mirror of
https://github.com/Ponce/slackbuilds
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483 lines
16 KiB
Bash
483 lines
16 KiB
Bash
#!/bin/bash
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# A wrapper script to launch imagej from the UNIX command line
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# Images given as arguments will be opened, macros may also be given as arguments
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# Looks for macros in the imagej macro directory
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#
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# This program is free software, but comes with no warrenty or guarantee
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# send bug reports or feedback to jjackson at familyjackson dot net
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# Author: Jon Jackson
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# Last modified date: $Date: 2008-09-17 10:31:27 +0100 (Wed, 17 Sep 2008) $
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# $Revision: 51 $
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#
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# INSTALLATION INSTRUCTIONS
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#
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### WARNING ###########################################################
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# This file must be edited with a program that supports unix new line characters
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# - it won't run if edited in 'Notepad' !
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#######################################################################
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# Source location: http://rsb.info.nih.gov/ij/download/linux/unix-script.txt
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# 1) Save this script in the ImageJ directory as 'imagej'
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# 2) Modify path variables according to your system
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# 3) Give the new file execute permission
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# 4) Be sure the 'imagej' wrapper is in the 'PATH'
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### MODIFICATION ###
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# With minor modifications to use with Slackware, by Petar Petrov 2012
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# ppetrov at paju dot oulu dot fi
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####################
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# setup environment
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set +u # don't give error for unset variables (matters for environment variables)
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shopt -s extglob # allow extended pattern matching
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############ SITE SPECIFIC VARIABLES #########################
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# Trailing / is not required for path variables
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# IMAGEJ PATH - production installation
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ij_path='/usr/share/ImageJ'
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# Path to ImageJ development installation
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#ij_path_dev='/home/jjackson/ImageJ'
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# JAVA PATH
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# assumes executable is ${java_home}/bin/java
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# set java_home variables ='' to use JAVA_HOME environment variable
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#if [[ -d /usr/java/jdk1.5 ]] ; then
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# java_home='/usr/java/jdk1.5'
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#else
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# # Optionally specify java path for all available OS / architecture combinations
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# java_home_Linux="${ij_path}/jre"
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# java_home_Linux_x86_64="${ij_path}/jre64"
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# java_home_SunOS="${ij_path}/jre64"
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# #
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#fi
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ijadmin=''
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# DOCUMENTATION URL
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doc_url='http://rsb.info.nih.gov/ij/'
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# TEMP FOLDER
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ij_tmp='/tmp/imagej'
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# LOG FILE
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#ij_log="${ij_tmp}/log.txt"
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# default behaviour when an ImageJ window is already open
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newwindow='true'
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#newwindow='false'
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# macro argument delimiter character
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separator=':'
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# a ' ' may work provided no arguments would contain spaces
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# use macro functions: args=getArgument(); argArray=split(args, ':');
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# to recover macro arguments
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############ DEFAULT MEMORY SETTINGS #########################
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declare -i default_mem=768
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declare -i min_mem=32
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declare -i max_32bit=1800 # empirical
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declare -i max_64bit=17000000000 # conservative
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############ SITE SPECIFIC MODULES #########################
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# JAR libraries for additional modules may be placed in ${ij_path}/lib
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# jmf.jar jai_codec.jar jai_core.jar mlibwrapper_jai.jar
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# Native libraries may be placed in ${ij_path}/lib/$OS
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# where OS matches the output of the 'uname' command
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############ END SITE SPECIFIC VARIABLES #########################
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OS=$(uname)
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processor=$(uname -m) # -p doesn't work on ubuntu
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declare -i mem
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declare -i max_mem
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declare -i free_mem
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java_home="${java_home:-$JAVA_HOME}"
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if [[ "$OS" == 'SunOS' ]] ; then
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java_arch='-d64'
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JAVA_HOME="${java_home_SunOS:-$java_home}"
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max_mem=`vmstat | awk 'BEGIN{maxMem='$max_64bit'} NR == 3 {fmem=int($5 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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free_mem="max_mem"
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mem=${free_mem}/2
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if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
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elif [[ "$OS" == 'Linux' ]] ; then
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if [[ "$processor" == 'x86_64' ]] ; then
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java_arch='-d64'
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JAVA_HOME="${java_home_Linux_x86_64:-$java_home}"
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max_mem=`free | awk -v maxMem=$max_64bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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free_mem=`free | awk -v maxMem=$max_64bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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mem=${free_mem}/3*2
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if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
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else
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java_arch='-d32'
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JAVA_HOME="${java_home_Linux:-$java_home}"
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max_mem=`free | awk -v maxMem=$max_32bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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free_mem=`free | awk -v maxMem=$max_32bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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mem=${free_mem}/3*2
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if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
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fi
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fi
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# if tools.jar is not in ${ij_path}/jre/lib/ext/ edit the 'tools=' line
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# to point to tools.jar. The -compile switch will load tools.jar into the
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# classpath and enable plugins to be compiled in imagej
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if [[ -f "${ij_path}/tools.jar" ]] ; then
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tools="${ij_path}/tools.jar"
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else
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tools=''
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fi
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# End Site specific variables ---------------------------------------------------------
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# other variables
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dir=`pwd`
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user=`whoami`
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host=`hostname`
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if [[ -z "$DISPLAY" ]] ; then
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echo 'Display variable not set'
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echo 'If ImageJ fails to load, try '
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echo '% setenv DISPLAY yourcomputer:0'
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echo 'if you use the "csh" or for "bash" try'
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echo '% export DISPLAY=yourcomputer:0'
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display='default'
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else
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display="$DISPLAY"
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fi
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declare -i port=0
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declare -i verbosity=0
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images=''
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macrocmd=''
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macroargs=''
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function usage {
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echo
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echo 'Image display and analysis program. Opens formats including:'
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echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
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echo
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echo 'imagej [options] image [ image2 ... image3 ]'
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echo ' -h print help and more options'
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echo ' -o open images in an open ImageJ panel'
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echo ' -p <N> open images in ImageJ panel number <N>'
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echo " -x <MB> set available memory (default=${mem} max=${max_mem})"
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echo
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}
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function fullusage {
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echo
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echo 'Image display and analysis program. Opens formats including:'
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echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
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echo
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echo 'imagej [options] image [ image2 ... image3 ] -> open images'
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echo
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echo 'basic options:'
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echo ' -h print help and more options'
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echo ' -o open images in existing ImageJ panel if one exists'
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echo ' -p <N> open images in existing ImageJ panel number <N>'
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echo " -x <MB> set available memory (default=${mem} max=${max_mem})"
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echo
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echo 'advanced options:'
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echo ' -c enable plugin compilation within imagej'
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echo ' -d use development version'
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echo ' -v be verbose (vv or vvv increases verbosity)'
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echo
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echo 'options for batch processing:'
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echo " -e 'Macro Code' execute macro code"
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echo " -r 'Menu Command' run menu command"
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echo "Quotation marks '' are required around commands including spaces"
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echo 'Commands can be sent to open ImageJ panels with the -p option'
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echo
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echo 'options for macros:'
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echo 'imagej [-i image] [-b|-m] [arg1 ... argN] '
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echo ' -b macro run macro without graphics window'
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echo ' -m macro run macro'
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echo '"image" will be opened before macro is run'
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echo 'all following arguments are passed to macro'
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echo
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echo "Documentation - $doc_url "
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echo "Report problems with this software to $ijadmin"
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echo
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}
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function macroCmdError {
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fullusage
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echo 'Only one command option (-b -e -m OR -r) may be specified' 1>&2
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exit 1
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}
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function getFullPath {
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# Return full path to file
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# treats multiple arguments as a single file with spaces
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if (( $# == 0 )) ; then
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echo "error getting full path for '${*}'" 1>&2
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fi
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pwd_getFullPath="$PWD"
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\cd $(dirname "${*}") > /dev/null
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dir_getFullPath="$PWD"
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\cd "$pwd_getFullPath" > /dev/null
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echo "$dir_getFullPath"/$(basename "${*}")
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}
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function derefln {
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# Returns the full path of file to which link points
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# following multiple levels of symbolic links.
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# NOTE: if you use this function in a script, don't use any
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# of the variable names used here
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if (( $# == 0 )) ; then
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return
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fi
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local the_link="$1"
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local link_dir
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local current_dir="$PWD"
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while file "$the_link" | grep symbolic > /dev/null ; do # resolve links until target is regular file
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if [[ "$the_link" == */* ]] ; then # path contains /
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\cd $(dirname "${the_link}") > /dev/null
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the_link=$(basename "$the_link")
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fi
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link_dir="$PWD"
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# some versions of 'file' surround the path in `' quotes, hence the tr to remove them
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the_link=$(file "${the_link}" | awk '/symbolic link/ {print $NF}' | tr -d "\140\047" )
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if [[ "$the_link" != /* ]] ; then # path is not absolute path - make it one
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the_link="$link_dir/$the_link"
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fi
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\cd "$current_dir" > /dev/null
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done
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echo $the_link
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}
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# parse input arguments
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while getopts b:cde:hi:m:nop:r:vx: options
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do
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case $options in
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b) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
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macrocmd="-batch ${OPTARG}"
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;;
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c) modules="${modules:-}${modules+:}${tools}"
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;;
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d) ij_path="$ij_path_dev"
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;;
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e) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
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macrocmd='-eval'
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macroargs="'${OPTARG}'"
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;;
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h) fullusage
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exit 0
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;;
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i) images="${images}'${OPTARG}' "
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;;
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m) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
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macrocmd="-macro ${OPTARG}"
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;;
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n) newwindow='true'
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;;
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o) newwindow='false'
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;;
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p) newwindow='false'
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port="${OPTARG}"
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if (( "$port" < 1 || "$port" > 99 )) ; then
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echo "${OPTARG} is not a permissible value for port number (-p)" 1>&2
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exit 1
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fi
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;;
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r) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
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macrocmd='-run'
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macroargs="'${OPTARG}'"
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;;
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v) verbosity=verbosity+1
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if (( $verbosity == 2 )) ; then set -x ; fi
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if (( $verbosity == 3 )) ; then set -v ; fi
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;;
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x) mem="${OPTARG}"
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newwindow='true'
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if (( $mem < $min_mem || $mem > $max_mem )) ; then
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echo "${OPTARG} is not a permissible value for memory (-x)" 1>&2
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echo "min=${min_mem}, max=${max_mem}" 1>&2
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exit 1
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fi
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;;
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\?) usage
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exit 1
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;;
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esac
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done
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#for ((i=1; i < $OPTIND; i++))
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#do
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# shift
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#done
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## above syntax not supported in bash < 2.05
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declare -i i=1
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while (( i < $OPTIND )) ; do
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shift
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i=i+1
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done
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if [[ "$#" == 0 && -z "$macrocmd" ]] ; then
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usage
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fi
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# The best way to install .jar libraries required by plugins is to copy them
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# to the imagej plugins/jars directory
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# Alternatively, either copy them to ${ij_path}/jre/lib/ext/ or add the .jar
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# filepath to the modules line below. Paths are separated by a colon
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# Classpath must follow command line arguments, as ij_path is dependent on the -d option
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# Resolving ij.jar path. If ij.jar is a symbolic link to ij_<version>.jar
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# this allows updating ij.jar without crashing running sessions
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ij_jar_path=$(derefln ${ij_path}/ij.jar)
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for mod_jar in ${ij_path}/lib/*jar ; do
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modules="${modules:-}${modules+:}$mod_jar"
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done
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modules="-cp ${ij_jar_path}:${modules+:}${modules:-}"
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#${ij_path}/plugins/jars/dcmie.jar
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export LD_LIBRARY_PATH="${ij_path}/lib/${OS}_$processor"
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if (( $verbosity > 0 )) ; then
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echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
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fi
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# -b and -m options only:
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# remaining command line arguments are passed as macro arguments
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# separated by $separator
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if [[ -n "$macrocmd" && -z "$macroargs" ]] ; then
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while (( "$#" > 0 )) ; do
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if [[ -z "$macroargs" ]] ; then
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macroargs="${1}"
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else
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macroargs="${macroargs}${separator}${1}"
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fi
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shift
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done
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macroargs="'$macroargs'"
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fi
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# PROTECT POSSIBLE SPACES IN IMAGE FILENAMES
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if (( "$#" > 0 )) ; then
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while (( "$#" > 0 )) ; do
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filearg="${1}"
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# full file path required when sending images to running ImageJ panel
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if [[ "${newwindow}" == 'false' && -f "${filearg}" ]] && ! expr "${filearg}" : '/.*' > /dev/null; then
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filearg="$(getFullPath ${filearg})"
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fi
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images="${images}'$filearg' "
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shift
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done
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fi
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# CREATE IMAGEJ SOCKET-LOCK DIRECTORY IF NON EXISTANT
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if [[ ! -d "$ij_tmp" ]] ; then
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mkdir "$ij_tmp"
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chmod 777 "$ij_tmp"
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fi
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# CREATE IMAGEJ LOG FILE IF NON EXISTANT
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if [[ -n "$ij_log" && ! -f "$ij_log" ]] ; then
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touch "$ij_log"
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chmod 666 "$ij_log"
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fi
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# CREATES A TEMP FILE INDICATING A PORT IS IN USE BY IMAGEJ
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cd "$ij_tmp"
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declare -i count=1
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portopen='false'
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lockFileCreated='false'
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declare -a locklist=(`ls | grep '[0-9][0-9]-.*'`)
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[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tNew Window = $newwindow" >> "$ij_log" 2> /dev/null
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[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tPort = $port" >> "$ij_log" 2> /dev/null
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[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tlocklist: \n ${locklist[*]}" >> "$ij_log" 2> /dev/null
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if (( $verbosity > 0 )) ; then echo -e "locklist: \n ${locklist[*]}" ; fi
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# PORT SPECIFIED BY USER
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if (( $port > 0 )) ; then
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# look for a lock on the port specified
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for lockname in ${locklist[*]} ; do
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prefix=`printf '%02u' $port`
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if [[ "$lockname" == ${prefix}-${user}-${host}* ]] ; then
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# found lock on the requested port, owned by user on current display
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portopen='true'
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if (( $verbosity > 0 )) ; then echo "Using socket lock: $lockname" ; fi
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count=$port
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break
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elif [[ "$lockname" == ${prefix}-* ]] ; then
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echo "Port $port is in use by some other user or a different host" 1>&2
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if (( $verbosity > 0 )) ; then echo "Port lock: $lockname" ; fi
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exit 1
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fi
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done
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# specified port not in use
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count=$port
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# IF EXISTING WINDOW IS REQUESTED, LOOK FOR LISTENING PORT
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elif [[ "$newwindow" == 'false' && ${#locklist} != 0 ]] ; then
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# look for a lock on the current display for this user
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for lockname in ${locklist[*]} ; do
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if [[ "$lockname" == [0-9][0-9]-${user}-${host}-${display} ]] ; then
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portopen='true'
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if (( $verbosity > 0 )) ; then echo "Found socket lock: $lockname" ; fi
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# if a matching user/display is found, use this one
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count="${lockname%-*-*-*}"
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#count=`echo $lockname | sed -e 's/^\([0-9][0-9]\).*/\1/' -e 's/^0//'` # csh?
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break
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fi
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done
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fi
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# IF A NEW PORT IS TO BE USED
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if [[ "$portopen" == 'false' ]] ; then
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# new window requested or no matching port found
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# if port is not specified, look for first free port
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if (( "$port" == 0 )) ; then
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if (( ${#locklist} == 0 )) ; then
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# no active locks - use first port
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count=1
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else
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# active locks - check each port number so see if it is in use
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# this is not synchronised!!
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count=0
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inuse='true'
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while [[ "$inuse" == 'true' ]] ; do
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count=count+1
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prefix=`printf '%02u' $count`
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inuse='false'
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for lockname in ${locklist[*]} ; do
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if [[ "$lockname" == ${prefix}-* ]] ; then
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inuse='true'
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fi
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done
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done
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fi
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fi
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# CREATING A NEW PORT LOCK
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prefix=`printf '%02u' $count`
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lockname=${prefix}-${user}-${host}-${display}
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[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null
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if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
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touch $lockname
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trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tReleasing lock\t$lockname" >> "$ij_log" 2> /dev/null' EXIT TERM KILL
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# Quitting ImageJ sends EXIT, as does a kill/kill -9
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# CTRL+C in terminal sends INT + EXIT
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# System shutdown sends TERM (+EXIT??)
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if (( $verbosity > 0 )) ; then echo 'done' ; fi
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lockFileCreated='true'
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if [[ -z "$macrocmd" ]] ; then
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echo 'Open other images in this ImageJ panel as follows:'
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|
echo " imagej -p $count <image1> [<image2> ... <imageN>]"
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fi
|
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[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tSocket lock:\t$lockname" >> "$ij_log" 2> /dev/null
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if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi
|
|
echo
|
|
fi
|
|
|
|
if (( $verbosity > 0 )) ; then
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|
echo ${JAVA_HOME}/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs}
|
|
fi
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|
|
|
cd "$dir"
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|
eval "${JAVA_HOME}/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs} "
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exit 0
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