#!/bin/bash # # Developed by Fred Weinhaus 3/24/2009 .......... revised 4/25/2015 # # ------------------------------------------------------------------------------ # # 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: stdimage [-m mode] [-c] infile1 ... infileN outfile # USAGE: stdimage [-h or -help] # # OPTIONS: # # -m mode output statistic; mode=s or std (for standard deviation) # or mode=v or var (for variance) # -c apply contrast stretch to output # # Note: all images must be the same size ### # # NAME: STDIMAGE # # PURPOSE: To compute a pixel-by-pixel standard deviation or variance image # from multiple input images. # # DESCRIPTION: STDIMAGE computes a pixel-by-pixel standard deviation or variance # image from multiple input images. # # # OPTIONS: # # # -m mode ... MODE statistical measure generated in the output image. Choices # are either mode=s or std (for standard deviation) or mode=v or var # (for variance). The default=std. # # -c ... Apply contrast stretch to output. # # 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 mode="std" # mode: s or std (standard deviation) or v or var (variance) cs="no" # constrast stretch output # set directory for temporary files dir="." # suggestions are dir="." or dir="/tmp" # 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 [ $# -lt 3 ] then errMsg "--- TOO FEW ARGUMENTS WERE PROVIDED ---" else while [ $# -gt 0 ] do # get parameter values case "$1" in -h|-help) # help information echo "" usage2 exit 0 ;; -m) # mode shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID MODE SPECIFICATION ---" checkMinus "$1" # test mode values mode="$1" #convert mode to lowercase mode=`echo "$mode" | tr "[:upper:]" "[:lower:]"` case "$mode" in s|std) mode=std ;; v|var) mode=var ;; *) errMsg "--- MODE=$mode IS AN INVALID VALUE ---" esac ;; -c) # contrast stretch cs="yes" ;; -) # STDIN, end of arguments break ;; -*) # any other - argument errMsg "--- UNKNOWN OPTION ---" ;; *) # end of arguments break ;; esac shift # next option done fi # get infiles and outfile fileArray=($@) nfiles=$# [ $nfiles -lt 3 ] && errMsg "--- TOO FEW IMAGES WERE PROVIDED ---" lastfile=`expr $nfiles - 1` outfile="${fileArray[$lastfile]}" # test that each infile is valid and put names into list i=0 infilelist="" while [ $i -lt $lastfile ]; do # test if image an ordinary, readable and non-zero size testfile="${fileArray[$i]}" if [ -f $testfile -a -r $testfile -a -s $testfile ] then infilelist="$infilelist $testfile" else errMsg "--- FILE $testfile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAS ZERO SIZE ---" exit 1 fi i=`expr $i + 1` done # remove leading space infilelist=${infilelist# } # test that infilelist provided [ "$infilelist" = "" ] && errMsg "NO INPUT FILES SPECIFIED" # test that outfile provided [ "$outfile" = "" ] && errMsg "NO OUTPUT FILE SPECIFIED" # set up temp files tmp0="$dir/stdimage_0_$$.miff" trap "rm -f $tmp0;" 0 trap "rm -f $tmp0; exit 1" 1 2 3 15 trap "rm -f $tmp0; exit 1" ERR # 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 stdimage # with IM 6.7.4.10, 6.7.6.10, 6.7.9.0 if [ "$im_version" -lt "06070607" -o "$im_version" -gt "06070707" ]; then setcspace="-set colorspace RGB" else setcspace="" fi # no need for setcspace for grayscale or channels after 6.8.5.4 if [ "$im_version" -gt "06080504" ]; then setcspace="" fi # Process images # get size of first image ww=`convert "${fileArray[0]}" -ping -format "%w" info:` hh=`convert "${fileArray[0]}" -ping -format "%h" info:` # set up contrast stretch if [ "$cs" = "no" ]; then stretch="" else stretch="$setcspace -contrast-stretch 0" fi # set up empty first frame of temporary convert -size ${ww}x${hh} xc: $tmp0 # add all other images to multi-frame miff for img in $infilelist; do convert $tmp0 $img $tmp0 done # compute variance result # note -gamma 0.5 is same as -evaluate pow 2 and is same as square # var=ave(frames^2) - (ave(frames))^2 # use -coalesce to separate frames and then delete intial bogus frame if [ "$im_version" -ge "06060904" ]; then convert \( $tmp0 -delete 0 -gamma 0.5 -evaluate-sequence mean \) \ \( $tmp0 -delete 0 -evaluate-sequence mean -gamma 0.5 \) \ +swap -compose minus -composite $tmp0 else convert \( $tmp0 -delete 0 -gamma 0.5 -average \) \ \( $tmp0 -delete 0 -average -gamma 0.5 \) \ +swap -compose minus -composite $tmp0 fi if [ "$mode" = "var" ]; then convert $tmp0 $stretch "$outfile" elif [ "$mode" = "std" ]; then # note -gamma 2 is same as -evaluate pow 0.5 and is same as square root convert $tmp0 -gamma 2 $stretch "$outfile" fi exit 0