#!/bin/bash # # Developed by Fred Weinhaus 10/2/2012 .......... 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: noisecleaner [-m method] [-n numiter] [-s stopdiff] [-f format] # [-p] infile outfile # # USAGE: noisecleaner [-h or -help] # # OPTIONS: # # -m method method of cleaning noise; choices are: 1 using # IM -enhance and 2 using IM -despeckle; default=1 # -n numiter number of iterations; integer>0; default=5 # -s stopdiff rmse stopping difference between between iterations; # 0<=float<=1; default=0 (do not stop until numiter reached) # -f format output image format; choices are last (iteration) or # all (iterations); default=last # -p show progress to terminal # ### # # NAME: NOISECLEANER # # PURPOSE: To iteratively clean noise from an image. # # DESCRIPTION: NOISECLEANER iteratively cleans noise from an image. Two # methods are available using either IM -enhance or IM -despeckle. # # # ARGUMENTS: # # -m method ... METHOD of cleaning noise. The choices are: 1 using # IM -enhance and 2 using IM -despeckle. The default=1 # # -n numiter ... NUMITER is the number of iterations to apply. Values are \ # integers>0. The default=5. # # -s stopdiff ... STOPDIFF is the rmse stopping difference between between # iterations. Values are 0<=floats<=1. The default=0 which indicates not to # stop until numiter is reached. If a value larger than zero is specified, then # processing will quit when the rmse difference between iterations is less than # or equal to this value. Values larger than 0 will slow the processing in # order to compute the rmse difference. # # -f format ... FORMAT is the desired output image format. The choices are # last (l), which saves only the last iteration reached or all (a), which saves # a multiframe (multilayer) tiff file with each iteration as a frame (layer). # The default is last. Note the output image file name will have its suffix # replaced by .tif # # -p ... show iteration PROGRESS to terminal # # 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=1 # 1 for -enhance and 2 for -despeckle numiter=5 # number of iterations; integer>0; default=5 stopdiff=0 # rmse stopping difference between between iterations; float>0; default ignore; nominal 0.005 format="last" # output saves last interation or all iterations progress="no" # show progress to terminal # 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 11 ] 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) # get method shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID METHOD SPECIFICATION ---" checkMinus "$1" method=`expr "$1" : '\([0-9]*\)'` [ $method -ne 1 -a $method -ne 2 ] && errMsg "--- METHOD=$method MUST BE EITHER 1 OR 2 ---" ;; -n) # get numiter shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID NUMITER SPECIFICATION ---" checkMinus "$1" numiter=`expr "$1" : '\([0-9]*\)'` [ "$numiter" = "" ] && errMsg "--- NUMITER=$numiter MUST BE A NON-NEGATIVE INTEGER ---" test1=`echo "$numiter <= 0" | bc` [ $test1 -eq 1 ] && errMsg "--- NUMITER=$numiter MUST BE AN INTEGER GREATER THAN 0 ---" ;; -s) # get stopdiff shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID STOPDIFF SPECIFICATION ---" checkMinus "$1" stopdiff=`expr "$1" : '\([.0-9]*\)'` [ "$stopdiff" = "" ] && errMsg "--- STOPDIFF=$stopdiff MUST BE A NON-NEGATIVE FLOAT VALUE (with no sign) ---" test1=`echo "$stopdiff < 0" | bc` test2=`echo "$stopdiff > 1" | bc` [ $test1 -eq 1 -o $test2 -eq 1 ] && errMsg "--- STOPDIFF=$stopdiff MUST BE A FLOAT BETWEEN 0 AND 1 ---" ;; -f) # get format shift # to get the next parameter # test if parameter starts with minus sign errorMsg="--- INVALID FORMAT SPECIFICATION ---" checkMinus "$1" format=`echo "$1" | tr '[A-Z]' '[a-z]'` case "$format" in last|l) format="last" ;; all|a) format="all" ;; *) errMsg "--- FORMAT=$format IS AN INVALID VALUE ---" ;; esac ;; -p) # get progress progress="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" # test that outfile provided [ "$outfile" = "" ] && errMsg "NO OUTPUT FILE SPECIFIED" # set directory for temporary files # tmpdir="/tmp" tmpdir="." dir="$tmpdir/NOISECLEANER.$$" 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 $dir; exit 1" ERR # test input image convert -quiet "$infile" +repage "$dir/tmpI.mpc" || errMsg "--- FILE $infile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAS ZERO SIZE ---" # get output file name and suffix outname=`echo "$outfile" | sed -n 's/^\(.*\)[\.].*$/\1/p'` suffix=`echo "$outfile" | sed -n 's/^.*[\.]\(.*\)$/\1/p'` if [ "$method" = "1" ]; then proc="-enhance" elif [ "$method" = "2" ]; then proc="-despeckle" fi if [ "$progress" = "yes" ]; then echo "" fi if [ "$format" = "last" ]; then convert $dir/tmpI.mpc $dir/tmpR_0.mpc for ((i=1; i<=numiter; i++)); do j=$((i-1)) convert $dir/tmpR_$j.mpc $proc $dir/tmpR_$i.mpc if [ "$stopdiff" = "0" -a "$progress" = "yes" ]; then echo "$i" elif [ "$stopdiff" != "0" -a "$progress" = "yes" ]; then diff=`compare -metric rmse $dir/tmpR_$j.mpc $dir/tmpR_$i.mpc null: 2>&1 | sed -n 's/^.*[(]\(.*\)[)].*$/\1/p'` echo "$i $diff" test=`convert xc: -format "%[fx:($diff<=$stopdiff)?1:0]" info:` # note if loop runs to completion it will add 1 to i, which has to be subtracted afterwards # if loop breaks it does not add 1 to i, so add it here if [ $test -eq 1 ]; then i=$((i+1)) break fi fi done k=$((i-1)) # echo "i=$i; k=$k" convert $dir/tmpR_$k.mpc "${outname}.${suffix}" elif [ "$format" = "all" ]; then convert $dir/tmpI.mpc $dir/tmpR_0.mpc # use subshell to save all images to miff ( for ((i=1; i<=numiter; i++)); do j=$((i-1)) convert $dir/tmpR_$j.mpc $proc $dir/tmpR_$i.mpc convert $dir/tmpR_$i.mpc miff:- #subshell variables need to be sent to stderr to show on terminal if [ "$stopdiff" = "0" -a "$progress" = "yes" ]; then echo >&2 "$i" elif [ "$stopdiff" != "0" -a "$progress" = "yes" ]; then diff=`compare -metric rmse $dir/tmpR_$j.mpc $dir/tmpR_$i.mpc null: 2>&1 | sed -n 's/^.*[(]\(.*\)[)].*$/\1/p'` echo >&2 "$i $diff" test=`convert xc: -format "%[fx:($diff<=$stopdiff)?1:0]" info:` # note if loop runs to completion it will add 1 to i, which has to be subtracted afterwards # if loop breaks it does not add 1 to i, so add it here if [ $test -eq 1 ]; then i=$((i+1)) break fi fi done ) | convert - "${outname}.tif" fi if [ "$progress" = "yes" ]; then echo "" fi exit 0