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[gnuastro-commits] master 45cd88cf 2/2: astscript-color-faint-gray: not
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From: |
Mohammad Akhlaghi |
|
Subject: |
[gnuastro-commits] master 45cd88cf 2/2: astscript-color-faint-gray: not using realpath for portability |
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Date: |
Sat, 3 Feb 2024 10:24:13 -0500 (EST) |
branch: master
commit 45cd88cf59be6639e8be5dc8139f2663190ce81a
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>
astscript-color-faint-gray: not using realpath for portability
Until now, this script used 'realpath' internally to avoid copying extra
files. However, 'realpath' is only reliably available on GNU-based
operating systems. For example it crashed after a check of Conda builds on
macOS. Also, the script used many variables with capital letters which is
contrary to Gnuastro's convention.
With this commit, both issues have been addressed: all 'realpaths' have
been removed and variables only have small-case names.
---
bin/script/color-faint-gray.sh | 222 +++++++++++++++++++++--------------------
1 file changed, 114 insertions(+), 108 deletions(-)
diff --git a/bin/script/color-faint-gray.sh b/bin/script/color-faint-gray.sh
index 2620f94b..209653e2 100644
--- a/bin/script/color-faint-gray.sh
+++ b/bin/script/color-faint-gray.sh
@@ -139,9 +139,8 @@ $scriptname options:
Contrast, bias, and marks
-b, --bias Constant (bias) to add to all the pixels (linear).
-c, --contrast Change the contrast of the final image (linear).
- -G, --gamma Gamma parameter (nonlinear, overrides bias/contrast).
- --markoptions=STR Options to mark/label the output (passed to
ConvertType).
-
+ -G, --gamma Gamma (nonlinear, overrides bias/contrast).
+ --markoptions=STR Options to add marks (passed to ConvertType).
Color and gray parameters
--coloronly No grayscale regions, background in color (black).
@@ -184,7 +183,7 @@ License GPLv3+: GNU General public license version 3 or
later.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
-Written/developed by Raul Infante-Sainz
+Written/developed by Raul Infante-Sainz and Mohammad Akhlaghi.
EOF
}
@@ -571,7 +570,7 @@ bclipped="$tmpdir/B_clipped.fits"
kclipped="$tmpdir/K_clipped.fits"
if [ x"$rmin" = x ]; then
- ln -sf $(realpath $rimage) $rclipped
+ cp $rimage $rclipped
else
astarithmetic $rimage --hdu=$rhdu set-i $quiet \
i i $rmin lt 0 where --output=$rclipped
@@ -579,7 +578,7 @@ else
fi
if [ x"$gmin" = x ]; then
- ln -sf $(realpath $gimage) $gclipped
+ cp $gimage $gclipped
else
astarithmetic $gimage --hdu=$ghdu set-i $quiet \
i i $gmin lt 0 where --output=$gclipped
@@ -587,7 +586,7 @@ else
fi
if [ x"$bmin" = x ]; then
- ln -sf $(realpath $bimage) $bclipped
+ cp $bimage $bclipped
else
astarithmetic $bimage --hdu=$bhdu set-i $quiet \
i i $bmin lt 0 where --output=$bclipped
@@ -596,7 +595,7 @@ fi
# kclipped is constructed only if a fourth image has been given.
if [ x"$kmin" = x ] && [ x$kimage != x ]; then
- ln -sf $(realpath $kimage) $kclipped
+ cp $kimage $kclipped
elif [ x$kimage != x ]; then
astarithmetic $kimage --hdu=$khdu set-i $quiet \
i i $kmin lt 0 where --output=$kclipped
@@ -640,9 +639,9 @@ if [ x$rweight = x"1.0000" ] &&
[ x$gweight = x"1.0000" ] &&
[ x$bweight = x"1.0000" ] &&
[ x"$rzero" = x ]; then
- ln -sf $(realpath $rclipped) $rscaled
- ln -sf $(realpath $gclipped) $gscaled
- ln -sf $(realpath $bclipped) $bscaled
+ ln -sf $rclipped $rscaled
+ ln -sf $gclipped $gscaled
+ ln -sf $bclipped $bscaled
# If diferent weights but same zeropoints, then scale the images.
elif [ x$rweight != x"1.0000" ] ||
@@ -676,17 +675,17 @@ fi
-# Stacked image: I_RGB = (R+G+B)/3
+# Stacked image: i_rgb = (R+G+B)/3
# --------------------------------
#
# 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 \
- --output=$I_RGB_stack $quiet
+ --output=$i_rgb_stack $quiet
@@ -697,33 +696,32 @@ astarithmetic $rscaled --hdu=$rhdu \
#
# Once the necessary parameters have been obtained, here the asinh
# 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"
-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"
-astarithmetic $I_RGB_stack -h1 set-stack \
- $I_RGB_asinh -h1 set-asinh \
- asinh stack / --output=$I_RGB_asinh_norm $quiet
+# transformation is done, it is normalized by 'i_rgb'. Finally, the range
+# of pixel values is linear transformed to [minvalrange - maxvalrange].
+i_rgb_asinh="$tmpdir/rgb_mean-asinh.fits"
+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"
+astarithmetic $i_rgb_stack -h1 set-stack \
+ $i_rgb_asinh -h1 set-asinh \
+ asinh stack / --output=$i_rgb_asinh_norm $quiet
-# Compute the R, G, B images
+# Compute the r, g, b images
# --------------------------
#
# Each input image is multiplied by the transformed and normalized averaged
-# image (I_RGB_asinh_norm).
-I_R="$tmpdir/R.fits"
-I_G="$tmpdir/G.fits"
-I_B="$tmpdir/B.fits"
-astarithmetic $rscaled --hdu=$rhdu $I_RGB_asinh_norm x $quiet --output=$I_R
-astarithmetic $gscaled --hdu=$ghdu $I_RGB_asinh_norm x $quiet --output=$I_G
-astarithmetic $bscaled --hdu=$bhdu $I_RGB_asinh_norm x $quiet --output=$I_B
+# image (i_rgb_asinh_norm).
+i_r="$tmpdir/r.fits"
+i_g="$tmpdir/g.fits"
+i_b="$tmpdir/b.fits"
+astarithmetic $rscaled --hdu=$rhdu $i_rgb_asinh_norm x $quiet --output=$i_r
+astarithmetic $gscaled --hdu=$ghdu $i_rgb_asinh_norm x $quiet --output=$i_g
+astarithmetic $bscaled --hdu=$bhdu $i_rgb_asinh_norm x $quiet --output=$i_b
@@ -734,17 +732,17 @@ astarithmetic $bscaled --hdu=$bhdu $I_RGB_asinh_norm x
$quiet --output=$I_B
#
# Compute the maximum of the R, G, B images and divide each image by that
# value. This step is done in order to represent the true color.
-I_R_norm="$tmpdir/R_norm.fits"
-I_G_norm="$tmpdir/G_norm.fits"
-I_B_norm="$tmpdir/B_norm.fits"
-maxR=$(aststatistics $I_R --maximum -q)
-maxG=$(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 / $maxvalrange x float32 --output=$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 $quiet
+i_r_norm="$tmpdir/r_norm.fits"
+i_g_norm="$tmpdir/g_norm.fits"
+i_b_norm="$tmpdir/b_norm.fits"
+maxr=$(aststatistics $i_r --maximum -q)
+maxg=$(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 / $maxvalrange x float32 -o$i_r_norm $quiet
+astarithmetic $i_g $maxrgb / $maxvalrange x float32 -o$i_g_norm $quiet
+astarithmetic $i_b $maxrgb / $maxvalrange x float32 -o$i_b_norm $quiet
@@ -767,30 +765,35 @@ astarithmetic $I_B $maxRGB / $maxvalrange x float32
--output=$I_B_norm $quiet
# After this transformation is done, all values are clipped by the
# maxvalrange value. So, all pixels above maxrangevalue become equal to
# maxrangevalue.
-
-I_R_enhanced="$tmpdir/R_enhanced.fits"
-I_G_enhanced="$tmpdir/G_enhanced.fits"
-I_B_enhanced="$tmpdir/B_enhanced.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_enhanced
$quiet
- astarithmetic $I_G_norm $maxvalrange / $gamma pow $maxvalrange x set-t \
- 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_enhanced
$quiet
+ astarithmetic $i_r_norm $maxvalrange / $gamma pow $maxvalrange x set-t \
+ 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_enhanced $quiet
+ astarithmetic $i_b_norm $maxvalrange / $gamma pow $maxvalrange x set-t \
+ 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_enhanced
$quiet
- astarithmetic $I_G_norm $contrast x $bias + set-t \
- 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_enhanced
$quiet
+ astarithmetic $i_r_norm $contrast x $bias + set-t \
+ 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_enhanced $quiet
+ astarithmetic $i_b_norm $contrast x $bias + set-t \
+ t t $maxvalrange gt $maxvalrange where \
+ --output=$i_b_enhanced $quiet
else
- 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
+ cp $i_r_norm $i_r_enhanced # Not using 'ln -s' because there will
+ cp $i_g_norm $i_g_enhanced # be too many links and 'realpath' is
+ cp $i_b_norm $i_b_enhanced # not portable on non-GNU OSs.
fi
@@ -808,9 +811,9 @@ if [ x$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_enhanced -h1 \
- $I_G_enhanced -h1 \
- $I_B_enhanced -h1 \
+ astconvertt $i_r_enhanced -h1 \
+ $i_g_enhanced -h1 \
+ $i_b_enhanced -h1 \
$markoptions \
--output=$output $quiet
@@ -868,28 +871,28 @@ else
# asinh-transformed image for the background. Otherwise, if four images
# are provided, we use the fourth image with no modifications for the
# background.
- I_COLORGRAY_threshold="$tmpdir/COLORGRAY_threshold.fits"
+ i_colorgray_threshold="$tmpdir/colorgray_threshold.fits"
if [ x$ninputs = x3 ]; then
- I_BACK=$I_RGB_asinh
+ i_back=$i_rgb_asinh
khdu=1
# Convolve the background image
# -----------------------------
#
# If the user wants to convolve the background image.
- I_BACK_convolved="$tmpdir/BACK_convolved.fits"
+ i_back_convolved="$tmpdir/back_convolved.fits"
if [ $graykernelfwhm = 0 ]; then
- ln -sf $(realpath $I_BACK) $I_BACK_convolved
+ cp $i_back $i_back_convolved
else
- I_BACK_kernel="$tmpdir/BACK_kernel.fits"
+ i_back_kernel="$tmpdir/back_kernel.fits"
astmkprof --kernel=gaussian,$graykernelfwhm,3 \
- --oversample=1 --output=$I_GRAY_kernel $quiet
- astconvolve $I_BACK --hdu=$khdu --kernel=$I_BACK_kernel \
- --domain=spatial --output=$I_BACK_convolved $quiet
+ --oversample=1 --output=$i_gray_kernel $quiet
+ astconvolve $i_back --hdu=$khdu --kernel=$i_back_kernel \
+ --domain=spatial --output=$i_back_convolved $quiet
fi
# Change pixel values to the wanted range
- astarithmetic $I_BACK_convolved -h1 set-image \
+ astarithmetic $i_back_convolved -h1 set-image \
image minvalue set-oldmin \
image maxvalue set-oldmax \
$minvalrange set-newmin \
@@ -897,11 +900,11 @@ else
oldmax oldmin - set-oldrange \
newmax newmin - set-newrange \
image oldmin - newrange x oldrange / newmin + \
- float32 --output=$I_COLORGRAY_threshold $quiet
+ float32 --output=$i_colorgray_threshold $quiet
else
- I_BACK_convolved=$kclipped
- ln -sf $(realpath $kclipped) $I_COLORGRAY_threshold
+ i_back_convolved=$kclipped
+ ln -sf $kclipped $i_colorgray_threshold
fi
@@ -917,12 +920,14 @@ else
# asinh-transformed image. If the user does not provide a value then use
# ghe computed one (guessed). If the user provide a value, then use it
# directly. Note that the guessed value is computed in any case.
- colorval_estimated=$(aststatistics $I_COLORGRAY_threshold --median --quiet)
+ colorval_estimated=$(aststatistics $i_colorgray_threshold \
+ --median --quiet)
if [ x$colorval = x"" ]; then
colorval=$colorval_estimated
fi
- grayval_estimated=$(aststatistics $I_COLORGRAY_threshold --median --quiet)
+ grayval_estimated=$(aststatistics $i_colorgray_threshold \
+ --median --quiet)
if [ x$grayval = x"" ]; then
grayval=$grayval_estimated
fi
@@ -942,17 +947,17 @@ else
# This image is computed by default from the colorval and grayval
# parameters. Alternatively, it can be provided by the user.
if [ x$regions = x ]; then
- TOTAL_MASK="$tmpdir/TOTAL_mask-2color-1black-0gray.fits"
- astarithmetic $I_COLORGRAY_threshold set-i \
+ total_mask="$tmpdir/total_mask-2color-1black-0gray.fits"
+ astarithmetic $i_colorgray_threshold set-i \
i $colorval gt 2 uint8 x set-c \
i $colorval lt i $grayval gt and 1 uint8 x set-b \
i $colorval lt 0 uint8 x set-g \
- c b g 3 sum uint8 --output $TOTAL_MASK
+ c b g 3 sum uint8 --output $total_mask
rhdu=1
else
grayval="$regions"
colorval="$regions"
- TOTAL_MASK=$regions
+ total_mask=$regions
fi
@@ -982,9 +987,10 @@ else
# (Note that 'grayscale' will transform the pixel value in case of any
# function is specified. E.g., log, sqrt, asinh, etc.)
grayscale=""
- I_GRAY_colormasked="$tmpdir/GRAY_colormasked.fits"
- astarithmetic $I_BACK_convolved -h1 set-values \
- $TOTAL_MASK -h$rhdu 2 uint8 eq set-mask \
+ i_gray_colormasked="$tmpdir/gray_colormasked.fits"
+ echo here1
+ astarithmetic $i_back_convolved -h1 set-values \
+ $total_mask -h$rhdu 2 uint8 eq set-mask \
values mask nan where $grayscale set-masked \
masked minvalue set-oldmin \
masked maxvalue set-oldmax \
@@ -994,7 +1000,7 @@ else
newmax newmin - set-newrange \
masked oldmin - newrange x oldrange / newmin + \
set-transformed \
- transformed float32 --output=$I_GRAY_colormasked $quiet
+ transformed float32 --output=$i_gray_colormasked $quiet
@@ -1005,11 +1011,11 @@ else
#
# Put black pixels (pixels=1 in TOTAL_MASK) equal to zero. By doing
# this, those pixels will be set to pure black color.
- I_GRAY_colormasked_zeroblack="$tmpdir/GRAY_colormasked_zeroblack.fits"
- astarithmetic $I_GRAY_colormasked -h1 set-i \
- $TOTAL_MASK -h$rhdu 1 uint8 eq -h1 set-b \
+ i_gray_colormasked_zeroblack="$tmpdir/gray_colormasked_zeroblack.fits"
+ astarithmetic $i_gray_colormasked -h1 set-i \
+ $total_mask -h$rhdu 1 uint8 eq -h1 set-b \
i b 0.0 where float32 \
- --output=$I_GRAY_colormasked_zeroblack
+ --output=$i_gray_colormasked_zeroblack
@@ -1022,14 +1028,14 @@ 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_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 $I_B_enhanced; do
+ i_r_black_gray="$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_zeroblack isblank not \
- $I_GRAY_colormasked_zeroblack \
+ $i_gray_colormasked_zeroblack isblank not \
+ $i_gray_colormasked_zeroblack \
where -g1 --output=$outputname $quiet;
done
@@ -1043,9 +1049,9 @@ 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_black_gray -h1 \
- $I_G_black_gray -h1 \
- $I_B_black_gray -h1 \
+ astconvertt $i_r_black_gray -h1 \
+ $i_g_black_gray -h1 \
+ $i_b_black_gray -h1 \
$markoptions \
--output=$output $quiet
fi
@@ -1070,14 +1076,14 @@ if [ ! x$quiet = x"--quiet" ]; then
# that are going to be used. This will helps to guess appropiate parameters
if [ x$checkparams = x1 ]; then
echo " "
- echo "FOR ASINH-TRANSFORMATION ('--strech' and '--qbright' parameters)."
- aststatistics $I_RGB_stack
+ echo "For asinh-transformation ('--strech' and '--qbright' parameters)."
+ aststatistics $i_rgb_stack
echo " "
- echo "FOR COLOR and GRAY THRESHOLDS"
- echo "Separation between color and black regions (--colorval)"
- echo "Separation between black and gray regions (--grayval)"
- aststatistics $I_COLORGRAY_threshold
+ echo "For color and gray thresholds."
+ echo "separation between color and black regions (--colorval)"
+ echo "separation between black and gray regions (--grayval)"
+ aststatistics $i_colorgray_threshold
fi
@@ -1097,7 +1103,7 @@ TIPS:
This is highest value of the threshold image that is shown in gray.
# Use '--checkparams' to check the pixel value distributions.
# Use '--keeptmp' to not remove the threshold image and check it:
- '$I_COLORGRAY_threshold'
+ '$i_colorgray_threshold'
EOF
echo
printf "%-17s %-15s %-15s\n" Option Default Used