academic/ImageJ: Added (Image processing and analysis in Java)

Signed-off-by: dsomero <xgizzmo@slackbuilds.org>

1 files changed, 483 insertions, 0 deletions

diff --git a/academic/ImageJ/imagej b/academic/ImageJ/imagej
new file mode 100644
index 0000000000..44922f4fd7
--- /dev/null
+++ b/academic/ImageJ/imagej
@@ -0,0 +1,483 @@
+#!/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