diverse:commandline:imagej
Table of Contents
Wrapper script for ImageJ
Description
A command line wrapper script to launch ImageJ on Linux / Mac OS / Cygwin platforms, with the following features
- Open images from the command line
- Launch macros / execute commands
- Send images / commands to running ImageJ windows
- Set available memory
Author
Jonathan Jackson (jjackson a.t familyjackson dot net)
Change List
- 2008-12-04: First posted on the ImageJ Wiki
- 2009-08-21: Now works with MacOS X (tested on 10.5). Fixed bug with assignment of lock files to open ports.
Limitations
- Can't open files in existing ImageJ panel on MacOS X
- Not tested on Cygwin
Usage
#!/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: 2008-12-04 18:38:47 +0000 (Thu, 04 Dec 2008) $ # $Revision: 64 $ # # INSTALLATION INSTRUCTIONS # ### WARNING ########################################################### # This file won't run if edited in 'Notepad' or similar programs # that don't support unix new line characters ####################################################################### # 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' ### DEPENDENCIES ###################################################### # readlink: This script works better with GNU readlink, which is not # installed by default on MacOS (or Solaris 8) # MacOS X: readlink can be installed with 'MacPorts': # Install MacPorts and Apple xCode, then run # 'sudo port install coreutils' and set the PATH variable appropriately # ALL: If no version of readlink is avaliable, hard code the ij_path and ij_jar_paths # sending images to a running ImageJ panel may not work (around line 357) ####################################################################### # setup environment set +u # don't give error for unset variables (matters for environment variables) shopt -s extglob # allow extended pattern matching shopt -s expand_aliases # Detect readlink version # if GNU readlink is known to be installed, this code can be replaced by "alias ReadLink='readlink -f'" alias ReadLink='readlink' # Default if [[ $(uname) == Darwin ]] && which greadlink &>/dev/null ; then # Using GNU readlink on MacOS X alias ReadLink='greadlink -f' elif [[ -f $(which readlink) ]] && readlink --version | grep coreutils &>/dev/null ; then alias ReadLink='readlink -f' # use GNU readlink else alias ReadLink='echo' echo "Please install GNU readlink. Symbolic links may not be resolved properly" >&2 fi ############ SITE SPECIFIC VARIABLES ######################### # Trailing / is not required for path variables # IMAGEJ PATH - production installation #ij_path='/local/ImageJ' ij_path="$(dirname $(ReadLink $0))" # IMAGEJ PATH - development installation (optional) ij_path_dev='/Users/jjackson/ImageJ' # JAVA PATH # assumes executable is ${java_home}/bin/java # set java_home variables ='' to use JAVA_HOME environment variable # Get a sensible default if which java > /dev/null ; then java_home="$(dirname $(ReadLink $(which java)))" fi # The following allow platform specific defaults for the java path # these take preference over the default if set if [[ -d /usr/java/jdk1.6_x64 ]] ; then java_home='/usr/java/jdk1.5' java_home_Linux_x86_64='/usr/java/jdk1.5' java_home_dev='/usr/java/jdk1.6_x64' else # Optionally specify java path for all available OS / architecture combinations java_home_Linux="${ij_path}/jre" java_home_Linux_x86_64="${ij_path}/jre64" java_home_SunOS="${ij_path}/jre64" java_home_Darwin="" # fi ijadmin='j.jackson AT ion.ucl.ac.uk' # DOCUMENTATION URL #doc_url='http://rsb.info.nih.gov/ij/' doc_url='http://saturn/~jjackson/imagej' # 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=900 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 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($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'` else java_arch='-d32' JAVA_HOME="${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($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'` fi elif [[ "$OS" == Darwin ]] ; then java_arch='-d64' JAVA_HOME="${java_home_Darwin:-$java_home}" max_mem=`vm_stat | awk 'NR == 2 {free=$3} NR == 3 {active=$3} NR == 4 {inactive=$3} END{print int((free+active+inactive)/256)}'` free_mem=`vm_stat | awk 'BEGIN{maxMem='$max_64bit'} NR == 2 {fmem=int($3 / 256)} NR == 4 {imem=int($3 / 256)} END{amem=fmem+imem ; if (amem < maxMem) {print amem} else {print maxMem}}'` fi mem=${free_mem}/3*2 (( $mem > $default_mem || $mem < $min_mem )) && mem=$default_mem if [[ -f ${JAVA_HOME}/bin/java ]] ; then JAVA=${JAVA_HOME}/bin/java else JAVA=${JAVA_HOME}/java unset JAVA_HOME # confuses Mac java 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="${ij_path}/tools.jar" else tools='' fi # End Site specific variables --------------------------------------------------------- # other variables dir=`pwd` user=`whoami` host=`hostname` # `hostname -s` is better but not solaris 8 compat. if [[ -z "$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="${DISPLAY##*/}" # display variable on Darwin can look like this: '/tmp/launch-si9S06/:0' fi declare -i port=0 declare -i verbosity=0 declare -i max_attempts=10 images='' macrocmd='' macroargs='' function usage { echo echo 'Image display and analysis program. Opens formats including:' echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...' echo echo 'imagej [options] image [ image2 ... image3 ]' echo ' -h print help and more options' echo ' -o open images in an open ImageJ panel' echo ' -p <N> open images in ImageJ panel number <N>' echo " -x <MB> set available memory (default=${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=${max_mem})" echo echo 'advanced options:' echo ' -c enable plugin compilation within imagej' echo ' -d use development version' echo " -j use development java version ($java_home_dev)" 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 echo "Macro commands can't be used with the '-o' option" 1>&2 exit 1 } # parse input arguments while getopts b:cde:hi:jm:nop:r:vx: options do case $options in b) [[ -n "$macrocmd" ]] && macroCmdError # exits macrocmd="-batch ${OPTARG}" display='batch' newwindow='false' ;; c) modules="${modules:-}${modules+:}${tools}" ;; d) ij_path="$ij_path_dev" ;; e) [[ -n "$macrocmd" ]] && macroCmdError # exits macrocmd='-eval' macroargs="'${OPTARG}'" ;; h) fullusage exit 0 ;; i) images="${images}'${OPTARG}' " ;; j) JAVA_HOME="$java_home_dev" ;; m) [[ -n "$macrocmd" ]] && macroCmdError # exits macrocmd="-macro ${OPTARG}" ;; n) newwindow='true' ;; o) [[ -n "$macrocmd" ]] && macroCmdError # exits 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) [[ -n "$macrocmd" ]] && macroCmdError # exits macrocmd='-run' macroargs="'${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 && -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 ${ij_path}/jre/lib/ext/ or add the .jar # filepath to the modules line below. Paths are separated by a colon # Classpath must follow command line arguments, as ij_path is dependent on the -d option # Resolving ij.jar path. If ij.jar is a symbolic link to ij_<version>.jar # this allows updating ij.jar without crashing running sessions ij_jar_path=$(ReadLink ${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'" # if user hasn't requested a specific port number # and it's not a batch mode macro, set display to 'macro' # to prevent other instances accessing this ImageJ window if [[ "$display" != "batch" && "$port" == 0 ]] ; then display="macro" newwindow='true' # should be redundant fi fi # PROTECT POSSIBLE SPACES IN IMAGE FILENAMES if (( "$#" > 0 )) ; then while (( "$#" > 0 )) ; do filearg="${1}" if [[ ! -f "$filearg" ]] ; then echo "Warning: image '$filearg' may not exist" >&2 fi # full file path required when sending images to running ImageJ panel if [[ "${newwindow}" == 'false' && -f "${filearg}" ]] && ! expr "${filearg}" : '/.*' > /dev/null; then filearg="$(ReadLink ${filearg})" fi images="${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 declare -i attempts=0 while [[ "$portopen" == 'false' ]] ; do # new window requested or no matching port found # if port is not specified, look for first free port if (( "$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 "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null (( $verbosity > 0 )) && echo -n "creating lock $lockname ... " echo $$ > $lockname 2> /dev/null if [[ "$(head -n 1 $lockname 2> /dev/null)" == $$ ]] ; then # port lock successful trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; [[ -n "$ij_log" ]] && echo -e "$$\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??) portopen='true' 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 "$$\t$(date)\tSocket lock:\t$lockname" >> "$ij_log" 2> /dev/null if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi echo else # port lock unsuccessful (simultaneous instances?) [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tAttempted lock failed\t$lockname" >> "$ij_log" 2> /dev/null if (( $attempts > $max_attempts )) ; then echo "Failed to secure a port lock for ImageJ after $max_attempts" >&2 [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tGiving up\t$lockname" >> "$ij_log" 2> /dev/null fi # REREAD LOCK LIST declare -a locklist=(`ls | grep '[0-9][0-9]-.*'`) fi attempts=$attempts+1 done if (( $verbosity > 0 )) ; then echo ${JAVA} ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs} fi cd "$dir" eval "${JAVA} ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs} " exit 0
diverse/commandline/imagej.txt ยท Last modified: 2019/04/12 13:13 by 127.0.0.1