#!/bin/bash # # Developed by Fred Weinhaus 4/22/2010 .......... revised 4/29/2015 # # ------------------------------------------------------------------------------ # # 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: denoise [-m method] [-f filter] [-s subsection] [-n nstd] # [-u unsharp] [-g gain] infile outfile # USAGE: denoise [-h or -help] # # OPTIONS: # # -m method method of filtering; mean or median; default=mean # -f filter filter size; float>0; default=2 # -s subsection subsection of image to compute noise standard deviation; # WIDTHxHEIGHT+XOFF+YOFF; default is no subsection # and get noise standard deviation from nstd argument # -n nstd noise standard deviation estimate expressed as # percentage of std value in range 0 to 1; # 0<=float<=100; default is estimated automatically # -u unsharp unsharp masking sigma to apply after filtering; # float>=0; default is no unsharp masking # -g gain unsharp masking gain to apply after filtering; # float>=0; default=1 # ### # # NAME: DENOISE # # PURPOSE: To reduces the noise in an image. # # DESCRIPTION: DENOISE reduces the noise in an image. It uses the formula: # input + gain*(input - mean), where mean is a local mean computed in the # neighborhood of each pixel and gain=max(0,(std-nstd)/std), where std is the # local standard deviation computed in the neighborhood of each pixel. This is # an implementation of the Lee Filter. See Lee, J.S., 1981. Speckle Analysis # and Smoothing of Synthetic Aperture Radar Images. Computer Graphics and Image # Processing, Vol. 17:24-32. # # # ARGUMENTS: # # -m method ... METHOD of filtering. Choices are: mean or median. Default=mean. # # -f filter ... FILTER size. Values are floats>0. The default=2. # # -s subsection ... Subsection is a rectangular homogeneous region where the # noise standard deviation will be computed if provided. Otherwise, nstd, # must be provided. The values are in the form of the usual IM subsection # expressed as WIDTHxHEIGHT+XOFF+YOFF. The default is no subsection provided. # # -n nstd ... NSTD is an estimate of the noise standard deviation in the image # expressed as a percentage (100 times std values in the range of 0 to 1). Thus # values for nstd are 0<=float<=100. The default is estimated automatically. # # -u unsharp ... UNSHARP masking sigma to apply as a post processing step to # sharpen the image. Values are floats>=0. The default=0 for no unsharp masking. # # -g gain ... UNSHARP masking gain to apply as a post processing step to # sharpen the image. Values are floats>=0. The default=1. # # References: # Lee, J.S., 1981. Speckle Analysis and Smoothing of Synthetic Aperture Radar Images. Computer Graphics and Image Processing, Vol. 17:24-32. # http://www.isprs.org/proceedings/XXXVI/1-W41/makaleler/Rajabi_Specle_Noise.pdf # J. Immerkaer, "Fast Noise Variance Estimation", Comput. Vis. Image Understand., vol. 64, pp. 300-302, Sep. 1996 # http://www.iaeng.org/IJCS/issues_v37/issue_1/IJCS_37_1_09.pdf # # NOTE: This script may be a bit slow due to the use of -fx for version of IM # prior to 6.8.0.5. # # 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 method="mean" # mean or median filter=2 # filter size; float>0 subsection="" # subsection for computing noise std nstd="" # noise standard deviation percent; float unsharp=0 # unsharp filtering sigma; float>0 gain=0 # unsharp filtering gain; float>0 # 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 [ $# -gt 16 ] then errMsg "--- TOO MANY ARGUMENTS WERE PROVIDED ---" else while [ $# -gt 0 ] do # get parameter values case "$1" in -h|-help) # help information echo "" usage2 exit 0 ;; -m) # method shift # to get the next parameter - mode # test if parameter starts with minus sign errorMsg="--- INVALID METHOD SPECIFICATION ---" checkMinus "$1" # test mode values method="$1" [ "$method" != "mean" -a "$method" != "median" ] && errMsg "--- METHOD=$method IS NOT A VALID VALUE ---" ;; -f) # get filter shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID FILTER SPECIFICATION ---" checkMinus "$1" filter=`expr "$1" : '\([.0-9]*\)'` [ "$filter" = "" ] && errMsg "--- FILTER=$filter MUST BE A NON-NEGATIVE FLOAT ---" test=`echo "$filter <= 0" | bc` [ $test -eq 1 ] && errMsg "--- FILTER=$filter MUST BE A POSITIVE FLOAT ---" ;; -s) # get subsection shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID SUBSECTION SPECIFICATION ---" checkMinus "$1" subsection=`expr "$1" : '\([x+0-9]*\)'` [ "$subsection" = "" ] && errMsg "--- SUBSECTION=$subsection MUST BE INTEGERS IN THE FORM OF WIDTHxHEIGHT+XOFF+YOFF ---" ;; -n) # get nstd shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID NSTD SPECIFICATION ---" checkMinus "$1" nstd=`expr "$1" : '\([.0-9]*\)'` [ "$nstd" = "" ] && errMsg "--- NSTD=$nstd MUST BE A NON-NEGATIVE FLOAT (with no sign) ---" test1=`echo "$nstd < 0" | bc` test2=`echo "$nstd > 100" | bc` [ $test1 -eq 1 -o $test2 -eq 1 ] && errMsg "--- NSTD=$nstd MUST BE A FLOAT BETWEEN 0 AND 100 ---" ;; -u) # get unsharp shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID UNSHARP SPECIFICATION ---" checkMinus "$1" unsharp=`expr "$1" : '\([.0-9]*\)'` [ "$unsharp" = "" ] && errMsg "--- UNSHARP=$unsharp MUST BE A NON-NEGATIVE FLOAT ---" ;; -g) # get gain shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID GAIN SPECIFICATION ---" checkMinus "$1" gain=`expr "$1" : '\([.0-9]*\)'` [ "$gain" = "" ] && errMsg "--- GAIN=$gain MUST BE A NON-NEGATIVE FLOAT ---" ;; -) # 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" # test that outfile provided [ "$outfile" = "" ] && errMsg "NO OUTPUT FILE SPECIFIED" # setup temporary images and auto delete upon exit tmpI1="$dir/denoise_I_$$.mpc" tmpI2="$dir/denoise_I_$$.cache" tmpM1="$dir/denoise_M_$$.mpc" tmpM2="$dir/denoise_M_$$.cache" tmpS1="$dir/denoise_S_$$.mpc" tmpS2="$dir/denoise_S_$$.cache" tmpG1="$dir/denoise_G_$$.mpc" tmpG2="$dir/denoise_G_$$.cache" trap "rm -f $tmpI1 $tmpI2 $tmpM1 $tmpM2 $tmpS1 $tmpS2 $tmpG1 $tmpG2;" 0 trap "rm -f $tmpI1 $tmpI2 $tmpM1 $tmpM2 $tmpS1 $tmpS2 $tmpG1 $tmpG2; exit 1" 1 2 3 15 trap "rm -f $tmpI1 $tmpI2 $tmpM1 $tmpM2 $tmpS1 $tmpS2 $tmpG1 $tmpG2; exit 1" ERR # read the input image and filter image into the temp files and test validity. convert -quiet "$infile" +repage "$tmpI1" || errMsg "--- FILE $infile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAS ZERO SIZE ---" # 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` # set up for biasing if [ "$im_version" -ge "07000000" ]; then biasing="-define convolve:bias=50%" else biasing="-bias 50%" fi # estimate noise std from nearly constant region if [ "$nstd" = "" -a "$subsection" = "" ]; then nstd=`convert $tmpI1 -define convolve:scale='!' $biasing \ -morphology Convolve Laplacian:3 -solarize 50% -level 0x50% -negate \ -format "%[fx:2*(mean/standard_deviation)*sqrt(pi/2)]" info:` elif [ "$nstd" = "" -a "$subsection" != "" ]; then nstd=`convert $tmpI1[$subsection] -format "%[fx:100*standard_deviation]" info:` fi echo "" echo "nstd=$nstd" echo "" #correct for change in median at IM 6.6.8-6 from radius to widthxheight #and from -median to -statistic median if [ "$im_version" -ge "06060806" -a "$method" = "median" ]; then filter=`convert xc: -format "%[fx:2*$filter+1]" info:` proc="-statistic median" else proc="-median" fi # set up for gamma or evaluate pow # don't want gamma to change meta value of gamma from 0.4545, so use -evaluate pow if [ "$im_version" -lt "06040109" ]; then sqrt="-gamma 2" else sqrt="-evaluate pow 0.5" fi #create mean (or median) and std if [ "$method" = "mean" ]; then convert $tmpI1 -blur 0x$filter $tmpM1 elif [ "$method" = "median" ]; then convert $tmpI1 $proc $filter $tmpM1 fi convert $tmpI1 \( -clone 0 -blur 0x$filter \) \ \( -clone 0 -clone 0 -compose multiply -composite -blur 0x$filter \) \ \( -clone 1 -clone 1 -compose multiply -composite \) \ -delete 0,1 +swap -compose minus -composite $sqrt $tmpS1 # create gain image convert $tmpS1 \( +clone -evaluate subtract ${nstd}% \) \ -compose divide -composite -evaluate max 0 $tmpG1 # set up for unsharp masking if [ "$unsharp" = "0" ]; then unsharpen="" else unsharpen="-unsharp 0x${unsharp}+${gain}" fi # denoise : ' # slower convert $tmpI1 $tmpM1 $tmpG1 \ -fx "(u[0]-u[1])*u[2]+u[1]" $unsharpen "$outfile" ' if [ "$im_version" -lt "06080005" ]; then proc2="-monitor -fx 'u[0]-u[1]+u[2]' +monitor $unsharpen " else proc2="-poly '1,1 -1,1 1,1' $unsharpen " fi # faster eval 'convert $tmpI1 $tmpM1 $tmpG1 \ \( -clone 0 -clone 2 -compose multiply -composite \) \ \( -clone 1 -clone 2 -compose multiply -composite \) \ -delete 0,2 -swap 0,1 -swap 1,2 \ '"$proc2"' "$outfile"' exit 0