#!/bin/bash # # Developed by Fred Weinhaus 12/8/2011 .......... revised 6/17/2017 # # ------------------------------------------------------------------------------ # # Licensing: # # Copyright © Fred Weinhaus # # My scripts are available free of charge for non-commercial use, ONLY. # # For use of my scripts in commercial (for-profit) environments or # non-free applications, please contact me (Fred Weinhaus) for # licensing arrangements. My email address is fmw at alink dot net. # # If you: 1) redistribute, 2) incorporate any of these scripts into other # free applications or 3) reprogram them in another scripting language, # then you must contact me for permission, especially if the result might # be used in a commercial or for-profit environment. # # My scripts are also subject, in a subordinate manner, to the ImageMagick # license, which can be found at: http://www.imagemagick.org/script/license.php # # ------------------------------------------------------------------------------ # #### # # USAGE: maxima [-r rad ] [-s shape] [-n num] [-t thresh] [-u units] [-d dist] # [-m metric] [-c color] [-g graphic] infile [outfile] # # USAGE: maxima [-h or -help] # # OPTIONS: # # -r rad x,y ${radx},${rady} for masking out peaks; integer>0; # one value will be used for both dimensions; # default=5; # -s shape shape for masking; choices are: ellipse or rectangle; # default=ellipse # -n num stopping number of maxima; integer>0; default=1 # -t thresh graylevel (maxima amplitude) stopping threshold; # integer>0; default=ignore argument # -u units units for graylevel threshold; choices are: # percent (p), raw (r), 8bit (8); default=percent # -d dist pixel distance for stopping; integer>0; # default=ignore argument # -m metric compare metric; any valid IM metric; default=rmse # -c color masking color if output image is specified; any valid # opaque IM color is allowed; default=black # -g display intermediate images # # An optional output image may be specified which will be the input # image with the masked areas showing where the maxima are located. # ### # # NAME: MAXIMA # # PURPOSE: To locate one or more local maxima in a grayscale image. # # DESCRIPTION: MAXIMA locates one or more local maxima in a grayscale # image. It does this by finding the highest graylevel value and its # location (via the compare function). Then it draws a black circle # (ellipse) at that location and repeats the process. The process can # be stopped by any combination of more than some number of maxima, # the graylevel (amplitude) at a maxima is lower than some threshold # value or the distance between any two maxima are less than some # spacing distance. Each maxima location and its graylevel will be # returned to the terminal. If the input is not grayscale it will be # converted to grayscale. # # Arguments: # # -r rad ... RAD are the x,y ${radx},${rady} for masking out peaks. Values are # integers>0. One value will be used for both dimensions. The default=5. # # -s shape ... SHAPE for masking. The choices are: ellipse or rectangle. # The default=ellipse. # # -n num ... NUM is the number of maxima used to stop the iterative # process. Stopping occurs when the iteration exceeds the num value. # Values are integers>0. The default=1. Note that a number must be set # even if one uses thresh. # # -t thresh ... THRESH is the graylevel (maxima amplitude) used as the # stopping threshold. Stopping occurs when a maxima graylevel is less # than thresh. Values are integers>0. The default=ignore this argument. # # -u units ... UNITS for the graylevel threshold. Choices are: # percent (or p), raw (or r), 8bit (or 8). The default=percent. # # -d dist ... DISTANCE in pixels between maxima used for stopping. # Stopping occurs when any two maxima are too close together, i.e. # less than dist. Values are integers>0. The default=ignore this # argument. # # -m metric ... METRIC is the compare metric used to locate the maxima. # Any valid IM metric may be used. The default=rmse. Only needed for # Imagemagick versions less than 6.8.6-10. # # -c color ... masking COLOR, if an output image is specified. Any valid opaque # IM color is allowed. The default=black. # # -g ... Indicates to display the intermediate masked images. # # An optional output image may be specified which will be the input # image with the masked areas showing where the maxima are located. # # CAVEAT: No guarantee that this script will work on all platforms, # nor that trapping of inconsistent parameters is complete and # foolproof. Use At Your Own Risk. # ###### # # set default values rad=5 # mask x,y ${radx},${rady}; default=5; integer>0 shape="ellipse" # ellipse or rectangle num=1 # stopping number of maxima; ; integer>0; default=1 thresh=0 # graylevel stopping threshold; integer>0; default=ignore units="percent" # units for threshold: percent, 8bit, raw; default=percent dist=0 # pixel distance stopping; integer>0; default=ignore metric="rmse" # compare metric color="black" # masking color for output image graphic="no" # display intermediate images # set directory for temporary files tmpdir="." # suggestions are tmpdir="." or tmpdir="/tmp" dir="$tmpdir/MAXIMA.$$" mkdir "$dir" || errMsg "--- FAILED TO CREATE TEMPORARY FILE DIRECTORY ---" trap "rm -rf $dir;" 0 trap "rm -rf $dir; exit 1" 1 2 3 15 #trap "rm -rf $dir; exit 1" ERR # set up functions to report Usage and Usage with Description PROGNAME=`type $0 | awk '{print $3}'` # search for executable on path PROGDIR=`dirname $PROGNAME` # extract directory of program PROGNAME=`basename $PROGNAME` # base name of program usage1() { echo >&2 "" echo >&2 "$PROGNAME:" "$@" sed >&2 -e '1,/^####/d; /^###/g; /^#/!q; s/^#//; s/^ //; 4,$p' "$PROGDIR/$PROGNAME" } usage2() { echo >&2 "" echo >&2 "$PROGNAME:" "$@" sed >&2 -e '1,/^####/d; /^######/g; /^#/!q; s/^#*//; s/^ //; 4,$p' "$PROGDIR/$PROGNAME" } # function to report error messages errMsg() { echo "" echo $1 echo "" usage1 exit 1 } # function to test for minus at start of value of second part of option 1 or 2 checkMinus() { test=`echo "$1" | grep -c '^-.*$'` # returns 1 if match; 0 otherwise [ $test -eq 1 ] && errMsg "$errorMsg" } # test for correct number of arguments and get values if [ $# -eq 0 ] then # help information echo "" usage2 exit 0 elif [ $# -gt 19 ] then errMsg "--- TOO MANY ARGUMENTS WERE PROVIDED ---" else while [ $# -gt 0 ] do # get parameters case "$1" in -h|-help) # help information echo "" usage2 ;; -r) # rad shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID RAD SPECIFICATION ---" checkMinus "$1" rad=`expr "$1" : '\([0-9]*,*[0-9]*\)'` [ "$rad" = "" ] && errMsg "--- RAD=$rad MUST BE TWO COMMA SEPARATED NON-NEGATIVE INTEGER (with no sign) ---" ;; -s) # shape shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID SHAPE SPECIFICATION ---" checkMinus "$1" # test mode values shape="$1" shape=`echo "$shape" | tr "[:upper:]" "[:lower:]"` case "$shape" in ellipse|e) shape="ellipse";; rectangle|r) shape="rectangle";; *) errMsg "--- SHAPE=$shape IS AN INVALID VALUE ---" esac ;; -n) # num shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID NUM SPECIFICATION ---" checkMinus "$1" num=`expr "$1" : '\([0-9]*\)'` [ "$num" = "" ] && errMsg "--- NUM=$num MUST BE A NON-NEGATIVE INTEGER (with no sign) ---" test=`echo "$num <= 0" | bc` [ $test -eq 1 ] && errMsg "--- NUM=$num MUST BE A POSITIVE INTEGER ---" ;; -t) # thresh shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID THRESH SPECIFICATION ---" checkMinus "$1" thresh=`expr "$1" : '\([0-9]*\)'` [ "$thresh" = "" ] && errMsg "--- THRESH=$thresh MUST BE A NON-NEGATIVE INTEGER (with no sign) ---" test=`echo "$thresh <= 0" | bc` [ $test -eq 1 ] && errMsg "--- THRESH=$thresh MUST BE A POSITIVE INTEGER ---" ;; -u) # units shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID UNITS SPECIFICATION ---" checkMinus "$1" # test mode values units="$1" units=`echo "$units" | tr "[:upper:]" "[:lower:]"` case "$units" in percent|p) units="percent";; raw|r) units="raw";; 8bit|8) units="8bit";; *) errMsg "--- UNITS=$units IS AN INVALID VALUE ---" esac ;; -d) # dist shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID DIST SPECIFICATION ---" checkMinus "$1" dist=`expr "$1" : '\([0-9]*\)'` [ "$dist" = "" ] && errMsg "--- DIST=$dist MUST BE A NON-NEGATIVE INTEGER (with no sign) ---" test=`echo "$dist <= 0" | bc` [ $test -eq 1 ] && errMsg "--- DIST=$dist MUST BE A POSITIVE INTEGER ---" ;; -m) # metric shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID METRIC SPECIFICATION ---" checkMinus "$1" # test mode values metric="$1" metric=`echo "$metric" | tr "[:upper:]" "[:lower:]"` case "$metric" in ae) ;; fuzz) ;; mae) ;; mepp) ;; mse) ;; ncc) ;; pae) ;; psnr) ;; rmse) ;; *) errMsg "--- METRIC=$metric IS AN INVALID VALUE ---" esac ;; -c) # color shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID COLOR SPECIFICATION ---" checkMinus "$1" color="$1" ;; -g) # set show graphic="yes" ;; -) # STDIN and end of arguments break ;; -*) # any other - argument errMsg "--- UNKNOWN OPTION ---" ;; *) # end of arguments break ;; esac shift # next option done # get infile and outfile infile="$1" outfile="$2" fi # test that infile provided [ "$infile" = "" ] && errMsg "--- NO INPUT FILE SPECIFIED ---" if [ "$outfile" != "" -a "$color" != "black" ]; then proc0="-evaluate max 1" else proc0="" fi # test input image convert -quiet "$infile" -alpha off -colorspace gray $proc0 +repage "$dir/tmpI.mpc" || errMsg "--- FILE $infile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAS ZERO SIZE ---" # get quantumrange qrange=`convert xc: -format "%[fx:quantumrange]" info:` # get im version im_version=`convert -list configure | \ sed '/^LIB_VERSION_NUMBER */!d; s//,/; s/,/,0/g; s/,0*\([0-9][0-9]\)/\1/g' | head -n 1` # colorspace RGB and sRGB swapped between 6.7.5.5 and 6.7.6.7 # though probably not resolved until the latter # then -colorspace gray changed to linear between 6.7.6.7 and 6.7.8.2 # then -separate converted to linear gray channels between 6.7.6.7 and 6.7.8.2, # though probably not resolved until the latter # so -colorspace HSL/HSB -separate and -colorspace gray became linear # but we need to use -set colorspace RGB before using them at appropriate times # so that results stay as in original script # The following was determined from various version tests using maxima. # with IM 6.7.4.10, 6.7.6.10, 6.8.5.10 if [ "$im_version" -lt "06070606" ]; then cspace="RGB" else cspace="sRGB" fi # set up use of -subimage-search if [ "$im_version" -ge "06060306" ]; then subimagesearch="-subimage-search" else subimagesearch="" fi # set up ${radx},${rady} radx=`echo $rad | cut -d, -f1` rady=`echo $rad | cut -d, -f2` test1=`echo "$radx <= 0" | bc` test2=`echo "$rady <= 0" | bc` [ $test1 -eq 1 -o $test2 -eq 1 ] && errMsg "--- RAD=$rad MUST BE TWO COMMA SEPARATED POSITIVE INTEGER ---" # set up for using (new) %[max] or (old) %[maxima] # notation changed somewhere between 6.7.4.10 and 6.7.7.7, but don't know where test=`convert -quiet xc:white xc:black +append -format "%[maxima]" info:` if [ "$test" != "" ]; then # old maximum="maxima" else # new maximum="max" fi # find first maxima value val=`convert $dir/tmpI.mpc -format "%[$maximum]" info:` valfrac=`convert xc: -format "%[fx:$val/$qrange]" info:` valpct=`convert xc: -format "%[fx:100*$val/$qrange]" info:` val8=`convert xc: -format "%[fx:round(255*$valfrac)]" info:` [ "$units" = "percent" ] && threshold=$valpct [ "$units" = "8bit" ] && threshold=$val8 [ "$units" = "raw" ] && threshold=$val # find first maxima location number=1 if [ "$im_version" -lt "06080610" ]; then match=`compare -metric $metric $subimagesearch $dir/tmpI.mpc \( -size 1x1 xc:"gray($valpct%)" \) null: 2>&1` oldlocation=`echo $match | cut -d\ -f4` else data=`identify -precision 5 -define identify:locate=maximum -define identify:limit=1 $dir/tmpI.mpc | tail -n +2 | tr -cs "[0-9,.]*" " " | sed 's/^ *//g'` oldlocation=`echo "$data" | cut -d\ -f3` fi echo "max=$number $oldlocation gray=$val,$val8,$valpct%" # mask image if [ "$shape" = "ellipse" ]; then convert $dir/tmpI.mpc -fill black -draw "translate $oldlocation ellipse 0,0 ${radx},${rady} 0,360" $dir/tmpI.mpc elif [ "$shape" = "rectangle" ]; then convert $dir/tmpI.mpc -fill black -draw "translate $oldlocation rectangle -${radx},-${rady} ${radx},${rady}" $dir/tmpI.mpc fi if [ "$im_version" -lt "06080610" ]; then flag="" for ((number=2; number<=num; number++)); do [ "$graphic" = "yes" ] && convert $dir/tmpI.mpc show: val=`convert $dir/tmpI.mpc -format "%[$maximum]" info:` valfrac=`convert xc: -format "%[fx:$val/$qrange]" info:` valpct=`convert xc: -format "%[fx:100*$val/$qrange]" info:` val8=`convert xc: -format "%[fx:round(255*$valfrac)]" info:` [ "$units" = "percent" ] && threshold=$valpct [ "$units" = "8bit" ] && threshold=$val8 [ "$units" = "raw" ] && threshold=$val match=`compare -metric $metric $subimagesearch $dir/tmpI.mpc \( -size 1x1 xc:"gray($valpct%)" \) null: 2>&1` location=`echo $match | cut -d\ -f4` test=`convert xc: -format "%[fx:$threshold < $thresh?1:0]" info:` [ $test -eq 1 ] && break if [ "$dist" != "0" ]; then x1=`echo $location | cut -d, -f1` y1=`echo $location | cut -d, -f2` for loc in $oldlocation; do x2=`echo $loc | cut -d, -f1` y2=`echo $loc | cut -d, -f2` distance=`convert xc: -format "%[fx:round(hypot($x1-$x2,$y1-$y2))]" info:` if [ $distance -lt $dist ]; then flag="stop" break fi done fi [ "$flag" = "stop" ] && break echo "max=$number $location gray=$val,$val8,$valpct%" if [ "$shape" = "ellipse" ]; then convert $dir/tmpI.mpc -fill black -draw "translate $location ellipse 0,0 ${radx},${rady} 0,360" $dir/tmpI.mpc elif [ "$shape" = "rectangle" ]; then convert $dir/tmpI.mpc -fill black -draw "translate $location rectangle -${radx},-${rady} ${radx},${rady}" $dir/tmpI.mpc fi oldlocation="$oldlocation $location" done else flag="" for ((number=2; number<=num; number++)); do [ "$graphic" = "yes" ] && convert $dir/tmpI.mpc show: data=`identify -precision 5 -define identify:locate=maximum -define identify:limit=1 $dir/tmpI.mpc | tail -n +2 | tr -cs "[0-9,.]*" " " | sed 's/^ *//g'` location=`echo "$data" | cut -d\ -f3` valfrac=`echo "$data" | cut -d\ -f2` val=`convert xc: -format "%[fx:round($valfrac*$qrange)]" info:` valpct=`convert xc: -format "%[fx:100*$valfrac]" info:` val8=`convert xc: -format "%[fx:round(255*$valfrac)]" info:` [ "$units" = "percent" ] && threshold=$valpct [ "$units" = "8bit" ] && threshold=$val8 [ "$units" = "raw" ] && threshold=$val test=`convert xc: -format "%[fx:$threshold < $thresh?1:0]" info:` [ $test -eq 1 ] && break if [ "$dist" != "0" ]; then x1=`echo $location | cut -d, -f1` y1=`echo $location | cut -d, -f2` for loc in $oldlocation; do x2=`echo $loc | cut -d, -f1` y2=`echo $loc | cut -d, -f2` distance=`convert xc: -format "%[fx:round(hypot($x1-$x2,$y1-$y2))]" info:` if [ $distance -lt $dist ]; then flag="stop" break fi done fi [ "$flag" = "stop" ] && break echo "max=$number $location gray=$val,$val8,$valpct%" if [ "$shape" = "ellipse" ]; then convert $dir/tmpI.mpc -fill black -draw "translate $location ellipse 0,0 ${radx},${rady} 0,360" $dir/tmpI.mpc elif [ "$shape" = "rectangle" ]; then convert $dir/tmpI.mpc -fill black -draw "translate $location rectangle -${radx},-${rady} ${radx},${rady}" $dir/tmpI.mpc fi oldlocation="$oldlocation $location" done fi if [ "$outfile" != "" -a "$color" != "black" ]; then proc1="-fill $color -opaque black" else proc1="" fi [ "$outfile" != "" ] && convert $dir/tmpI.mpc -set colorspace $cspace $proc1 "$outfile" exit 0