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Diffstat (limited to 'bin/localthresh')
| -rw-r--r-- | bin/localthresh | 347 |
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diff --git a/bin/localthresh b/bin/localthresh new file mode 100644 index 0000000..03d6f06 --- /dev/null +++ b/bin/localthresh @@ -0,0 +1,347 @@ +#!/bin/bash +# +# Developed by Fred Weinhaus 10/30/2008 .......... revised 11/3/2015 +# +# ------------------------------------------------------------------------------ +# +# 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: localthresh [-m method] [-s size] [-b bias] [-n negate] infile outfile +# USAGE: localthresh [-help] +# +# OPTIONS: +# +# -m method method for computing threshold statistics; +# method=1 uses only the local mean; +# method=2 uses the local mean and standard deviation; +# method=3 used the local mean and mean absolute deviation; +# default=1 +# -r radius radius of window to use; float; radius>=3; default=15 +# -b bias bias parameter (in percent) for thresholding; +# float; bias>=0; default=20 +# -n negate negate indicates whether to negate the image +# before and after processing; negate=yes or no; +# default=no +# +### +# +# NAME: LOCALTHRESH +# +# PURPOSE: To threshold an image to binary (b/w) format using a moving +# window adaptive thresholding approach. +# +# DESCRIPTION: LOCALTHRESH thresholds an image to binary (b/w) format +# using a moving window adaptive thresholding approach. For each window +# placement the center pixel is compared to some measure of either mean or +# combination of mean and either standard deviation or mean absolute +# deviation within the window. If the center pixel is larger than this +# measure by some bias value, then the center pixel is made white; +# otherwise it is made black. The moving window is a circle with Gaussian +# profile. NOTE: the image MUST have the "objects" or foreground as white +# and the "non-objects" or background as black. Thus the image must either +# be preprocessed using the IM function -negate or have the script do that +# using its negate parameter. IMPORTANT: For acceptable results, the +# window size generally should be larger than the dimension of the +# "objects" to be detected in the image by the thresholding. Consequently, +# this method is best applied to images of text, small objects or edges. +# +# OPTIONS: +# +# -m method ... METHOD specifies what statistical measure to use to +# compute the threshold for each window placement. Method 1 compares +# the center pixel to the window mean, and if larger than the bias, +# the center is made white; otherwise black. Method 2 compares the +# center pixel to the window mean plus the bias times the window +# standard deviation, and if the center pixels is larger, it is made +# white; otherwise black. Method 3 compares the center pixel to the +# window mean plus the bias times the square root of window mean +# absolute deviation and if the center pixel is larger, it is made white; +# otherwise black. The default is method=1. Note that method=1 is similar +# to the IM function -lat (but uses a circular gaussian weighted window +# rather than a square uniform weighted window and more importantly +# does not suffer from the image shift resulting with the IM -lat +# function). +# +# -r radius ... RADIUS specifies the radius for the gaussian profile +# window. The value may be a float, but must be greater than or equal +# to 3. The default=15. For acceptable results, the radius generally +# must be larger than the feature dimension that is to be detected by +# the thresholding. +# +# -b bias ... BIAS is the bias parameter used in each of the two +# methods to determine the threshold. Larger bias values will have +# the effect of removing more "noise" from the result, but too large +# a value may remove parts of the foreground objects that are detected. +# Values for bias are expressed as (percent) floats where bias>=0. +# The default=20. +# +# -n negate ... NEGATE indicates whether to negate the image before +# and after processing, since this technique only works when the "object" +# or foreground is white and the "non-object" or background is black. +# Values may be either yes or no. The default=yes. +# +# REFERENCES: see the following: +# http://www.dfki.uni-kl.de/~shafait/papers/Shafait-efficient-binarization-SPIE08.pdf +# http://www.busim.ee.boun.edu.tr/~sankur/SankurFolder/Threshold_survey.pdf +# +# 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=mean, 2=mean and std, 3=mean and sqrt(mad) +radius=15 #radius>=3 +bias=20 #percent bias>=0 +negate="no" #yes or no + +# 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 10 ] + 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" : '\([0-9]*\)'` + [ "$method" = "" ] && errMsg "--- METHOD=$method MUST BE A NON-NEGATIVE INTEGER ---" + [ $method -lt 1 -o $method -gt 3 ] && errMsg "--- METHOD=$method MUST BE EITHER 1 OR 2 ---" + ;; + -r) # get radius + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID RADIUS SPECIFICATION ---" + checkMinus "$1" + radius=`expr "$1" : '\([.0-9]*\)'` + [ "$radius" = "" ] && errMsg "--- RADIUS=$radius MUST BE A NON-NEGATIVE FLOAT ---" + radiustest=`echo "$radius < 3" | bc` + [ $radiustest -eq 1 ] && errMsg "--- RADIUS=$radius MUST BE A FLOAT GREATER THAN OR EQUAL TO 3 ---" + ;; + -b) # get bias + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID BIAS SPECIFICATION ---" + checkMinus "$1" + bias=`expr "$1" : '\([.0-9]*\)'` + [ "$bias" = "" ] && errMsg "--- BIAS=$bias MUST BE A NON-NEGATIVE FLOAT ---" + ;; + -n) # get negate + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID NEGATE SPECIFICATION ---" + checkMinus "$1" + negate="$1" + negate=`echo "$negate" | tr '[A-Z]' '[a-z]'` + case "$negate" in + yes|y) negate="yes";; + no|n) negate="no";; + *) errMsg "--- NEGATE=$negate MUST BE EITHER YES OR NO ---";; + esac + ;; + -) # 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 +[ "$outfile" = "" ] && errMsg "NO OUTPUT FILE SPECIFIED" + +tmpA1="$dir/autothresh1_A_$$.mpc" +tmpA2="$dir/autothresh1_A_$$.cache" +tmpT1="$dir/autothresh1_T_$$.mpc" +tmpT2="$dir/autothresh1_T_$$.cache" +tmpM1="$dir/autothresh1_M_$$.mpc" +tmpM2="$dir/autothresh1_M_$$.cache" +tmpS1="$dir/autothresh1_S_$$.mpc" +tmpS2="$dir/autothresh1_S_$$.cache" +trap "rm -f $tmpA1 $tmpA2 $tmpT1 $tmpT2 $tmpM1 $tmpM2 $tmpS1 $tmpS2; exit 0" 0 +trap "rm -f $tmpA1 $tmpA2 $tmpT1 $tmpT2 $tmpM1 $tmpM2 $tmpS1 $tmpS2; exit 1" 1 2 3 15 + +# 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 localthresh. +# with IM 6.7.4.10, 6.7.6.10, 6.7.8.10 +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 [ "$im_version" -gt "06080504" ]; then + setcspace="" +fi + + +if convert -quiet "$infile" $setcspace -colorspace gray -alpha off +repage "$tmpA1" + then + : ' do nothing ' +else + errMsg "--- FILE $infile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAG ZERO SIZE ---" +fi + +# setup window filters + radius=`convert xc: -format "%[fx:$radius/3]" info:` + size="0x${radius}" + + +# process image +[ "$negate" = "yes" ] && convert $tmpA1 -negate $tmpA1 + +# get mean image +convert $tmpA1 -blur "$size" $tmpM1 + +# NOTE: to form (image1-image2), +# use convert image2 image1 -compose minus -composite +# or convert image1 image2 +swap -compose minus -composite + +# get sos=second order statistic = either std or sqrt(mad) +if [ $method -eq 2 ]; then + # get standard deviation=std image; std = sqrt( ave(x^2) - ave(x)^2 ); + # ave=mean; -gamma 2 is equivalent to sqrt + convert \( $tmpA1 $tmpA1 -compose multiply -composite -blur "$size" \) \ + \( $tmpM1 $tmpM1 -compose multiply -composite \) +swap \ + -compose minus -composite -gamma 2 $tmpS1 + +elif [ $method -eq 3 ]; then + # get sqrt(mean absolute deviation)=sqrt(mad) image; + # mad=absolute difference of (image - mean) + convert $tmpA1 $tmpM1 -compose difference -composite -gamma 2 $tmpS1 +fi + + +if [ $method -eq 1 ]; then + # threshold to white if image > (mean + K) or + # image - (mean + K) > 0 or + # (image - mean) - K > 0 or + # (image - mean) > K + # where K is percent + #convert $tmpA1 \( $tmpM1 -evaluate add ${bias}% \) +swap -compose minus -composite -threshold 1 $tmpT1 + #convert $tmpA1 $tmpM1 +swap -compose minus -composite -evaluate subtract ${bias}% -threshold 1 $tmpT1 + + convert $tmpA1 $tmpM1 +swap -compose minus -composite -threshold ${bias}% $tmpT1 + +else + # threshold to white if image > (mean +k*sos) or + # image - (mean +k*sos) > 0 or + # (image - mean) - k*sos > 0 + # where k is fraction, k=K/100 and K is percent + + bias=`convert xc: -format "%[fx:$bias/100]" info:` + convert $tmpA1 $tmpM1 +swap -compose minus -composite \ + \( $tmpS1 -evaluate multiply ${bias} \) \ + +swap -compose minus -composite \ + -threshold 1 \ + $tmpT1 +fi + +if [ "$negate" = "yes" ]; then + convert $tmpT1 -negate "$outfile" +else + convert $tmpT1 "$outfile" +fi + +exit 0 |