Initial import

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+#!/bin/bash
+
+# imagej.sh - a not so simple wrapper script used to run ImageJ
+#
+#   Copyright 2008 Paolo Ariano
+#   Authors: Paolo Ariano (paolo dot ariano at unito dot it)
+#   Last modified date: 19 Sept 2008
+#
+# This is a not so simple wrapper script used to run ImageJ in Unix but 
+# optimized for Debian GNU/Linux, this is a merge between my original script 
+# and a more exhaustive one from Jon Jackson (jjackson at familyjackson dot net)
+
+# Adapted for use with ArchLinux
+
+#   Edited 2009 Giulio Guzzinati
+#   Authors: Giulio Guzzinati (guzzinati.giulio at gmail)
+#   Last modified date: 24 May 2009
+
+#   Edited 2012/13 Michael Schubert
+#   Authors: Michael Schubert (mschu.dev at gmail)
+#   Last modified date: 17 Feb 2013
+
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public Licenseas published by
+# the Free Software Foundation, either version 3 of the License, or (at 
+# your option) any later version. See the file Documentation/LGPL3 in the
+# original distribution for details. There is ABSOLUTELY NO warranty.
+# This program is free software, but comes with no warrenty or guarantee
+# send bug reports or feedback to me or to debian bug tracking system
+
+
+# setup environment
+# dont give error for unset variables (matters for environment variables)
+set +u
+# allow extended pattern matching
+shopt -s extglob
+
+##################### CREATE THE RIGHT ENVIRONMENT #####################
+
+# ImageJ path
+ij_path=/usr/share/imagej
+
+#ImageJ user path
+ij_user_path=$HOME/.imagej
+
+# Documentation URL
+doc_url='http://rsb.info.nih.gov/ij/'
+
+# temp folder
+ij_tmp='/tmp/imagej'
+
+# default behaviour when an ImageJ window is already open
+newwindow='true'
+#newwindow='false'
+
+# macro argument conjoining character
+separator=':'
+# a ' ' may work provided no arguments would contain spaces
+# use macro functions:  args=getArgument(); argArray=split(args, ':'); 
+# to recover macro arguments
+
+# create plugins,macro,tmp dirs 
+mkdir -p ${ij_user_path}/{plugins,macros,luts}
+
+# makes symbolik links from shared plugins, macros and luts 
+find ${ij_path}/{plugins,macros,luts} -maxdepth 1 -mindepth 1 | while read p; do
+    if [ ! -e "${p/$ij_path/$ij_user_path}" ] ; then
+        ln -s "$p" "${p/$ij_path/$ij_user_path}"
+    fi
+done
+
+# remove symlinks for files that do no longer exist
+find ${ij_user_path} -type l | while read p; do
+    if ! readlink -qe "$p" > /dev/null; then 
+        rm "$p"
+    fi
+done
+
+# report errors to this user
+# ijadmin='paolo.ariano@unito.it'
+
+# other variables 
+dir=`pwd`
+user=`whoami`
+host=`hostname`
+if [[ -z "$DISPLAY" ]] ; then
+    echo 'Display variable not set'
+    echo 'If ImageJ fails to load, try '
+    echo '% setenv DISPLAY yourcomputer:0'
+    echo 'if you use the "csh" or for "bash" try'
+    echo '% export DISPLAY=yourcomputer:0'
+    display='default' 
+else
+    display="$DISPLAY"
+fi
+
+declare -i port=0
+declare -i verbosity=0
+images=''
+macrocmd=''
+macroargs=''
+
+############ DEFAULT MEMORY SETTINGS  #########################
+
+declare -i default_mem=768
+declare -i min_mem=32
+declare -i max_32bit=1800 # empirical
+declare -i max_64bit=17000000000 # conservative
+
+############ MEMORY ALLOCATION #########################
+
+OS=$(uname)
+processor=$(uname -m) # -p doesn't work on debian/ubuntu
+declare -i mem
+declare -i max_mem
+declare -i free_mem
+
+java_home="${java_home:-$JAVA_HOME}"
+
+if [[ "$OS" == 'SunOS' ]] ; then
+    java_arch='-d64'
+    JAVA_HOME="${java_home_SunOS:-$java_home}"  
+    max_mem=`vmstat | awk 'BEGIN{maxMem='$max_64bit'} NR == 3 {fmem=int($5 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
+    free_mem="max_mem"
+    mem=${free_mem}/2
+    if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
+elif [[ "$OS" == 'Linux' ]] ; then
+    if [[ "$processor" == 'x86_64' ]] ; then
+        java_arch='-d64'
+        JAVA_HOME="${java_home_Linux_x86_64:-$java_home}"
+        max_mem=`free | awk -v maxMem=$max_64bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
+        free_mem=`free | awk -v maxMem=$max_64bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
+        mem=${free_mem}/3*2
+        if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
+    else
+        java_arch='-d32'
+        JAVA_HOME="${java_home_Linux:-$java_home}"
+        max_mem=`free | awk -v maxMem=$max_32bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
+        free_mem=`free | awk -v maxMem=$max_32bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
+        mem=${free_mem}/3*2
+        if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi    
+    fi
+fi
+
+
+##################### USAGE DESCRIPTION #####################
+
+function usage {
+    echo 
+    echo 'Image display and analysis program. Opens formats including:'
+    echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'  
+    echo
+    echo 'imagej [options] image [ image2 ... image3 ]'
+    echo '    -h        print help and more options'
+    echo '    -o        open images in an open ImageJ panel'
+    echo '    -p <N>    open images in ImageJ panel number <N>' 
+    echo "    -x <MB>   set available memory (default=${mem} max=${max_mem})"     
+    echo 
+}
+
+function fullusage {
+    echo 
+    echo 'Image display and analysis program. Opens formats including:'
+    echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'  
+    echo 
+    echo 'imagej [options] image [ image2 ... image3 ] -> open images'
+    echo
+    echo 'basic options:'
+    echo '  -h        print help and more options'
+    echo '  -o        open images in existing ImageJ panel if one exists'
+    echo '  -p <N>    open images in existing ImageJ panel number <N>' 
+    echo "  -x <MB>   set available memory (default=${mem} max=${max_mem})"
+    echo
+    echo 'advanced options:'
+    echo '  -c        enable plugin compilation within imagej'
+    echo '  -d        use development version'
+    echo '  -v        be verbose (vv or vvv increases verbosity)'  
+    echo
+    echo 'options for batch processing:'
+    echo "  -e 'Macro Code'            execute macro code"
+    echo "  -r 'Menu Command'          run menu command"
+    echo "Quotation marks '' are required around commands including spaces"
+    echo 'Commands can be sent to open ImageJ panels with the -p option'
+    echo 
+    echo 'options for macros:'
+    echo 'imagej [-i image] [-b|-m] [arg1 ... argN] '
+    echo '  -b macro    run macro without graphics window' 
+    echo '  -m macro    run macro' 
+    echo '"image" will be opened before macro is run'
+    echo 'all following arguments are passed to macro'        
+    echo 
+    echo "Documentation - $doc_url "
+    echo "Report problems with this software to $ijadmin"
+    echo
+}
+
+function macroCmdError {
+    fullusage 
+    echo 'Only one command option (-b -e -m OR -r) may be specified' 1>&2
+    exit 1
+}
+
+function getFullPath {
+    # Return full path to file
+    # treats multiple arguments as a single file with spaces
+    if (( $# == 0 )) ; then
+        echo "error getting full path for '${*}'" 1>&2
+    fi
+    pwd_getFullPath="$PWD"
+    \cd $(dirname "${*}") > /dev/null
+    dir_getFullPath="$PWD"
+    \cd "$pwd_getFullPath" > /dev/null
+    echo "$dir_getFullPath"/$(basename "${*}")
+}
+function derefln { 
+    # Returns the full path of file to which link points
+    # following multiple levels of symbolic links.
+    # NOTE: if you use this function in a script, don't use any
+    # of the variable names used here
+    if (( $# == 0 )) ; then
+        return
+    fi
+    local the_link="$1"
+    local link_dir 
+    local current_dir="$PWD"
+    while file "$the_link" | grep symbolic > /dev/null ; do # resolve links until target is regular file
+        if [[ "$the_link" == */* ]] ; then # path contains  /
+            \cd $(dirname "${the_link}") > /dev/null
+            the_link=$(basename "$the_link")
+        fi
+        link_dir="$PWD" 
+        # some versions of 'file' surround the path in `' quotes, hence the tr to remove them
+        the_link=$(file "${the_link}" | awk '/symbolic link/ {print $NF}' | tr -d "\140\047" )
+        if [[ "$the_link" != /* ]] ; then # path is not absolute path  - make it one
+            the_link="$link_dir/$the_link"
+        fi
+        \cd "$current_dir" > /dev/null
+    done 
+    echo $the_link
+}
+
+
+# The best way to install .jar libraries required by plugins is to copy them 
+# to the imagej plugins/jars directory
+# Alternatively, either copy them to ${ij_path}/jre/lib/ext/ or add the .jar
+# filepath to the modules line below. Paths are separated by a colon
+# Classpath must follow command line arguments, as ij_path is dependent on the -d option
+
+# Resolving ij.jar path.  If ij.jar is a symbolic link to ij_<version>.jar
+# this allows updating ij.jar without crashing running sessions
+ij_jar_path=$(derefln ${ij_path}/ij.jar)    
+                                         
+for mod_jar in ${ij_path}/lib/*jar  ; do
+    modules="${modules:-}${modules+:}$mod_jar"
+done
+modules="-cp ${ij_jar_path}:${modules+:}${modules:-}"
+#${ij_path}/plugins/jars/dcmie.jar
+
+export LD_LIBRARY_PATH="${ij_path}/lib/${OS}_$processor"
+if (( $verbosity > 0 )) ; then
+    echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
+fi
+ 
+# enable plugins to be compiled in imagej
+tools="$JAVA_HOME/lib/tools.jar"
+
+
+#####################  ARGUMENTS PARSING #####################
+
+while getopts b:cde:hi:m:nop:r:vx: options
+do
+    case $options in
+        b)  if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
+            macrocmd="-batch ${OPTARG}"
+            ;;
+        c)  modules="${modules:-}${modules+:}${tools}"
+            ;;
+        d)  ij_path="$ij_path_dev"
+            ;;
+        e)  if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
+            macrocmd='-eval'
+            macroargs="'${OPTARG}'"
+            ;;
+        h)  fullusage
+            exit 0
+            ;;
+        i)  images="${images}'${OPTARG}' "
+            ;;
+        m)  if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
+            macrocmd="-macro ${OPTARG}"
+            ;;
+        n)  newwindow='true'
+            ;;
+        o)  newwindow='false'
+            ;;
+        p)  newwindow='false'
+            port="${OPTARG}"
+            if (( "$port" < 1 || "$port" > 99 )) ; then
+                echo "${OPTARG} is not a permissible value for port number (-p)" 1>&2
+                exit 1
+            fi
+            ;;
+        r)  if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
+            macrocmd='-run'
+            macroargs="'${OPTARG}'"
+            ;;
+        v)  verbosity=verbosity+1
+            if (( $verbosity == 2 )) ; then set -x ; fi
+            if (( $verbosity == 3 )) ; then set -v ; fi
+            ;;
+        x)  mem="${OPTARG}"
+            newwindow='true'
+            if (( $mem < $min_mem || $mem > $max_mem )) ; then
+                echo "${OPTARG} is not a permissible value for memory (-x)" 1>&2
+                echo "min=${min_mem}, max=${max_mem}" 1>&2
+                exit 1              
+            fi
+            ;;
+        \?) usage
+            exit 1 
+            ;;
+    esac
+done
+            
+        
+declare -i i=1
+while (( i < $OPTIND )) ; do
+    shift
+    i=i+1
+done
+
+#if (( "$#" == 0 )) ; then
+#   usage
+#fi 
+
+# -b and -m options only:
+# remaining command line arguments are passed as macro arguments 
+# separated by $separator
+if [[ -n "$macrocmd" && -z "$macroargs" ]] ; then
+    while (( "$#" > 0 )) ; do
+        if [[ -z "$macroargs" ]] ; then 
+            macroargs="${1}"
+        else
+            macroargs="${macroargs}${separator}${1}"
+        fi
+        shift       
+    done
+    macroargs="'$macroargs'"
+fi
+    
+# PROTECT POSSIBLE SPACES IN IMAGE FILENAMES
+if (( "$#" > 0 )) ; then
+    while (( "$#" > 0 )) ; do
+        filearg="${1}"
+        # full file path required when sending images to running ImageJ panel
+        if [[ "${newwindow}" == 'false' && -f "${filearg}" ]]  && ! expr "${filearg}" : '/.*' > /dev/null; then 
+            filearg="$(getFullPath ${filearg})"
+        fi
+        images="${images}'$filearg' "
+        shift 
+    done
+fi  
+
+##################### USING PORT #####################
+
+# CREATE IMAGEJ SOCKET-LOCK DIRECTORY IF NON EXISTANT 
+if [[ ! -d "$ij_tmp" ]] ; then
+    mkdir "$ij_tmp"
+    chmod 777 "$ij_tmp"
+fi
+
+# CREATE IMAGEJ LOG FILE IF NON EXISTANT 
+if [[ -n "$ij_log" && ! -f "$ij_log" ]] ; then
+    touch "$ij_log"
+    chmod 666 "$ij_log"
+fi
+
+# CREATES A TEMP FILE INDICATING A PORT IS IN USE BY IMAGEJ
+cd "$ij_tmp"
+declare -i count=1
+portopen='false'
+lockFileCreated='false'
+declare -a locklist=(`ls | grep '[0-9][0-9]-.*'`)
+
+[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tNew Window = $newwindow" >> "$ij_log" 2> /dev/null
+[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tPort = $port" >> "$ij_log" 2> /dev/null
+[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tlocklist: \n ${locklist[*]}" >> "$ij_log" 2> /dev/null
+if (( $verbosity > 0 )) ; then echo -e "locklist: \n ${locklist[*]}" ; fi
+
+# PORT SPECIFIED BY USER
+if (( $port > 0 )) ; then
+    # look for a lock on the port specified
+    for lockname in ${locklist[*]} ; do
+        prefix=`printf '%02u' $port`
+        if [[ "$lockname" == ${prefix}-${user}-${host}* ]] ; then
+            # found lock on the requested port, owned by user on current display
+            portopen='true'
+            if (( $verbosity > 0 )) ; then echo "Using socket lock: $lockname" ; fi
+            count=$port
+            break
+        elif [[ "$lockname" == ${prefix}-* ]] ; then
+            echo "Port $port is in use by some other user or a different host" 1>&2
+            if (( $verbosity > 0 )) ; then echo "Port lock: $lockname" ; fi
+            exit 1
+        fi
+    done 
+    # specified port not in use 
+    count=$port
+
+# IF EXISTING WINDOW IS REQUESTED, LOOK FOR LISTENING PORT
+elif [[ "$newwindow" == 'false' && ${#locklist} != 0 ]] ; then
+    # look for a lock on the current display for this user
+    for lockname in ${locklist[*]} ; do
+        if [[ "$lockname" == [0-9][0-9]-${user}-${host}-${display} ]] ; then
+            portopen='true'
+            if (( $verbosity > 0 )) ; then echo "Found socket lock: $lockname" ; fi
+            # if a matching user/display is found, use this one
+            count="${lockname%-*-*-*}"
+            #count=`echo $lockname | sed  -e 's/^\([0-9][0-9]\).*/\1/' -e 's/^0//'` # csh?
+            break
+        fi
+    done
+fi
+
+# IF A NEW PORT IS TO BE USED
+if [[ "$portopen" == 'false' ]] ; then
+    # new window requested or no matching port found
+    # if port is not specified, look for first free port
+    if (( "$port" == 0 )) ; then 
+        if (( ${#locklist} == 0 )) ; then
+            # no active locks - use first port
+            count=1
+        else
+            # active locks - check each port number so see if it is in use
+            # this is not synchronised!!
+            count=0
+            inuse='true'
+            while [[ "$inuse" == 'true' ]] ; do
+                count=count+1
+                prefix=`printf '%02u' $count`
+                inuse='false'
+                for lockname in ${locklist[*]} ; do
+                    if [[ "$lockname" == ${prefix}-* ]] ; then
+                        inuse='true'
+                    fi
+                done
+            done
+        fi
+    fi
+    # CREATING A NEW PORT LOCK
+    prefix=`printf '%02u' $count`
+    lockname=${prefix}-${user}-${host}-${display}
+    
+    [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null
+    if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
+    touch $lockname
+    trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; echo -e "$$\t$(date)\tReleasing lock\t$lockname" >> "$ij_log" 2> /dev/null' EXIT TERM KILL 
+    # Quitting ImageJ sends EXIT, as does a kill/kill -9 
+    # CTRL+C in terminal sends INT + EXIT
+    # System shutdown sends TERM (+EXIT??)
+    
+    if (( $verbosity > 0 )) ; then  echo 'done' ; fi
+
+    lockFileCreated='true'
+    if [[ -z "$macrocmd" ]] ; then 
+        echo 'Open other images in this ImageJ panel as follows:'
+        echo "  imagej -p $count <image1> [<image2> ... <imageN>]"
+    fi
+    [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tSocket lock:\t$lockname" >> "$ij_log" 2> /dev/null
+    if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi
+    echo
+fi
+
+##################### FINALLY RUN IMAGEJ #####################
+
+eval java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
+
+exit 0
+