[gnuastro-commits] master f1cfd384 25/69: PSF select stars: remove --input add --output and --catalog

[Mohammad Akhlaghi]

branch: master
commit f1cfd3842161ca83ffa490eb93b32b17c05e606a
Author: Sepideh Eskandarlou <sepideh.eskandarlou@gmail.com>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    PSF select stars: remove --input add --output and --catalog
    
    Until now, some parameters such as (the old) '--matchaperture' and
    '--minaxisrario' mistakenly had been written. Furthermore for inserting
    image we had a '--input' option, while in Gnuastro we do not have any
    option like that. We did not use '--output' for defining output of script,
    also '--extscript' option was extra.
    
    Also, this script is just used when the user has an image. Based on that
    image and by using 'astquery', this script downloads the corresponding
    catalog of stars from the Gaia data base. Then based on this catalog
    circular stars with good parallax and less than 9 neighbors were
    selected. If the user has already prepared the catalog and does not want to
    download it again, or the catalog of stars is not in Gaia, for instance in
    simulated images, this pipeline could not be used.
    
    With this commit, the parameters that have been written mistakenly are
    corrected. For instance, instead of '--matchaperture' we now have
    '--matchaperturedeg' and instead of '--minaxisrario' we now have
    '--minaxisratio'. The '--input' option also has been removed and we now
    have a new '--output' option for the result of the script, also
    '--extscript' was removed.
    
    Furthermore, if the user has prepared the catalog before or has a simulated
    images that won't be in Gaia s/he can use the new '--catalog' option. With
    this option, at first this script checks the overlap with the image and
    aborts with an error if there is not any overlap.
---
 bin/script/psf-create-select-stars.in | 140 +++++++++++++++++++++++++---------
 1 file changed, 105 insertions(+), 35 deletions(-)

diff --git a/bin/script/psf-create-select-stars.in 
b/bin/script/psf-create-select-stars.in
index 6f512ed2..1856b388 100755
--- a/bin/script/psf-create-select-stars.in
+++ b/bin/script/psf-create-select-stars.in
@@ -53,10 +53,9 @@ bdir=""
 show=""
 input=""
 quiet=""
+catalog=""
 segmented=""
 keepbuild=""
-extscript=""
-matchaperture=""
 minaxisratio=0.9
 version=@VERSION@
 mindistdeg=0.015277778
@@ -90,7 +89,7 @@ This script builds a catalogue, with column names "columns", 
of reference
 stars from an astquery "dataset", with a "field" magnitude value between "min"
 and "max" specified as a chunk of awk code.
 Additionaly, if a segmented file is provided, only stars which match clumps
-within a given "matchaperture", in pixels, and with an AXIS_RATIO >
+within a given "matchaperturedeg", in pixels, and with an AXIS_RATIO >
 "minaxisrario" are selected.
 
 $scriptname options:
@@ -103,12 +102,14 @@ $scriptname options:
                           ("phot_rp_mean_mag", etc.).
   -m, --min=FLT           Minimum value of field.
   -M, --max=FLT           Maximum value of field.
-  -a, --matchaperture=FLT Aperture, in pixels, to match catalogue ra and
+  -a, --matchaperturedeg=FLT Aperture, in pixels, to match catalogue ra and
                           dec coordinates with clumps' ra and dec.
   -Q, --minaxisratio=FLT  Minimum axis ratio of a clump to be accepted.
                           Default to 0.9.
   -D, --mindistdeg=FLT    Minimum distance to more brilliant neighbour stars
                           to be accepted, in degree.
+  -c, --catalog=STR       Catalog of stras contain of ra, desc, magnitude,
+                          parrallax and parrallax_error.
 
  Output:
   -k, --keepbuild         Keep the build directory.
@@ -221,6 +222,9 @@ do
        -d|--dataset)           dataset="$2";                                 
check_v "$1" "$dataset";  shift;shift;;
        -d=*|--dataset=*)       dataset="${1#*=}";                            
check_v "$1" "$dataset";  shift;;
        -d*)                    dataset=$(echo "$1" | sed -e's/-d//');        
check_v "$1" "$dataset";  shift;;
+       -c|--catalog)           catalog="$2";                                 
check_v "$1" "$catalog";  shift;shift;;
+       -c=*|--catalog=*)       catalog="${1#*=}";                            
check_v "$1" "$catalog";  shift;;
+       -c*)                    catalog=$(echo "$1" | sed -e's/-c//');        
check_v "$1" "$catalog";  shift;;
        -f|--field)             field="$2";                                   
check_v "$1" "$field";  shift;shift;;
        -f=*|--field=*)         field="${1#*=}";                              
check_v "$1" "$field";  shift;;
        -f*)                    field=$(echo "$1" | sed -e's/-f//');          
check_v "$1" "$field";  shift;;
@@ -230,11 +234,11 @@ do
        -M|--max)               max="$2";                                     
check_v "$1" "$max";  shift;shift;;
        -M=*|--max=*)           max="${1#*=}";                                
check_v "$1" "$max";  shift;;
        -M*)                    max=$(echo "$1" | sed -e's/-M//');            
check_v "$1" "$max";  shift;;
-       -a|--matchaperture)     matchaperture="$2";                           
check_v "$1" "$matchaperture";shift;shift;;
-       -a=*|--matchaperture=*) matchaperture="${1#*=}";                      
check_v "$1" "$matchaperture";  shift;;
-       -a*)                    matchaperture=$(echo "$1" | sed -e's/-a//');  
check_v "$1" "$matchaperture";  shift;;
+       -a|--matchaperturedeg)  matchaperturedeg="$2";                        
check_v "$1" "$matchaperturedeg";shift;shift;;
+       -a=*|--matchaperturedeg=*) matchaperturedeg="${1#*=}";                
check_v "$1" "$matchaperturedeg";  shift;;
+       -a*)                    matchaperturedeg=$(echo "$1" | sed -e's/-a//'); 
 check_v "$1" "$matchaperturedeg";  shift;;
        -Q|--minaxisratio)      minaxisratio="$2";                            
check_v "$1" "$minaxisratio";  shift;shift;;
-       -Q=*|--minaxisratio=*)  minaxisrario="${1#*=}";                       
check_v "$1" "$minaxisratio";  shift;;
+       -Q=*|--minaxisratio=*)  minaxisratio="${1#*=}";                       
check_v "$1" "$minaxisratio";  shift;;
        -Q*)                    minaxisratio=$(echo "$1" | sed -e's/-Q//');   
check_v "$1" "$minaxisratio";  shift;;
        -D|--mindistdeg)        mindistdeg="$2";                              
check_v "$1" "$mindistdeg";  shift;shift;;
        -D=*|--mindistdeg=*)    mindistdeg="${1#*=}";                         
check_v "$1" "$mindistdeg";  shift;;
@@ -266,7 +270,7 @@ do
 
        # Not an option (not starting with a '-'):
        # it's assumed to be detected.fits or segmented.fits
-       *) input="$1"; shift;;
+       *) input="$1 $input"; shift;;
    esac
 done
 
@@ -279,16 +283,17 @@ done
 #
 # If the input image has not been given at all.
 if [ x"$input" = x ]; then
-       echo "No input image file specified"
+    echo " $scriptname: no input image file specified."
+    echo "Run with '--help' for more information on how to run."
        exit 1
 fi
 
-# Check that if 'matchaperture' is not specified as input,
+# Check that if 'matchaperturedeg' is not specified as input,
 # Set its value to'3.0/3600'
 arcsec_per_pixel=$(astfits $input --hdu=$hdu --pixelscale -q \
                       | awk '{print $1*3600}')
-if [ x"$matchaperture" = x ]; then
-   matchaperturedeg=$(echo $matchaperture $arcsec_per_pixel \
+if [ x"$matchaperturedeg" = x ]; then
+   matchaperturedeg=$(echo $matchaperturedeg $arcsec_per_pixel \
                            | awk '{print $1*$2/3600}')
 fi
 
@@ -310,12 +315,6 @@ fi
 
 
 
-
-
-
-
-
-
 # Make a directory for output files.
 #-----------------------------------
 #
@@ -332,18 +331,78 @@ fi
 
 
 
-# Download the catalog.
-#----------------------
+# Catalog of stars
+#-----------------
 #
-# Downdowd catalouge of stars from Gaia with use
-# of 'astquery'.
-query=$bdir/query.fits
-if [ -f $query ]; then
-    echo "External Cataloge already exists "
+# At first check that user have catalog of stars or no. If the user geive a
+# catalog to script at first with help of "--skycoverage" check the
+# catalog's minimum (maximum) ra and dec are smaller (larger) than the
+# image edge. If it is true with "asttable" just choose stars that have
+# magnitude between 0 to maximum of magitude. If it isn't stop script. If
+# user don't provide catalog with help of "--astquery" download the
+# catalog.
+if [ -f $catalog ]; then
+    # Find minimum value of image's ra.
+    minraimg=$(astfits $input --skycoverage | grep 'RA' | awk '{print $2}')
+
+    # Find minimum value of image's dec.
+    mindecimg=$(astfits $input --skycoverage | grep 'DEC' | awk '{print $2}')
+
+    # Find maximum value of image's ra.
+    maxraimg=$(astfits $input --skycoverage | grep 'RA' | awk '{print $3}')
+
+    # Find maximum value of image's dec.
+    maxdecimg=$(astfits $input --skycoverage | grep 'DEC' | awk '{print $3}')
+
+    # Find minimum value of catalog's ra.
+    minracatalog=$(asttable $catalog -cRA | aststatistics --minimum)
+
+    # Find minimum value of catalog's dec.
+    mindeccatalog=$(asttable $catalog -cDEC | aststatistics --minimum)
+
+    # Find maximum value of catalog's ra.
+    maxracatalog=$(asttable $catalog -cRA | aststatistics --maximum)
+
+    # Find maximum value of catalog's dec.
+    maxdeccatalog=$(asttable $catalog -cDEC | aststatistics --maximum)
+
+    # Check that catalog overlap the image or not.
+    check=$(echo $minraimg $minracatalog $mindecimg $mindeccatalog \
+                 $maxraimg $maxracatalog $maxdecimg $maxdeccatalog \
+                | awk '{print ($1 >= $2 && $3 >= $4 && $5 <= $6 && $7 <= $8)}')
+
+    # If catalog overlap the image, just select stars with magnitude
+    # between 0 to maximmum range that user choose.
+    if [ "$check" = 1 ]; then
+
+        # Make a file for output of 'asttable'.
+        query=$bdir/query.fits
+        if [ -f $query ]; then
+            echo "External Cataloge already exists "
+        else
+            # Select stars with magnitude between 0 to maximum.
+            asttable $catalog --range=$field,0:$max --sort=$field \
+                     --output=$query
+        fi
+    else
+        # If catalog doesn't overlap the image stop.
+        echo "Tha catalog is smaller than the image and don't overlap image."
+        exit 1
+    fi
+# If user doesn't provide catalog, with use of 'astquery' catalog of stars
+# with magnitude between 0 to max from gaia has been downloaded.
 else
-    astquery $dataset --output=$query --overlapwith=$input \
-            --hdu=$hdu --column=ra,dec,$field,parallax,parallax_error \
-            --range=$field,0:$max --sort=$field $quiet
+    # Make a 'query.fits' for output of 'astquery'.
+    query=$bdir/query.fits
+    if [ -f $query ]; then
+        echo "External Cataloge already exists "
+    else
+        # Download catalog of stars with magnitude between 0 to max from
+        # Gaia with '--astquery'.
+        astquery $dataset --output=$query --overlapwith=$input \
+                --hdu=$hdu --column=ra,dec,$field,parallax,parallax_error \
+                --range=$field,0:$max --sort=$field $quiet
+    fi
 fi
 
 
@@ -417,11 +476,14 @@ fi
 # minimumm distance and based on '--noblank' and 'where' remove
 # stars tha have distance larger than minimumm distance. Then
 # remove each circular stars that have more than 9 neighbors.
-lessneighbor=$bdir/less-than-9-stars.fits
-moreneighbor=$bdir/more-than-9-stars.fits
+lessneighbor=$bdir/less-than-9-stars.txt
+moreneighbor=$bdir/more-than-9-stars.txt
+echo "# Column 1: ra [deg,f64] Right ascension" >> $lessneighbor
+echo "# Column 2: dec [deg,f64] Declination" >> $lessneighbor
+echo "# Column 3: photo-g-mean-mag [mag,f64] Magnitude" >> $lessneighbor
 
 # Find ra and dec of each circul star.
-asttable $circular -cra,dec | while read r d; do
+asttable $circular -cra,dec -c$field | while read r d mag; do
 
    # Make a file for number of neighbourhood.
    numberneighbor=$bdir/"$r"th-star-neighbor.fits
@@ -431,16 +493,16 @@ asttable $circular -cra,dec | while read r d; do
            --colinfoinstdout \
            -c'arith ra dec '$r' '$d' distance-on-sphere \
                      set-i i i '$mindistdeg' gt nan where' \
-            --noblank=4
+            --noblank=4 \
             --output=$numberneighbor
 
    # Check number of neighborhod and remove each star that
    # has more than 9 neighbors.
    lof=$(cat $numberneighbor | wc -l)
    if [ $lof -le 9 ]; then
-       echo $r $d >> $lessneighbor
+       echo $r $d $mag >> $lessneighbor
    else
-       echo $r $d >> $moreneighbor
+       echo $r $d $mag >> $moreneighbor
    fi
 done
 
@@ -448,6 +510,14 @@ done
 
 
 
+# Output of selected circular stars with good parallax and
+# less than 9 neighbors in fits format.
+asttable $lessneighbor --output=$output
+
+
+
+
+
 # Run script quiet or not
 #------------------------
 #