[gnuastro-commits] master 81f37667 02/23: astscript-rgb-image: select black or gray background

[Mohammad Akhlaghi]

branch: master
commit 81f3766759404ed4e8041050b10a6b93b8447e19
Author: Raul Infante-Sainz <infantesainz@gmail.com>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    astscript-rgb-image: select black or gray background
    
    Until this commit, the rgb-image script generates two output images. One
    image with color and black background, and another one with color and gray
    background. While this is good because both images are obtained at once, it
    is not good in other scenarios like in pipelines or just if one of the two
    images is not wanted. In addition to that, a predefined output name for the
    gray-background image was selected. This is not good.
    
    With this commit, a new option has been added: --grayback. This option
    allows the user to ask for the gray-background image and not generate the
    black-background image. As a consequence, time is saved. Also, now the
    script can be easily used in pipelines where systematic inputs and output
    names are required.
---
 bin/script/rgb-image.sh | 433 ++++++++++++++++++++++++------------------------
 1 file changed, 217 insertions(+), 216 deletions(-)

diff --git a/bin/script/rgb-image.sh b/bin/script/rgb-image.sh
index e0a57a12..b92a6b85 100644
--- a/bin/script/rgb-image.sh
+++ b/bin/script/rgb-image.sh
@@ -80,7 +80,9 @@ quiet=""
 tmpdir=""
 keeptmp=0
 checkparams=0
-output="color-image.jpg"
+output="rgb-image.jpg"
+
+grayback=0
 
 version=@VERSION@
 scriptname=@SCRIPT_NAME@
@@ -146,6 +148,7 @@ $scriptname options:
                           this overrides --brightness or --contrast)
 
  Color and gray parameters
+      --grayback            Generate the gray-background color image.
       --grayval=FLT         Value that defines the black and white (for gray 
regions).
       --colorval=FLT        Value that defines the separation between color 
and gray.
       --graykernelfwhm=FLT  Kernel FWHM for convolving the background image.
@@ -179,7 +182,7 @@ EOF
 print_version() {
     cat <<EOF
 $scriptname (GNU Astronomy Utilities) $version
-Copyright (C) 2021, Free Software Foundation, Inc.
+Copyright (C) 2021-2023, Free Software Foundation, Inc.
 License GPLv3+: GNU General public license version 3 or later.
 This is free software: you are free to change and redistribute it.
 There is NO WARRANTY, to the extent permitted by law.
@@ -282,6 +285,7 @@ do
         -b=*|--brightness=*) brightness="${1#*=}";                       
check_v "$1" "$brightness";  shift;;
         -b*)                 brightness=$(echo "$1"  | sed -e's/-b//');  
check_v "$1" "$brightness";  shift;;
 
+        --grayback)         grayback=1; shift;;
         --grayval)          grayval="$2";                              check_v 
"$1" "$grayval";  shift;shift;;
         --grayval=*)        grayval="${1#*=}";                         check_v 
"$1" "$grayval";  shift;;
         --colorval)         colorval="$2";                             check_v 
"$1" "$colorval";  shift;shift;;
@@ -292,7 +296,7 @@ do
         --colorkernelfwhm=*) colorkernelfwhm="${1#*=}";                check_v 
"$1" "$colorkernelfwhm";  shift;;
 
         # Output parameters
-        --checkparams) checkparams=1; shift;;
+        --checkparams)    checkparams=1; shift;;
         -k|--keeptmp)     keeptmp=1; shift;;
         -k*|--keeptmp=*)  on_off_option_error --keeptmp -k;;
         -t|--tmpdir)      tmpdir="$2";                          check_v "$1" 
"$tmpdir";  shift;shift;;
@@ -771,251 +775,246 @@ fi
 
 
 
-# Make the color figure
-# ---------------------
-#
-# Once all the previous treatment has been done for each image, then combine
-# all with Convert program to obtain the colored image. Limit fluxes used
-# 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 \
-            $I_B_transformed -h1 \
-            --output=$output $quiet
-
+# If the user wants the gray background image
+if [ x$grayback = x1 ]; then
+
+    # Until now, all necessary threshold and parameters have been computed (if
+    # the user did not specify any value) from the R,G,B images. The following
+    # steps are necessary for constructing the gray background color image. So,
+    # low brightness will be showed in gray while high brightness wil be showed
+    # in color.
+
+    # Convolve the gray threshold image and set it to 0-100 range values
+    # ------------------------------------------------------------------
+    #
+    # Convolve the image that is going to be used for defining the threshold
+    # for splitting the COLOR and GRAY parts. By doing this, instead of having
+    # a noised frontier, the border would be more clear. If the user don't want
+    # to convolve, just make a symbolic link.
+    I_COLORGRAY_threshold="$tmpdir/COLORGRAY_threshold.fits"
+    if [ $colorkernelfwhm = 0 ]; then
+      # Change pixel values to the wanted range
+      astarithmetic $I_RGB_asinh_norm -h1 set-image \
+                    image minvalue set-oldmin \
+                    image maxvalue set-oldmax \
+                    $minvalrange set-newmin \
+                    $maxvalrange set-newmax \
+                    oldmax oldmin - set-oldrange \
+                    newmax newmin - set-newrange \
+                    image oldmin - newrange x oldrange / newmin + 
set-transformed \
+                    transformed --output=$I_COLORGRAY_threshold $quiet
+    else
+      I_COLORGRAY_kernel="$tmpdir/COLORGRAY_kernel.fits"
+      astmkprof --kernel=gaussian,$colorkernelfwhm,3 \
+                --output=$I_COLORGRAY_kernel $quiet
+
+      I_COLORGRAY_convolved="$tmpdir/COLORGRAY_kernel.fits"
+      astconvolve $I_RGB_asinh_norm --hdu=1 --kernel=$I_COLORGRAY_kernel \
+                  --domain=spatial --output=$I_COLORGRAY_convolved $quiet
+
+      # Change pixel values to the wanted range
+      astarithmetic $I_COLORGRAY_convolved -h1 set-image \
+                    image minvalue set-oldmin \
+                    image maxvalue set-oldmax \
+                    $minvalrange set-newmin \
+                    $maxvalrange set-newmax \
+                    oldmax oldmin - set-oldrange \
+                    newmax newmin - set-newrange \
+                    image oldmin - newrange x oldrange / newmin + 
set-transformed \
+                    transformed --output=$I_COLORGRAY_threshold $quiet
+    fi
 
 
 
 
-# Remove images
-if [ $keeptmp = 0 ]; then
-  rm $rscaled $gscaled $bscaled \
-     $rclipped $gclipped $bclipped
-fi
 
+    # Find the COLOR threshold
+    # ------------------------
+    #
+    # The color image with the gray background is constructed by separating the
+    # original image into two regimes: COLOR and GRAY. Here, the pixel value
+    # used for separate these two regions is computed. It is obtained from the
+    # asinh-transformed image. If the user does not provide a value then use
+    # ghe computed one (guessed). If the user provide a value, then use it
+    # directly. Note that the guessed value is computed in any case.
+    colorval_guessed=$(aststatistics $I_COLORGRAY_threshold --median -q)
+    if [ x$colorval = x"" ]; then
+      colorval=$colorval_guessed
+    fi
 
 
 
 
-# GRAY BACKGROUND
-# ---------------
-#
-# Until now, all necessary threshold and parameters have been computed (if
-# the user did not specify any value) from the R,G,B images. The following
-# steps are necessary for constructing the gray background color image. So,
-# low brightness will be showed in gray while high brightness wil be showed
-# in color.
 
+    # Binary mask for COLOR (1) and GRAY (0) parts
+    # --------------------------------------------
+    #
+    # Here the image is separated into two parts: COLOR (pixels=1) and GRAY
+    # (pixels = 0). To obtain this mask, the colorval is considered as the
+    # threshold on the asinhed image. So:
+    #   asinhed < colorval -->  COLOR = 1
+    #   asinhed > colorval -->  GRAY  = 0
+    I_COLORGRAY_mask="$tmpdir/COLORGRAY_mask-1color-0gray.fits"
+    astarithmetic $I_COLORGRAY_threshold set-ref \
+                  ref $colorval lt -o $I_COLORGRAY_mask $quiet
 
 
 
 
 
-# Convolve the gray threshold image and set it to 0-100 range values
-# ------------------------------------------------------------------
-#
-# Convolve the image that is going to be used for defining the threshold
-# for splitting the COLOR and GRAY parts. By doing this, instead of having
-# a noised frontier, the border would be more clear. If the user don't want
-# to convolve, just make a symbolic link.
-I_COLORGRAY_threshold="$tmpdir/COLORGRAY_threshold.fits"
-if [ $colorkernelfwhm = 0 ]; then
-  # Change pixel values to the wanted range
-  astarithmetic $I_RGB_asinh_norm -h1 set-image \
-                image minvalue set-oldmin \
-                image maxvalue set-oldmax \
-                $minvalrange set-newmin \
-                $maxvalrange set-newmax \
-                oldmax oldmin - set-oldrange \
-                newmax newmin - set-newrange \
-                image oldmin - newrange x oldrange / newmin + set-transformed \
-                transformed --output=$I_COLORGRAY_threshold $quiet
-else
-  I_COLORGRAY_kernel="$tmpdir/COLORGRAY_kernel.fits"
-  astmkprof --kernel=gaussian,$colorkernelfwhm,3 \
-            --output=$I_COLORGRAY_kernel $quiet
-
-  I_COLORGRAY_convolved="$tmpdir/COLORGRAY_kernel.fits"
-  astconvolve $I_RGB_asinh_norm --hdu=1 --kernel=$I_COLORGRAY_kernel \
-              --domain=spatial --output=$I_COLORGRAY_convolved $quiet
-
-  # Change pixel values to the wanted range
-  astarithmetic $I_COLORGRAY_convolved -h1 set-image \
-                image minvalue set-oldmin \
-                image maxvalue set-oldmax \
-                $minvalrange set-newmin \
-                $maxvalrange set-newmax \
-                oldmax oldmin - set-oldrange \
-                newmax newmin - set-newrange \
-                image oldmin - newrange x oldrange / newmin + set-transformed \
-                transformed --output=$I_COLORGRAY_threshold $quiet
-fi
+    # Convolve the GRAY background reference image
+    # --------------------------------------------
+    #
+    # Convolve the image that is going to be used for the gray parts. This is
+    # done for smoothing the image and increase the signal to noise ratio of
+    # the black-white regions.
+    if [ x$ninputs = x3 ]; then
+      I_GRAY=$I_RGB_stack
+      khdu=1
+    else
+      I_GRAY=$kclipped
+    fi
 
+    I_GRAY_convolved="$tmpdir/GRAY_convolved.fits"
+    if [ $graykernelfwhm = 0 ]; then
+      ln -sf $(realpath $I_GRAY) $I_GRAY_convolved
+    else
+      I_GRAY_kernel="$tmpdir/GRAY_kernel.fits"
+      astmkprof --kernel=gaussian,$graykernelfwhm,3 \
+                --oversample=1 --output=$I_GRAY_kernel $quiet
 
+      astconvolve $I_GRAY --hdu=$khdu --kernel=$I_GRAY_kernel \
+                  --domain=spatial --output=$I_GRAY_convolved $quiet
+    fi
 
 
 
-# Find the COLOR threshold
-# ------------------------
-#
-# The color image with the gray background is constructed by separating the
-# original image into two regimes: COLOR and GRAY. Here, the pixel value
-# used for separate these two regions is computed. It is obtained from the
-# asinh-transformed image. If the user does not provide a value then use
-# ghe computed one (guessed). If the user provide a value, then use it
-# directly. Note that the guessed value is computed in any case.
-colorval_guessed=$(aststatistics $I_COLORGRAY_threshold --median -q)
-if [ x$colorval = x"" ]; then
-  colorval=$colorval_guessed
-fi
 
 
+    # Gray background image
+    # ---------------------
+    #
+    # We use the specified gray background image after some modifications to
+    # obtain the GRAY part. For futher highlight the interesting diffuse flux,
+    # we need to invert it the brigher pixels are darker.
+    #
+    # Here is the logic of the steps we take:
+    #   1. We call the convolved image 'values'.
+    #   2. We call the mask image 'mask'.
+    #   3. Pixels equal to 1 in 'mask' are set to nan in 'values': 'masked'.
+    #   4. The min value of this image is 'oldmin'.
+    #   5. The max value of this image is 'oldmax'.
+    #   6. The new min value of the final image is 'newmin'.
+    #   7. The new max value of the final image is 'newmax'.
+    #   (Note that they are equal but inverted of the general range values).
+    #   7. The old range (oldmax - oldmin) is 'oldrange'.
+    #   8. The new range (newmax - newmin) is 'newrange'.
+    #   9. The 'masked' image is transformed to have the new range of values.
+    #   (Note that 'grayscale' will transform the pixel value in case of any
+    #   function is specified. E.g., log, sqrt, asinh, etc.)
+    grayscale=""
+    I_GRAY_colormasked="$tmpdir/GRAY_colormasked.fits"
+    astarithmetic $I_GRAY_convolved -h1 set-values \
+                  $I_COLORGRAY_mask -h1 set-mask \
+                  values mask nan where $grayscale set-masked \
+                  masked minvalue set-oldmin \
+                  masked maxvalue set-oldmax \
+                  $maxvalrange set-newmin \
+                  $minvalrange set-newmax \
+                  oldmax oldmin - set-oldrange \
+                  newmax newmin - set-newrange \
+                  masked oldmin - newrange x oldrange / newmin + 
set-transformed \
+                  transformed --output=$I_GRAY_colormasked $quiet
+
+
+
+
+
+    # Find the GRAY thresholds
+    # ------------------------
+    #
+    # Once the COLOR and GRAY parts have been separated, the gray part can be
+    # also separated into BLACK and WHITE. To separate these two parts, here a
+    # threshold is estimated as the median of the GRAY values.
+    I_GRAY_colormasked_clipped="$tmpdir/GRAY_colormasked_clipped.fits"
+    grayval_guessed=$(aststatistics $I_GRAY_colormasked --median -q)
+
+    if [ x$grayval = x"" ]; then
+      ln -sf $(realpath $I_GRAY_colormasked) $I_GRAY_colormasked_clipped
+    else
+      astarithmetic $I_GRAY_colormasked -h1 set-i \
+                    i i $grayval lt $minvalrange where \
+                    --output=$I_GRAY_colormasked_clipped
+    fi
 
 
 
-# Binary mask for COLOR (1) and GRAY (0) parts
-# --------------------------------------------
-#
-# Here the image is separated into two parts: COLOR (pixels=1) and GRAY
-# (pixels = 0). To obtain this mask, the colorval is considered as the
-# threshold on the asinhed image. So:
-#   asinhed < colorval -->  COLOR = 1
-#   asinhed > colorval -->  GRAY  = 0
-I_COLORGRAY_mask="$tmpdir/COLORGRAY_mask-1color-0gray.fits"
-astarithmetic $I_COLORGRAY_threshold set-ref \
-              ref $colorval lt -o $I_COLORGRAY_mask $quiet
-             #2 fill-holes
 
 
+    # Use color for high S/N and gray for low S/N
+    # -------------------------------------------
+    #
+    # Once the gray-mask has been obtained, use it for replace all pixels less
+    # 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/')
+      astarithmetic $f \
+                    $I_GRAY_colormasked_clipped isblank not \
+                    $I_GRAY_colormasked_clipped \
+                    where -g1 --output=$outputname $quiet;
+    done
 
 
 
-# Convolve the GRAY background reference image
-# --------------------------------------------
-#
-# Convolve the image that is going to be used for the gray parts. This is
-# done for smoothing the image and increase the signal to noise ratio of
-# the black-white regions.
-if [ x$ninputs = x3 ]; then
-  I_GRAY=$I_RGB_stack
-  khdu=1
-else
-  I_GRAY=$kclipped
-fi
 
-I_GRAY_convolved="$tmpdir/GRAY_convolved.fits"
-if [ $graykernelfwhm = 0 ]; then
-  ln -sf $(realpath $I_GRAY) $I_GRAY_convolved
-else
-  I_GRAY_kernel="$tmpdir/GRAY_kernel.fits"
-  astmkprof --kernel=gaussian,$graykernelfwhm,3 \
-            --oversample=1 --output=$I_GRAY_kernel $quiet
 
-  astconvolve $I_GRAY --hdu=$khdu --kernel=$I_GRAY_kernel \
-              --domain=spatial --output=$I_GRAY_convolved $quiet
-fi
+    # Make the color-gray image
+    # -------------------------
+    #
+    # 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 \
+                $I_B_transformed_gray -h1 \
+                --output=$output $quiet
 
 
 
 
 
-# Gray background image
-# ---------------------
-#
-# We use the specified gray background image after some modifications to
-# obtain the GRAY part. For futher highlight the interesting diffuse flux,
-# we need to invert it the brigher pixels are darker.
-#
-# Here is the logic of the steps we take:
-#   1. We call the convolved image 'values'.
-#   2. We call the mask image 'mask'.
-#   3. Pixels equal to 1 in 'mask' are set to nan in 'values': 'masked'.
-#   4. The min value of this image is 'oldmin'.
-#   5. The max value of this image is 'oldmax'.
-#   6. The new min value of the final image is 'newmin'.
-#   7. The new max value of the final image is 'newmax'.
-#   (Note that they are equal but inverted of the general range values).
-#   7. The old range (oldmax - oldmin) is 'oldrange'.
-#   8. The new range (newmax - newmin) is 'newrange'.
-#   9. The 'masked' image is transformed to have the new range of values.
-#   (Note that 'grayscale' will transform the pixel value in case of any
-#   function is specified. E.g., log, sqrt, asinh, etc.)
-grayscale=""
-I_GRAY_colormasked="$tmpdir/GRAY_colormasked.fits"
-astarithmetic $I_GRAY_convolved -h1 set-values \
-              $I_COLORGRAY_mask -h1 set-mask \
-              values mask nan where $grayscale set-masked \
-              masked minvalue set-oldmin \
-              masked maxvalue set-oldmax \
-              $maxvalrange set-newmin \
-              $minvalrange set-newmax \
-              oldmax oldmin - set-oldrange \
-              newmax newmin - set-newrange \
-              masked oldmin - newrange x oldrange / newmin + set-transformed \
-              transformed --output=$I_GRAY_colormasked $quiet
-
-
-
-
-
-# Find the GRAY thresholds
-# ------------------------
-#
-# Once the COLOR and GRAY parts have been separated, the gray part can be
-# also separated into BLACK and WHITE. To separate these two parts, here a
-# threshold is estimated as the median of the GRAY values.
-I_GRAY_colormasked_clipped="$tmpdir/GRAY_colormasked_clipped.fits"
-grayval_guessed=$(aststatistics $I_GRAY_colormasked --median -q)
-
-if [ x$grayval = x"" ]; then
-  ln -sf $(realpath $I_GRAY_colormasked) $I_GRAY_colormasked_clipped
+# If user does not want the gray background image
 else
-  astarithmetic $I_GRAY_colormasked -h1 set-i \
-                i i $grayval lt $minvalrange where \
-                --output=$I_GRAY_colormasked_clipped
-fi
-
-
-
-
-
-# Use color for high S/N and gray for low S/N
-# -------------------------------------------
-#
-# Once the gray-mask has been obtained, use it for replace all pixels less
-# 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/')
-  astarithmetic $f \
-                $I_GRAY_colormasked_clipped isblank not \
-                $I_GRAY_colormasked_clipped \
-                where -g1 --output=$outputname $quiet;
-done
-
 
+    # Make the color figure
+    # ---------------------
+    #
+    # Once all the previous treatment has been done for each image, then 
combine
+    # all with Convert program to obtain the colored image. Limit fluxes used
+    # 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 \
+                $I_B_transformed -h1 \
+                --output=$output $quiet
 
 
 
 
 
+    # Remove images
+    if [ $keeptmp = 0 ]; then
+      rm $rscaled $gscaled $bscaled \
+         $rclipped $gclipped $bclipped
+    fi
 
-# Make the color-gray image
-# -------------------------
-#
-# 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).
-output_gray=$(echo "$output" | sed -e's/.jpg/-gray.jpg/')
-astconvertt $I_R_transformed_gray -h1 \
-            $I_G_transformed_gray -h1 \
-            $I_B_transformed_gray -h1 \
-            --output=$output_gray $quiet
+fi
 
 
 
@@ -1049,34 +1048,36 @@ if [ ! x$quiet = x"--quiet" ]; then
   aststatistics $I_GRAY_colormasked
   fi
 
-
   cat <<EOF
 
-PARAMETERS:
-  Guessed: --qbright=$qbright_guessed --stretch=$stretch_guessed 
--colorval=$colorval_guessed --grayval=$grayval_guessed
-  Used   : --qbright=$qbright_value --stretch=$stretch_value 
--colorval=$colorval --grayval=$grayval
-
 TIPS:
+  # Use '--checkparams'to check the pixel value distributions.
   # First use the default options to guess the parameters.
   # Select a good sky background value of the images.
-    A minimum value of zero could be a good option: --minimum=0.0
+      A minimum value of zero could be a good option: --minimum=0.0
   # Focus on the bright regions and twek '--stretch' and '-qbright'.
-    Try low values of '--qbright' tho show the bright parts.
-    Then, adjust '--stretch' for showing the fainter regions around bright 
parts.
-    Overall, play with these two parameters to show the color regions 
appropiately.
+      Try low values of '--qbright' tho show the bright parts.
+      Then, adjust '--stretch' for showing the fainter regions around bright 
parts.
+      Overall, play with these two parameters to show the color regions 
appropriately.
+  # (next tips only for gray background image: --grayback)
   # Change '--colorval' to select the value that separates the color and gray 
regions.
-    --colorval=100 means all will be shown in color.
-    --colorval=0 means everything will become gray.
+      --colorval=100 means all will be shown in color.
+      --colorval=0 means everything will become gray.
   # Change '--grayval' to change the gray pixels to black (from 
$grayval_guessed to 100.0).
-    --grayval=100 means all gray regions will become black.
-  # Use the '-c' or '--checkparams'to see the distributions.
+      --grayval=100 means all gray regions will become black.
+
+PARAMETERS:
+  Guessed: --qbright=$qbright_guessed --stretch=$stretch_guessed 
--colorval=$colorval_guessed --grayval=$grayval_guessed
+  Used   : --qbright=$qbright_value --stretch=$stretch_value 
--colorval=$colorval --grayval=$grayval
 
+Output written to '$output'.
 EOF
 fi
 
 
 
 
+
 # Remove temporal files
 # ---------------------
 #