_transformed_gray -h1 \
+    astconvertt $I_R_black_gray -h1 \
+                $I_G_black_gray -h1 \
+                $I_B_black_gray -h1 \
                 --output=$output $quiet
 fi
 
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index ccae4a11..fa641b5f 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -9135,7 +9135,7 @@ $ astscript-color-faint-gray $params 
--output=m51-cval.pdf \
                            --colorval=25
 @end example
 
-Open @file{m51-colorval.pdf} and check that it is true!
+Open @file{m51-cval.pdf} and check that it is true!
 Only the central part of the objects (very bright pixels, those between 100 
and 25 on the threshold image) are shown in color.
 Fainter pixels (below 25 on the threshold image) are shown in gray.
 However, in many situations it is good to be able to show the outskirts of 
galaxies and low surface brightness features in pure black, while showing the 
background in gray.
@@ -9152,14 +9152,14 @@ $ astscript-color-faint-gray $params 
--output=m51-cval-gval.pdf \
 Open the image and check that the regions shown in color are smaller (as 
before), and that now there is a region around those color pixels that are in 
pure black.
 After the black pixels toward the fainter ones, they are shown in gray.
 It is recomended to experiment with different values around the estimated one 
to have a feeling on how it changes the image.
-To have even better idea of those regions, please run the following example to 
keep temporary files and check the segmentation image 
@file{./aux/total-mask-2color-1black-0gray.fits}
+To have even better idea of those regions, please run the following example to 
keep temporary files and check the segmentation image 
@file{./aux/TOTAL-mask-2color-1black-0gray.fits}
 
 @example
 $ astscript-color-faint-gray $params --output=m51-cval-gval.pdf \
                            --colorval=25 --grayval=5 \
                            --tmpdir=./aux --keeptmp
 
-$ astscript-fits-view aux/total-mask-2color-1black-0gray.fits
+$ astscript-fits-view aux/TOTAL-mask-2color-1black-0gray.fits
 @end example
 
 In this segmentation image, pixels equal to 2 will be shown in color, pixels 
equal to 1 will be shown as pure black, and pixels equal to zero are shown in 
gray.
@@ -9204,7 +9204,6 @@ Two additional transformations are available to modify 
the appearance of the out
 The linear transformation combines bias adjustment and contrast enhancement 
through the @option{--bias} and @option{--contrast} options.
 In most cases, only the contrast adjustment is necessary to improve the 
quality of the color image.
 To illustrate the impact of adjusting image contrast, we will generate an 
image with higher contrast and compare with the previous one.
-Since we have decided to keep the weights, to keep the following commands, 
simple, we have modified the definition of each channel (and used the short 
version of the options to keep them short):
 
 @example
 $ astscript-color-faint-gray $params --output=m51-contrast.pdf \
@@ -9212,6 +9211,8 @@ $ astscript-color-faint-gray $params 
--output=m51-contrast.pdf \
 @end example
 
 When you compare this (@file{m51-contrast.pdf}) with the previous output 
(@file{m51-params.pdf}), you see that the colored parts are now much more clear!
+Use this option also with caution because it may happen that the bright parts 
become saturated.
+
 Congratulations!
 By following the tutorial up to this point, we have been able to reproduce 
three images of Infante-Sainz et al. (2023, @url{TBD}).
 You can see the commands that were used to generate them within the 
reproducible source of that paper at @url{TBD}.