imagej/imagej

   1 #!/bin/bash
   2
   3 # imagej.sh - a not so simple wrapper script used to run ImageJ
   4
   5 #       Copyright © 2008 Paolo Ariano
   6 #       Authors: Paolo Ariano (paolo dot ariano at unito dot it)
   7 #       Last modified date: 19 Sept 2008
   8
   9 # This is a not so simple wrapper script used to run ImageJ in Unix but
  10 # optimized for Debian GNU/Linux, this is a merge between my original script
  11 # and a more exhaustive one from Jon Jackson (jjackson at familyjackson dot net)
  12
  13 #       Edited 2009 Giulio Guzzinati
  14 #       Authors: Giulio Guzzinati (skarn86junk () gmail DOT it)
  15 #       Last modified date: 24 May 2009
  16
  17 #This script has been edited for usage with Arch Linux by Giulio Guzzinati
  18
  19 # This program is free software; you can redistribute it and/or modify it
  20 # under the terms of the GNU Lesser General Public Licenseas published by
  21 # the Free Software Foundation, either version 3 of the License, or (at
  22 # your option) any later version. See the file Documentation/LGPL3 in the
  23 # original distribution for details. There is ABSOLUTELY NO warranty.
  24 # This program is free software, but comes with no warrenty or guarantee
  25 # send bug reports or feedback to me or to debian bug tracking system
  26
  27
  28 # setup environment
  29 set +u # don't give error for unset variables (matters for environment variables)
  30 shopt -s extglob # allow extended pattern matching
  31
  32 ##################### DEFINE JAVA_HOME #####################
  33
  34 if [ -z "/opt/java/jre"  ] ; then
  35     JAVA_HOME=$(/opt/java/jre -l | head -1 | cut -d' ' -f 3)
  36 else
  37         JAVA_HOME=$(/usr -l | head -1 | cut -d' ' -f 3)
  38 fi
  39
  40
  41 ##################### CREATE THE RIGHT ENVIRONMENT #####################
  42
  43 # ImageJ path
  44 ij_path=/usr/share/imagej
  45
  46 #ImageJ user path
  47 ij_user_path=$HOME/.imagej
  48
  49 # Documentation URL
  50 doc_url='http://rsb.info.nih.gov/ij/'
  51
  52 # temp folder
  53 ij_tmp='/tmp/imagej'
  54
  55 # default behaviour when an ImageJ window is already open
  56 newwindow='true'
  57 #newwindow='false'
  58
  59 # macro argument conjoining character
  60 separator=':'
  61 # a ' ' may work provided no arguments would contain spaces
  62 # use macro functions:  args=getArgument(); argArray=split(args, ':');
  63 # to recover macro arguments
  64
  65 # create plugins,macro,tmp dirs
  66 mkdir -p ${ij_user_path}/plugins
  67 mkdir -p ${ij_user_path}/macros
  68 mkdir -p ${ij_user_path}/luts
  69
  70 # makes symbolik links from shared plugins, macros and luts
  71
  72 ls ${ij_path}/plugins | while read p ; do
  73   if [ ! -e "${ij_user_path}/plugins/$p" ] ; then
  74     ln -s ${ij_path}/plugins/$p ${ij_user_path}/plugins/$p
  75   fi
  76 done
  77
  78 ls ${ij_path}/macros | while read p; do
  79   if [ ! -e "${ij_user_path}/macros/$p" ] ; then
  80       ln -s ${ij_path}/macros/$p ${ij_user_path}/macros/$p
  81   fi
  82 done
  83
  84 ls ${ij_path}/luts | while read p ; do
  85     if [ ! -e "${ij_user_path}/luts/$p" ] ; then
  86         ln -s ${ij_path}/luts/$p ${ij_user_path}/luts/$p
  87     fi
  88 done
  89
  90
  91 # report errors to this user
  92 # ijadmin='paolo.ariano@unito.it'
  93
  94 # other variables
  95 dir=`pwd`
  96 user=`whoami`
  97 host=`hostname`
  98 if [[ -z "$DISPLAY" ]] ; then
  99     echo 'Display variable not set'
 100     echo 'If ImageJ fails to load, try '
 101     echo '% setenv DISPLAY yourcomputer:0'
 102     echo 'if you use the "csh" or for "bash" try'
 103     echo '% export DISPLAY=yourcomputer:0'
 104     display='default'
 105 else
 106     display="$DISPLAY"
 107 fi
 108
 109 declare -i port=0
 110 declare -i verbosity=0
 111 images=''
 112 macrocmd=''
 113 macroargs=''
 114
 115 ############ DEFAULT MEMORY SETTINGS  #########################
 116
 117 declare -i default_mem=768
 118 declare -i min_mem=32
 119 declare -i max_32bit=1800 # empirical
 120 declare -i max_64bit=17000000000 # conservative
 121
 122 ############ MEMORY ALLOCATION #########################
 123
 124 OS=$(uname)
 125 processor=$(uname -m) # -p doesn't work on debian/ubuntu
 126 declare -i mem
 127 declare -i max_mem
 128 declare -i free_mem
 129
 130 java_home="${java_home:-$JAVA_HOME}"
 131
 132 if [[ "$OS" == 'SunOS' ]] ; then
 133     java_arch='-d64'
 134         JAVA_HOME="${java_home_SunOS:-$java_home}"
 135         max_mem=`vmstat | awk 'BEGIN{maxMem='$max_64bit'} NR == 3 {fmem=int($5 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
 136         free_mem="max_mem"
 137         mem=${free_mem}/2
 138         if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
 139 elif [[ "$OS" == 'Linux' ]] ; then
 140         if [[ "$processor" == 'x86_64' ]] ; then
 141         java_arch='-d64'
 142         JAVA_HOME="${java_home_Linux_x86_64:-$java_home}"
 143         max_mem=`free | awk -v maxMem=$max_64bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
 144                 free_mem=`free | awk -v maxMem=$max_64bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
 145                 mem=${free_mem}/3*2
 146                 if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
 147         else
 148                 java_arch='-d32'
 149         JAVA_HOME="${java_home_Linux:-$java_home}"
 150         max_mem=`free | awk -v maxMem=$max_32bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
 151                 free_mem=`free | awk -v maxMem=$max_32bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
 152                 mem=${free_mem}/3*2
 153                 if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
 154         fi
 155 fi
 156
 157
 158 ##################### USAGE DESCRIPTION #####################
 159
 160 function usage {
 161     echo
 162     echo 'Image display and analysis program. Opens formats including:'
 163     echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
 164     echo
 165     echo 'imagej [options] image [ image2 ... image3 ]'
 166     echo '    -h        print help and more options'
 167     echo '    -o        open images in an open ImageJ panel'
 168     echo '    -p <N>    open images in ImageJ panel number <N>'
 169     echo "    -x <MB>   set available memory (default=${mem} max=${max_mem})"
 170     echo
 171 }
 172
 173 function fullusage {
 174     echo
 175     echo 'Image display and analysis program. Opens formats including:'
 176     echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
 177     echo
 178     echo 'imagej [options] image [ image2 ... image3 ] -> open images'
 179     echo
 180     echo 'basic options:'
 181     echo '  -h        print help and more options'
 182     echo '  -o        open images in existing ImageJ panel if one exists'
 183     echo '  -p <N>    open images in existing ImageJ panel number <N>'
 184     echo "  -x <MB>   set available memory (default=${mem} max=${max_mem})"
 185     echo
 186     echo 'advanced options:'
 187     echo '  -c        enable plugin compilation within imagej'
 188     echo '  -d        use development version'
 189     echo '  -v        be verbose (vv or vvv increases verbosity)'
 190     echo
 191     echo 'options for batch processing:'
 192     echo "  -e 'Macro Code'            execute macro code"
 193     echo "  -r 'Menu Command'          run menu command"
 194     echo "Quotation marks '' are required around commands including spaces"
 195     echo 'Commands can be sent to open ImageJ panels with the -p option'
 196     echo
 197     echo 'options for macros:'
 198     echo 'imagej [-i image] [-b|-m] [arg1 ... argN] '
 199     echo '  -b macro    run macro without graphics window'
 200     echo '  -m macro    run macro'
 201     echo '"image" will be opened before macro is run'
 202     echo 'all following arguments are passed to macro'
 203     echo
 204     echo "Documentation - $doc_url "
 205         echo "Report problems with this software to $ijadmin"
 206     echo
 207 }
 208
 209 function macroCmdError {
 210         fullusage
 211         echo 'Only one command option (-b -e -m OR -r) may be specified' 1>&2
 212         exit 1
 213 }
 214
 215 function getFullPath {
 216     # Return full path to file
 217     # treats multiple arguments as a single file with spaces
 218     if (( $# == 0 )) ; then
 219         echo "error getting full path for '${*}'" 1>&2
 220     fi
 221     pwd_getFullPath="$PWD"
 222     \cd $(dirname "${*}") > /dev/null
 223     dir_getFullPath="$PWD"
 224     \cd "$pwd_getFullPath" > /dev/null
 225     echo "$dir_getFullPath"/$(basename "${*}")
 226 }
 227 function derefln {
 228     # Returns the full path of file to which link points
 229     # following multiple levels of symbolic links.
 230     # NOTE: if you use this function in a script, don't use any
 231     # of the variable names used here
 232     if (( $# == 0 )) ; then
 233         return
 234     fi
 235     local the_link="$1"
 236     local link_dir
 237     local current_dir="$PWD"
 238     while file "$the_link" | grep symbolic > /dev/null ; do # resolve links until target is regular file
 239         if [[ "$the_link" == */* ]] ; then # path contains  /
 240             \cd $(dirname "${the_link}") > /dev/null
 241             the_link=$(basename "$the_link")
 242         fi
 243         link_dir="$PWD"
 244             # some versions of 'file' surround the path in `' quotes, hence the tr to remove them
 245         the_link=$(file "${the_link}" | awk '/symbolic link/ {print $NF}' | tr -d "\140\047" )
 246         if [[ "$the_link" != /* ]] ; then # path is not absolute path  - make it one
 247             the_link="$link_dir/$the_link"
 248         fi
 249         \cd "$current_dir" > /dev/null
 250     done
 251     echo $the_link
 252 }
 253
 254
 255 # The best way to install .jar libraries required by plugins is to copy them
 256 # to the imagej plugins/jars directory
 257 # Alternatively, either copy them to ${ij_path}/jre/lib/ext/ or add the .jar
 258 # filepath to the modules line below. Paths are separated by a colon
 259 # Classpath must follow command line arguments, as ij_path is dependent on the -d option
 260
 261 # Resolving ij.jar path.  If ij.jar is a symbolic link to ij_<version>.jar
 262 # this allows updating ij.jar without crashing running sessions
 263 ij_jar_path=$(derefln ${ij_path}/ij.jar)
 264
 265 for mod_jar in ${ij_path}/lib/*jar  ; do
 266     modules="${modules:-}${modules+:}$mod_jar"
 267 done
 268 modules="-cp ${ij_jar_path}:${modules+:}${modules:-}"
 269 #${ij_path}/plugins/jars/dcmie.jar
 270
 271 export LD_LIBRARY_PATH="${ij_path}/lib/${OS}_$processor"
 272 if (( $verbosity > 0 )) ; then
 273     echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
 274 fi
 275
 276 # enable plugins to be compiled in imagej
 277 tools="$JAVA_HOME/lib/tools.jar"
 278
 279
 280 #####################  ARGUMENTS PARSING #####################
 281
 282 while getopts b:cde:hi:m:nop:r:vx: options
 283 do
 284         case $options in
 285                 b)      if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
 286                         macrocmd="-batch ${OPTARG}"
 287                         ;;
 288                 c)      modules="${modules:-}${modules+:}${tools}"
 289                         ;;
 290                 d)      ij_path="$ij_path_dev"
 291                         ;;
 292                 e)  if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
 293                         macrocmd='-eval'
 294                         macroargs="'${OPTARG}'"
 295                         ;;
 296                 h)  fullusage
 297                         exit 0
 298                         ;;
 299                 i)  images="${images}'${OPTARG}' "
 300                         ;;
 301                 m)      if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
 302                         macrocmd="-macro ${OPTARG}"
 303                         ;;
 304         n)  newwindow='true'
 305             ;;
 306                 o)  newwindow='false'
 307                         ;;
 308                 p)      newwindow='false'
 309                         port="${OPTARG}"
 310                 if (( "$port" < 1 || "$port" > 99 )) ; then
 311                 echo "${OPTARG} is not a permissible value for port number (-p)" 1>&2
 312                 exit 1
 313                 fi
 314                         ;;
 315                 r)      if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
 316                         macrocmd='-run'
 317                         macroargs="'${OPTARG}'"
 318                         ;;
 319                 v)      verbosity=verbosity+1
 320                         if (( $verbosity == 2 )) ; then set -x ; fi
 321                         if (( $verbosity == 3 )) ; then set -v ; fi
 322                         ;;
 323                 x)      mem="${OPTARG}"
 324             newwindow='true'
 325                         if (( $mem < $min_mem || $mem > $max_mem )) ; then
 326                 echo "${OPTARG} is not a permissible value for memory (-x)" 1>&2
 327                 echo "min=${min_mem}, max=${max_mem}" 1>&2
 328                 exit 1
 329                         fi
 330                         ;;
 331                 \?) usage
 332                         exit 1
 333                         ;;
 334         esac
 335 done
 336
 337
 338 declare -i i=1
 339 while (( i < $OPTIND )) ; do
 340         shift
 341         i=i+1
 342 done
 343
 344 #if (( "$#" == 0 )) ; then
 345 #       usage
 346 #fi
 347
 348 # -b and -m options only:
 349 # remaining command line arguments are passed as macro arguments
 350 # separated by $separator
 351 if [[ -n "$macrocmd" && -z "$macroargs" ]] ; then
 352         while (( "$#" > 0 )) ; do
 353         if [[ -z "$macroargs" ]] ; then
 354             macroargs="${1}"
 355         else
 356             macroargs="${macroargs}${separator}${1}"
 357         fi
 358         shift
 359         done
 360         macroargs="'$macroargs'"
 361 fi
 362
 363 # PROTECT POSSIBLE SPACES IN IMAGE FILENAMES
 364 if (( "$#" > 0 )) ; then
 365         while (( "$#" > 0 )) ; do
 366         filearg="${1}"
 367         # full file path required when sending images to running ImageJ panel
 368         if [[ "${newwindow}" == 'false' && -f "${filearg}" ]]  && ! expr "${filearg}" : '/.*' > /dev/null; then
 369             filearg="$(getFullPath ${filearg})"
 370         fi
 371                 images="${images}'$filearg' "
 372                 shift
 373         done
 374 fi
 375
 376 ##################### USING PORT #####################
 377
 378 # CREATE IMAGEJ SOCKET-LOCK DIRECTORY IF NON EXISTANT
 379 if [[ ! -d "$ij_tmp" ]] ; then
 380     mkdir "$ij_tmp"
 381     chmod 777 "$ij_tmp"
 382 fi
 383
 384 # CREATE IMAGEJ LOG FILE IF NON EXISTANT
 385 if [[ -n "$ij_log" && ! -f "$ij_log" ]] ; then
 386     touch "$ij_log"
 387     chmod 666 "$ij_log"
 388 fi
 389
 390 # CREATES A TEMP FILE INDICATING A PORT IS IN USE BY IMAGEJ
 391 cd "$ij_tmp"
 392 declare -i count=1
 393 portopen='false'
 394 lockFileCreated='false'
 395 declare -a locklist=(`ls | grep '[0-9][0-9]-.*'`)
 396
 397 [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tNew Window = $newwindow" >> "$ij_log" 2> /dev/null
 398 [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tPort = $port" >> "$ij_log" 2> /dev/null
 399 [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tlocklist: \n ${locklist[*]}" >> "$ij_log" 2> /dev/null
 400 if (( $verbosity > 0 )) ; then echo -e "locklist: \n ${locklist[*]}" ; fi
 401
 402 # PORT SPECIFIED BY USER
 403 if (( $port > 0 )) ; then
 404     # look for a lock on the port specified
 405     for lockname in ${locklist[*]} ; do
 406         prefix=`printf '%02u' $port`
 407         if [[ "$lockname" == ${prefix}-${user}-${host}* ]] ; then
 408                 # found lock on the requested port, owned by user on current display
 409             portopen='true'
 410             if (( $verbosity > 0 )) ; then echo "Using socket lock: $lockname" ; fi
 411             count=$port
 412             break
 413         elif [[ "$lockname" == ${prefix}-* ]] ; then
 414             echo "Port $port is in use by some other user or a different host" 1>&2
 415             if (( $verbosity > 0 )) ; then echo "Port lock: $lockname" ; fi
 416             exit 1
 417         fi
 418     done
 419     # specified port not in use
 420     count=$port
 421
 422 # IF EXISTING WINDOW IS REQUESTED, LOOK FOR LISTENING PORT
 423 elif [[ "$newwindow" == 'false' && ${#locklist} != 0 ]] ; then
 424     # look for a lock on the current display for this user
 425     for lockname in ${locklist[*]} ; do
 426         if [[ "$lockname" == [0-9][0-9]-${user}-${host}-${display} ]] ; then
 427             portopen='true'
 428             if (( $verbosity > 0 )) ; then echo "Found socket lock: $lockname" ; fi
 429             # if a matching user/display is found, use this one
 430             count="${lockname%-*-*-*}"
 431             #count=`echo $lockname | sed  -e 's/^\([0-9][0-9]\).*/\1/' -e 's/^0//'` # csh?
 432             break
 433         fi
 434     done
 435 fi
 436
 437 # IF A NEW PORT IS TO BE USED
 438 if [[ "$portopen" == 'false' ]] ; then
 439     # new window requested or no matching port found
 440     # if port is not specified, look for first free port
 441     if (( "$port" == 0 )) ; then
 442         if (( ${#locklist} == 0 )) ; then
 443             # no active locks - use first port
 444             count=1
 445         else
 446             # active locks - check each port number so see if it is in use
 447             # this is not synchronised!!
 448             count=0
 449             inuse='true'
 450             while [[ "$inuse" == 'true' ]] ; do
 451                 count=count+1
 452                 prefix=`printf '%02u' $count`
 453                 inuse='false'
 454                 for lockname in ${locklist[*]} ; do
 455                     if [[ "$lockname" == ${prefix}-* ]] ; then
 456                         inuse='true'
 457                     fi
 458                 done
 459             done
 460         fi
 461     fi
 462     # CREATING A NEW PORT LOCK
 463     prefix=`printf '%02u' $count`
 464     lockname=${prefix}-${user}-${host}-${display}
 465
 466     [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null
 467         if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
 468         touch $lockname
 469         trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; echo -e "$$\t$(date)\tReleasing lock\t$lockname" >> "$ij_log" 2> /dev/null' EXIT TERM KILL
 470         # Quitting ImageJ sends EXIT, as does a kill/kill -9
 471         # CTRL+C in terminal sends INT + EXIT
 472         # System shutdown sends TERM (+EXIT??)
 473
 474         if (( $verbosity > 0 )) ; then  echo 'done' ; fi
 475
 476     lockFileCreated='true'
 477     if [[ -z "$macrocmd" ]] ; then
 478             echo 'Open other images in this ImageJ panel as follows:'
 479             echo "  imagej -p $count <image1> [<image2> ... <imageN>]"
 480     fi
 481     [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tSocket lock:\t$lockname" >> "$ij_log" 2> /dev/null
 482     if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi
 483         echo
 484 fi
 485
 486 ##################### FINALLY RUN IMAGEJ #####################
 487
 488 #popd > /dev/null
 489
 490 #if [ "$JAVA_HOME" ] ; then
 491 #       if (( $verbosity > 0 )) ; then
 492 #               echo ${modules}
 493 #               echo $JAVA_HOME/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
 494 #       else
 495 #       eval $JAVA_HOME/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
 496 #       fi
 497 #else
 498 #  echo "No JVM found to run ImageJ"
 499 #  echo "Please pacman -S java-runtime a JVM to run ImageJ or "
 500 #  echo "check JAVA_HOME."
 501 #  exit 1
 502 #fi
 503
 504 eval java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
 505
 506 exit 0
 507