[gnuastro-commits] master 220386cf 6/6: PSF scripts: homogenizing the way errors and warnings are printed

[Mohammad Akhlaghi]

branch: master
commit 220386cf8e4bc489c5c075e40f416997b3cec888
Author: Raul Infante-Sainz <infantesainz@gmail.com>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    PSF scripts: homogenizing the way errors and warnings are printed
    
    Until now, the different PSF scripts have different ways of printing
    warning and error messages on the standard output (command-line). Some of
    them use the "cat<<EOF [text] EOF" and other scripts use simply "echo
    text". However, it is better to print all messages following the same
    convention.
    
    With this commit, all messages are printed following the same standard:
    "cat<<EOF [text] EOF". Moreover, a label indicating if the message is a
    warning (WARNING:) or an error (ERROR:) is also printed at the start of the
    message. Errors cause the stop of the execution, while warnings are just
    useful information. Warnings are not printed if the user uses the option
    '--quiet'.
---
 bin/script/psf-scale-factor.in | 24 ++++++++++--------
 bin/script/psf-select-stars.in | 50 ++++++++++++++++++++++--------------
 bin/script/psf-stamp.in        | 57 ++++++++++++++++++++++++++----------------
 bin/script/psf-subtract.in     | 29 +++++++++++++--------
 bin/script/psf-unite.in        | 16 +++++++-----
 5 files changed, 107 insertions(+), 69 deletions(-)

diff --git a/bin/script/psf-scale-factor.in b/bin/script/psf-scale-factor.in
index 8b627208..e6210920 100644
--- a/bin/script/psf-scale-factor.in
+++ b/bin/script/psf-scale-factor.in
@@ -338,7 +338,7 @@ done
 # If an input image is not given at all.
 if [ x"$inputs" = x ]; then
     cat <<EOF
-$scriptname: no input FITS image files. Run with '--help' for more information 
on how to run
+$scriptname: ERROR: no input FITS image files. Run with '--help' for more 
information on how to run
 EOF
     exit 1
 elif [ ! -f "$inputs" ]; then
@@ -349,7 +349,7 @@ fi
 # If a PSF image (--psf) is not given.
 if [ x"$psf" = x ]; then
     cat <<EOF
-$scriptname: no PSF image or profile provided. A PSF image (profile) has to be 
specified with '--psf' (or '-p').
+$scriptname: ERROR: no PSF image or profile provided. A PSF image (profile) 
has to be specified with '--psf' (or '-p').
 EOF
     exit 1
 fi
@@ -357,14 +357,14 @@ fi
 # If center coordinates (--center) is not given at all.
 if [ x"$center" = x ]; then
     cat <<EOF
-$scriptname: no center coordinates provided. You can specify the object's 
central coordinate with '--center' ('-c')
+$scriptname: ERROR: no center coordinates provided. You can specify the 
object's central coordinate with '--center' ('-c')
 EOF
     exit 1
 else
     ncenter=$(echo $center | awk 'BEGIN{FS=","}END{print NF}')
     if [ x$ncenter != x2 ]; then
         cat <<EOF
-$scriptname: '--center' (or '-c') only take two values, but $ncenter were 
given in '$center'
+$scriptname: ERROR: '--center' (or '-c') only take two values, but $ncenter 
were given in '$center'
 EOF
         exit 1
     fi
@@ -373,14 +373,14 @@ fi
 # If a normalization range is not given at all.
 if [ x"$normradii" = x ]; then
     cat <<EOF
-$scriptname: no rign of normalization provided. You can use '--normradii' 
('-n') to give the radial interval to define normalization
+$scriptname: ERROR: no rign of normalization provided. You can use 
'--normradii' ('-n') to give the radial interval to define normalization
 EOF
     exit 1
 else
     nnormradii=$(echo $normradii | awk 'BEGIN{FS=","}END{print NF}')
     if [ x$nnormradii != x2 ]; then
         cat <<EOF
-$scriptname: '--normradii' (or '-n') only takes two values, but $nnormradii 
were given
+$scriptname: ERROR: '--normradii' (or '-n') only takes two values, but 
$nnormradii were given
 EOF
         exit 1
     fi
@@ -389,7 +389,7 @@ fi
 # If mode (--mode) is not given at all.
 if [ x"$mode" = x ]; then
     cat <<EOF
-$scriptname: no coordinate mode provided. You can use '--mode' (or '-O'), 
acceptable values are 'img' (for pixel coordinate) or 'wcs' (for celestial 
coordinates)
+$scriptname: ERROR: no coordinate mode provided. You can use '--mode' (or 
'-O'), acceptable values are 'img' (for pixel coordinate) or 'wcs' (for 
celestial coordinates)
 EOF
     exit 1
 
@@ -400,7 +400,7 @@ elif [ "$mode" = wcs     -o     "$mode" = img ]; then
     junk=1
 else
     cat <<EOF
-$scriptname: wrong value to --mode (-O) provided. Acceptable values are 'img' 
(for pixel coordinate) or 'wcs' (for celestial coordinates)
+$scriptname: ERROR: wrong value to --mode (-O) provided. Acceptable values are 
'img' (for pixel coordinate) or 'wcs' (for celestial coordinates)
 EOF
     exit 1
 fi
@@ -550,9 +550,11 @@ if [ x"$segment" != x ]; then
     # the user is informed of the situation (and that this is a bug: 'clab'
     # should be initialized!).
     if [ "$clab" = "not-initialized"   -o   "$olab" = "not-initialized" ]; then
-        cat <<EOF
+        if [ x"$quiet" = x ]; then
+            cat <<EOF
 $scriptname: WARNING: a bug! Please contact us at 'bug-gnuastro@gnu.org' to 
fix the problem. For some reason, no clump or object label could be initialized 
for the given coordinate within the given Segment image.
 EOF
+        fi
         cropped_masked=$cropped
 
     else
@@ -561,10 +563,10 @@ EOF
         cropobj=$tmpdir/cropped-objects-$objectid.fits
         astcrop $segment --hdu=OBJECTS --mode=img \
                 --center=$xcenter,$ycenter \
-                --width=$xstampwidth,$ystampwidth --output=$cropobj $quiet
+                --width=$stampwidth --output=$cropobj $quiet
         astcrop $segment --hdu=CLUMPS --mode=img \
                 --center=$xcenter,$ycenter \
-                --width=$xstampwidth,$ystampwidth --output=$cropclp $quiet
+                --width=$stampwidth --output=$cropclp $quiet
 
         # Mask all the undesired regions.
         cropped_masked=$tmpdir/cropped-masked-$objectid.fits
diff --git a/bin/script/psf-select-stars.in b/bin/script/psf-select-stars.in
index 186d1f1f..b7cc1e15 100644
--- a/bin/script/psf-select-stars.in
+++ b/bin/script/psf-select-stars.in
@@ -366,14 +366,17 @@ done
 
 # Basic sanity checks
 # ===================
-#
-# If the input image has not been given at all.
+
+# If an input image is not given at all.
 if [ x"$inputs" = x ]; then
-    echo " $scriptname: no input image file specified."
-    echo "Run with '--help' for more information on how to run."
+    cat <<EOF
+$scriptname: ERROR: no input FITS image files (outer part of the PSF to unite 
with an inner part). Run with '--help' for more information on how to run
+EOF
     exit 1
-elif [ ! -f "$inputs" ]; then
-    echo "$scriptname: $inputs: No such file or directory."
+elif [ ! -f $inputs ]; then
+    cat <<EOF
+$scriptname: ERROR: $inputs, no such file or directory
+EOF
     exit 1
 fi
 
@@ -384,25 +387,29 @@ if [ x"$segmented" != x ]; then
                | wc -l)
     if [ $nhdu != 2 ]; then
         cat <<EOF
-$scriptname: the file given to '--segmented' does not have 'CLUMPS' and
-'OBJECTS' HDUs. Please give an output from 'astsegment'
+$scriptname: ERROR: the file given to '--segmented' does not have 'CLUMPS' and 
'OBJECTS' HDUs. Please give an output from 'astsegment'
 EOF
         exit 1
     fi
 elif [ ! -f $segmented ]; then
-    echo "$scriptname: $segmented: No such file or directory."
+    cat <<EOF
+$scriptname: ERROR: $segmented, no such file or directory"
+EOF
     exit 1
 fi
 
 # If the brighter and fainter range of magnitude are not given at all.
 if [ x$magnituderange = x ]; then
-    echo "$scriptname: no magnitude range provided."
-    echo "$scriptname: Values to '--magnituderange' (or '-m') should be 
provided."
+    cat<<EOF
+$scriptname: ERROR:no magnitude range provided. Values to '--magnituderange' 
(or '-m') should be provided"
+EOF
     exit 1
 else
     nmagrange=$(echo $magnituderange | awk 'BEGIN{FS=","}END{print NF}')
     if [ x$nmagrange != x2 ]; then
-        echo "$scriptname: '--magnituderange' (or '-m') only take two values, 
but $nmagrange were given."
+        cat<<EOF
+$scriptname: ERROR: '--magnituderange' (or '-m') only take two values, but 
$nmagrange were given
+EOF
         exit 1
     fi
 fi
@@ -413,7 +420,9 @@ if [ x$parallaxanderrorcolumn = x ]; then
 else
     nmparallax=$(echo $parallaxanderrorcolumn | awk 'BEGIN{FS=","}END{print 
NF}')
     if [ x$nmparallax != x2 ]; then
-        echo "$scriptname: '--parallaxanderrorcolumn' (or '-p') only take two 
values, but $nmparallax were given."
+        cat<<EOF
+$scriptname: ERROR: '--parallaxanderrorcolumn' (or '-p') only take two values, 
but $nmparallax were given
+EOF
         exit 1
     else
         columnquery=$racolumn,$deccolumn,$field,$parallaxanderrorcolumn
@@ -422,22 +431,25 @@ fi
 
 # If the minimum axis ratio is not given at all.
 if [ x$minaxisratio = x ]; then
-    echo "$scriptname: no minimum axis ratio provided."
-    echo "$scriptname: Value to '--minaxisratio' (or '-Q') should be provided."
+    cat<<EOF
+$scriptname: ERROR: no minimum axis ratio provided. Value to '--minaxisratio' 
(or '-Q') should be provided
+EOF
     exit 1
 fi
 
 # If the minimum distance between contaminants is not given at all.
 if [ x$mindistdeg = x ]; then
-    echo "$scriptname: no minimum distance (for rejecting neighbors) provided. 
"
-    echo "$scriptname: value to '--mindistdeg' (or '-M') should be provided."
+    cat<<EOF
+$scriptname: ERROR: no minimum distance (for rejecting neighbors) provided. 
Value to '--mindistdeg' (or '-M') should be provided
+EOF
     exit 1
 fi
 
 # If the match aperture radius is not given at all.
 if [ x$matchaperturedeg = x ]; then
-    echo "$scriptname: no aperture matching radius provided."
-    echo "$scripname: value to '--matchaperturedeg' (or '-a') should be 
provided."
+    cat<<EOF
+$scriptname: ERROR: no aperture matching radius provided. Value to 
'--matchaperturedeg' (or '-a') should be provided
+EOF
     exit 1
 fi
 
diff --git a/bin/script/psf-stamp.in b/bin/script/psf-stamp.in
index a2bc47d6..0fe86ecb 100644
--- a/bin/script/psf-stamp.in
+++ b/bin/script/psf-stamp.in
@@ -351,11 +351,13 @@ done
 # If an input image is not given at all.
 if [ x"$inputs" = x ]; then
     cat <<EOF
-$scriptname: no input FITS image files. Run with '--help' for more information 
on how to run
+$scriptname: ERROR: no input FITS image files (outer part of the PSF to unite 
with an inner part). Run with '--help' for more information on how to run
 EOF
     exit 1
-elif [ ! -f "$inputs" ]; then
-    echo "$scriptname: $inputs: No such file or directory"
+elif [ ! -f $inputs ]; then
+    cat <<EOF
+$scriptname: ERROR: $inputs, no such file or directory
+EOF
     exit 1
 fi
 
@@ -373,14 +375,16 @@ if [ x"$center" = x ]; then
 
     # The center has been computed in pixels, assume pixel coordinates mode
     mode=img
+    if [ x"$quiet" = x ]; then
     cat <<EOF
-$scriptname: warning: no center provided ('--center' or '-c'). Considering 
that the center of the image is $xcoord,$ycoord
+$scriptname: WARNING: no center provided ('--center' or '-c'). Considering 
that the center of the image is $xcoord,$ycoord
 EOF
+    fi
 else
     ncenter=$(echo $center | awk 'BEGIN{FS=","}END{print NF}')
     if [ x$ncenter != x2 ]; then
         cat <<EOF
-$scriptname: '--center' (or '-c') only take two values, but $ncenter were 
given in '$center'
+$scriptname: ERROR: '--center' (or '-c') only take two values, but $ncenter 
were given in '$center'
 EOF
         exit 1
     fi
@@ -398,34 +402,39 @@ if [ x"$stampwidth" = x ]; then
 
     if [ x"$xsizetype" = xeven ]; then
         xstampwidth=$(echo $xsize | awk '{print $1+1}')
-        cat <<EOF
-$scriptname: warning: the image along the first dimension (NAXIS1) has an even 
number of pixels ($xsize). This may cause some problems with the centering of 
the stamp. Please, check and consider providing an image with an odd number of 
pixels
+        if [ x"$quiet" = x ]; then
+            cat <<EOF
+$scriptname: WARNING: the image along the first dimension (NAXIS1) has an even 
number of pixels ($xsize). This may cause some problems with the centering of 
the stamp. Please, check and consider providing an image with an odd number of 
pixels
 EOF
+        fi
     elif [ x"$xsizetype" = xodd ]; then
         xstampwidth=$xsize
     else
         cat <<EOF
-$scriptname: warning: the size of the image along the first dimension (NAXIS1) 
can not be obtained
+$scriptname: ERROR: the size of the image along the first dimension (NAXIS1) 
can not be obtained
 EOF
         exit 1
     fi
     if [ x"$ysizetype" = xeven ]; then
         ystampwidth=$(echo $ysize | awk '{print $1+1}')
-        cat <<EOF
-$scriptname: warning: the image along the second dimension (NAXIS2) has an 
even number of pixels ($ysize). This may cause some problems with the centering 
of the stamp. Please, check and consider providing an image with an odd number 
of pixels
+        if [ x"$quiet" = x ]; then
+            cat <<EOF
+$scriptname: WARNING: the image along the second dimension (NAXIS2) has an 
even number of pixels ($ysize). This may cause some problems with the centering 
of the stamp. Please, check and consider providing an image with an odd number 
of pixels
 EOF
+        fi
     elif [ x"$ysizetype" = xodd ]; then
         ystampwidth=$ysize
     else
         cat <<EOF
-$scriptname: warning: the size of the image along the second dimension 
(NAXIS2) can not be obtained
+$scriptname: ERROR: the size of the image along the second dimension (NAXIS2) 
can not be obtained
 EOF
         exit 1
     fi
-    cat <<EOF
-$scriptname: warning: no stamp width provided (--stampwidth or -W). 
Considering that the stamp width is $xstampwidth x $ystampwidth.
+    if [ x"$quiet" = x ]; then
+        cat <<EOF
+$scriptname: WARNING: no stamp width provided ('--stampwidth' or '-W'). 
Considering that the stamp width is $xstampwidth x $ystampwidth
 EOF
-
+    fi
 else
     nstampwidth=$(echo $stampwidth | awk 'BEGIN{FS=","}END{print NF}')
     if [ x$nstampwidth != x2 ]; then
@@ -441,14 +450,16 @@ fi
 
 # If a normalization range is not given at all.
 if [ x"$normradii" = x ]; then
-    cat <<EOF
-$scriptname: warning: no ring of normalization provided (--normradii). The 
stamp won't be normalized
+    if [ x"$quiet" = x ]; then
+        cat <<EOF
+$scriptname: WARNING: no ring of normalization provided ('--normradii' or 
'-n'). The stamp won't be normalized
 EOF
+    fi
 else
     nnormradii=$(echo $normradii | awk 'BEGIN{FS=","}END{print NF}')
     if [ x$nnormradii != x2 ]; then
         cat <<EOF
-$scriptname: '--normradii' (or '-n') only take two values, but $nnormradii 
were given in '$normradii'
+$scriptname: ERROR: '--normradii' (or '-n') only take two values, but 
$nnormradii were given in '$normradii'
 EOF
         exit 1
     fi
@@ -464,7 +475,7 @@ if [ "$mode" = wcs     -o      $mode = "img" ]; then
     junk=1
 else
     cat <<EOF
-$scriptname: value to '--mode' (or '-O') is not recognized ('$mode'). This 
option takes one of the following two values: 'img' (for pixel coordinates) or 
'wcs' (for celestial coordinates)
+$scriptname: ERROR: value to '--mode' (or '-O') is not recognized ('$mode'). 
This option takes one of the following two values: 'img' (for pixel 
coordinates) or 'wcs' (for celestial coordinates)
 EOF
     exit 1
 fi
@@ -473,8 +484,8 @@ fi
 
 
 
-# Define a temporal directory and thefinal output file
-# ----------------------------------------------------
+# Define a temporal directory and the final output file
+# -----------------------------------------------------
 #
 # Construct the temporary directory. If the user does not specify any
 # directory, then a default one with the base name of the input image will
@@ -614,7 +625,7 @@ EOF
 
         # Mask all the undesired regions.
         cropped_masked=$tmpdir/cropped-masked-$objectid.fits
-        astarithmetic $cropped --hdu=1 set-i --output=$cropped_masked \
+        astarithmetic $cropped --hdu=1 set-i --output=$cropped_masked $quiet \
                       $cropobj --hdu=1 set-o \
                       $cropclp --hdu=1 set-c \
                       \
@@ -714,9 +725,11 @@ astfits $output --write=NORMVAL,$normvalue,"Normalization 
value" \
 # script) because we dont want it to be mixed with the outputs of the
 # previus commands.
 if [ $normvalue = nan ]; then
-    cat <<EOF
+    if [ x"$quiet" = x ]; then
+        cat <<EOF
 $scriptname: WARNING: all the pixels in the requested normalization radius are 
NaN. Therefore the output stamp will be fully NaN. When you use this stamp with 
any stack operator of 'astsrithmetic' (for making the PSF) this image will 
effectively be ignored
 EOF
+    fi
 fi
 
 
diff --git a/bin/script/psf-subtract.in b/bin/script/psf-subtract.in
index 01b23373..ab030adc 100644
--- a/bin/script/psf-subtract.in
+++ b/bin/script/psf-subtract.in
@@ -324,29 +324,33 @@ done
 # If an input image is not given at all.
 if [ x"$inputs" = x ]; then
     cat <<EOF
-$scriptname: no input FITS image files. Run with '--help' for more information 
on how to run
+$scriptname: ERROR: no input FITS image files. Run with '--help' for more 
information on how to run
 EOF
     exit 1
 elif [ ! -f $inputs ]; then
-    echo "$scriptname: $inputs: No such file or directory."
+    cat <<EOF
+$scriptname: ERROR: $inputs, no such file or directory
+EOF
     exit 1
 fi
 
 # If a PSF image (--psf) is not given at all.
 if [ x"$psf" = x ]; then
     cat <<EOF
-$scriptname: no PSF image provided. The PSF image should be provided with 
'--psf' ('-p').
+$scriptname: ERROR: no PSF image provided. The PSF image should be provided 
with '--psf' (or '-p')
 EOF
     exit 1
 elif [ ! -f $psf ]; then
-    echo "$scriptname: $psf: No such file or directory."
+    cat <<EOF
+$scriptname: ERROR: $psf, no such file or directory
+EOF
     exit 1
 fi
 
 # If a scale factor (--scale) is not given at all.
 if [ x"$scale" = x ]; then
     cat <<EOF
-$scriptname: no scale factor provided. It can be given with '--scale' (or 
'-s'). You can derive this value with the 'astscript-psf-model-scale-factor'
+$scriptname: ERROR: no scale factor provided. It has to be given with 
'--scale' (or '-s'). You can derive this value with the 
'astscript-psf-model-scale-factor'
 EOF
     exit 1
 fi
@@ -354,28 +358,31 @@ fi
 # If center coordinates (--center) is not given at all.
 if [ x"$center" = x ]; then
     cat <<EOF
-$scriptname: no center coordinates provided (for the star that should be 
subtracted). You can use '--center' ('-c').
+$scriptname: ERROR: no center coordinates provided (for the star that should 
be subtracted). You can use '--center' ('-c')
 EOF
     exit 1
 else
     ncenter=$(echo $center | awk 'BEGIN{FS=","}END{print NF}')
     if [ x$ncenter != x2 ]; then
-        echo "$scriptname: '--center' (or '-c') only takes two values, but 
$ncenter were given."
+        cat <<EOF
+$scriptname: ERROR: $scriptname: '--center' (or '-c') only takes two values, 
but $ncenter were given
+EOF
         exit 1
     fi
 fi
-
 # If mode (--mode) is not given at all.
-modeerrorinfo="Depending on the nature of the star's coordinates, please give 
either 'img' (for pixel coordinates) or 'wcs' (for RA,Dec) to the '--mode' (or 
'-O') option."
+modeerrorinfo="Depending on the nature of the star's coordinates, please give 
either 'img' (for pixel coordinates) or 'wcs' (for RA,Dec) to the '--mode' (or 
'-O') option"
 if [ x"$mode" = x ]; then
-    echo "$scriptname: no coordinate mode provided! $modeerrorinfo"
+    cat <<EOF
+$scriptname: ERROR: no coordinate mode provided. $modeerrorinfo
+EOF
     exit 1
 # Make sure the value to '--mode' is either 'wcs' or 'img'.
 elif [ "$mode" = wcs    -o    "$mode" = img ]; then
     junk=1
 else
     cat <<EOF
-$scriptname: '$mode' not acceptable for '--mode' (or '-O'). $modeerrorinfo
+$scriptname: ERROR: '$mode' not acceptable for '--mode' (or '-O'). 
$modeerrorinfo
 EOF
     exit 1
 fi
diff --git a/bin/script/psf-unite.in b/bin/script/psf-unite.in
index 42921097..279066d4 100644
--- a/bin/script/psf-unite.in
+++ b/bin/script/psf-unite.in
@@ -327,29 +327,33 @@ done
 # If an input image is not given at all.
 if [ x"$inputs" = x ]; then
     cat <<EOF
-$scriptname: no input FITS image files (outer part of the PSF to unite with an 
inner part). Run with '--help' for more information on how to run
+$scriptname: ERROR: no input FITS image files (outer part of the PSF to unite 
with an inner part). Run with '--help' for more information on how to run
 EOF
     exit 1
 elif [ ! -f $inputs ]; then
-    echo "$scriptname: $inputs: No such file or directory."
+    cat <<EOF
+$scriptname: ERROR: $inputs, no such file or directory
+EOF
     exit 1
 fi
 
 # If an inner image (--inner) is not given at all.
 if [ x"$inner" = x ]; then
     cat <<EOF
-$scriptname: no inner FITS image provided. The inner part of the PSF (to unite 
with the outer part, which is the main argument) can be specified with the 
'--inner' (or '-i') option as a FITS image
+$scriptname: ERROR: no inner FITS image provided. The inner part of the PSF 
(to unite with the outer part, which is the main argument) can be specified 
with the '--inner' (or '-i') option as a FITS image
 EOF
     exit 1
 elif [ ! -f "$inner" ]; then
-    echo "$scriptname: $inner: No such file or directory."
+    cat <<EOF
+$scriptname: ERROR: $inner, no such file or directory
+EOF
     exit 1
 fi
 
 # If a radius (--radius) is not given at all.
 if [ x"$radius" = x ]; then
     cat <<EOF
-$scriptname: no radius (in pixels) provided. All pixels below this radius will 
be filled with the inner PSf image. You can use '--radius' (or '-r') to specify 
it
+$scriptname: ERROR: no radius (in pixels) provided. All pixels below this 
radius will be filled with the inner PSf image. You can use '--radius' (or 
'-r') to specify it
 EOF
     exit 1
 fi
@@ -357,7 +361,7 @@ fi
 # If a scale (--scale) is not given at all.
 if [ x"$scale" = x ]; then
     cat <<EOF
-$scriptname: no scale factor provided ('--scale' or '-s'). This is necessary 
to scale the inner region to the outer and is usually determined with the 
'astscript-psf-model-scale-factor'. See the Gnuastro tutorial on "Building the 
extended PSF" for more
+$scriptname: ERROR: no scale factor provided ('--scale' or '-s'). This is 
necessary to scale the inner region to the outer and is usually determined with 
the 'astscript-psf-model-scale-factor'. See the Gnuastro tutorial on "Building 
the extended PSF" for more
 EOF
     exit 1
 fi