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-#!/bin/bash
-# A wrapper script to launch imagej from the UNIX command line
-# Images given as arguments will be opened, macros may also be given as arguments
-# Looks for macros in the imagej macro directory
-#
-# This program is free software, but comes with no warrenty or guarantee
-# send bug reports or feedback to jjackson at familyjackson dot net
-# Author: Jon Jackson
-# Last modified date: $Date: 2008-09-17 10:31:27 +0100 (Wed, 17 Sep 2008) $
-# $Revision: 51 $
-#
-# INSTALLATION INSTRUCTIONS
-#
-### WARNING ###########################################################
-# This file must be edited with a program that supports unix new line characters
-# - it won't run if edited in 'Notepad' !
-#######################################################################
-
-# Source location: http://rsb.info.nih.gov/ij/download/linux/unix-script.txt
-# 1) Save this script in the ImageJ directory as 'imagej'
-# 2) Modify path variables according to your system
-# 3) Give the new file execute permission
-# 4) Be sure the 'imagej' wrapper is in the 'PATH'
-
-### MODIFICATION ###
-# With minor modifications to use with Slackware, by Petar Petrov 2012
-# ppetrov at paju dot oulu dot fi
-####################
-
-# setup environment
-set +u # don't give error for unset variables (matters for environment variables)
-shopt -s extglob # allow extended pattern matching
-
-############ SITE SPECIFIC VARIABLES #########################
-# Trailing / is not required for path variables
-# IMAGEJ PATH - production installation
-ij_path='/usr/share/ImageJ'
-# Path to ImageJ development installation
-#ij_path_dev='/home/jjackson/ImageJ'
-# JAVA PATH
-# assumes executable is ${java_home}/bin/java
-# set java_home variables ='' to use JAVA_HOME environment variable
-#if [[ -d /usr/java/jdk1.5 ]] ; then
-# java_home='/usr/java/jdk1.5'
-#else
-# # Optionally specify java path for all available OS / architecture combinations
-# java_home_Linux="${ij_path}/jre"
-# java_home_Linux_x86_64="${ij_path}/jre64"
-# java_home_SunOS="${ij_path}/jre64"
-# #
-#fi
-ijadmin=''
-# DOCUMENTATION URL
-doc_url='http://rsb.info.nih.gov/ij/'
-
-# TEMP FOLDER
-ij_tmp='/tmp/imagej'
-# LOG FILE
-#ij_log="${ij_tmp}/log.txt"
-# default behaviour when an ImageJ window is already open
-newwindow='true'
-#newwindow='false'
-# macro argument delimiter character
-separator=':'
-# a ' ' may work provided no arguments would contain spaces
-# use macro functions: args=getArgument(); argArray=split(args, ':');
-# to recover macro arguments
-
-############ 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
-
-############ SITE SPECIFIC MODULES #########################
-
-# JAR libraries for additional modules may be placed in ${ij_path}/lib
-# jmf.jar jai_codec.jar jai_core.jar mlibwrapper_jai.jar
-
-# Native libraries may be placed in ${ij_path}/lib/$OS
-# where OS matches the output of the 'uname' command
-
-############ END SITE SPECIFIC VARIABLES #########################
-
-OS=$(uname)
-processor=$(uname -m) # -p doesn't work on 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
-
-
-# if tools.jar is not in ${ij_path}/jre/lib/ext/ edit the 'tools=' line
-# to point to tools.jar. The -compile switch will load tools.jar into the
-# classpath and enable plugins to be compiled in imagej
-
-if [[ -f "${ij_path}/tools.jar" ]] ; then
- tools="${ij_path}/tools.jar"
-else
- tools=''
-fi
-
-# End Site specific variables ---------------------------------------------------------
-
-# other variables
-dir=`pwd`
-user=`whoami`
-host=`hostname`
-if [[ -z "$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="$DISPLAY"
-fi
-
-declare -i port=0
-declare -i verbosity=0
-images=''
-macrocmd=''
-macroargs=''
-
-
-function usage {
- echo
- echo 'Image display and analysis program. Opens formats including:'
- echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
- echo
- echo 'imagej [options] image [ image2 ... image3 ]'
- echo ' -h print help and more options'
- echo ' -o open images in an open ImageJ panel'
- echo ' -p <N> open images in ImageJ panel number <N>'
- echo " -x <MB> set available memory (default=${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
-}
-
-
-# parse input arguments
-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
-
-#for ((i=1; i < $OPTIND; i++))
-#do
-# shift
-#done
-## above syntax not supported in bash < 2.05
-declare -i i=1
-while (( i < $OPTIND )) ; do
- shift
- i=i+1
-done
-
-if [[ "$#" == 0 && -z "$macrocmd" ]] ; then
- usage
-fi
-
-# 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
-
-# -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}'$filearg' "
- shift
- done
-fi
-
-# CREATE IMAGEJ SOCKET-LOCK DIRECTORY IF NON EXISTANT
-if [[ ! -d "$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 "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null
- if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
- touch $lockname
- trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; [[ -n "$ij_log" ]] && echo -e "$$\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
-
-if (( $verbosity > 0 )) ; then
- echo ${JAVA_HOME}/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs}
-fi
-
-cd "$dir"
-eval "${JAVA_HOME}/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs} "
-exit 0
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