academic/ImageJ: Removed (Use fiji).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

8 files changed, 0 insertions, 632 deletions

diff --git a/academic/ImageJ/ImageJ.SlackBuild b/academic/ImageJ/ImageJ.SlackBuild
deleted file mode 100644
index 7ebfbc08b3..0000000000
--- a/academic/ImageJ/ImageJ.SlackBuild
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/bin/sh
-
-# Slackware build script for ImageJ
-
-# Copyright 2012-2018 Petar Petrov slackalaxy@gmail.com
-# All rights reserved.
-#
-# Redistribution and use of this script, with or without modification, is
-# permitted provided that the following conditions are met:
-#
-# 1. Redistributions of this script must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#
-#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
-#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
-#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-PRGNAM=ImageJ
-VERSION=${VERSION:-1.52}
-ARCH=noarch
-BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}
-
-SRCNAM=ij
-SRCVER=152
-
-CWD=$(pwd)
-TMP=${TMP:-/tmp/SBo}
-PKG=$TMP/package-$PRGNAM
-OUTPUT=${OUTPUT:-/tmp}
-
-set -e
-
-rm -rf $PKG
-mkdir -p $TMP $PKG $OUTPUT
-cd $TMP
-rm -rf $PRGNAM
-unzip $CWD/${SRCNAM}${SRCVER}.zip
-cd $PRGNAM
-chown -R root:root .
-find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
- -o -perm 511 \) -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
- -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
-
-mkdir -p $PKG/usr/share/$PRGNAM
-cp -a luts macros plugins ij.jar $PKG/usr/share/$PRGNAM
-
-mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
-cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
-
-# Fix permissions
-find $PKG -type d -exec chmod 755 {} \; -o \
-          -type f -exec chmod 644 {} \;
-
-# Install the wrapper of ij.jar, taken from the link below:
-# http://rsb.info.nih.gov/ij/download/linux/unix-script.txt
-install -D -m755 $CWD/imagej $PKG/usr/bin/imagej
-
-mkdir -p $PKG/usr/share/{applications,pixmaps}
-cp $CWD/imagej.desktop $PKG/usr/share/applications
-cp $CWD/imagej.png $PKG/usr/share/pixmaps
-
-mkdir -p $PKG/install
-cat $CWD/slack-desc > $PKG/install/slack-desc
-cat $CWD/doinst.sh > $PKG/install/doinst.sh
-
-cd $PKG
-/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/ImageJ/ImageJ.info b/academic/ImageJ/ImageJ.info
deleted file mode 100644
index 0fc4667ea3..0000000000
--- a/academic/ImageJ/ImageJ.info
+++ /dev/null
@@ -1,10 +0,0 @@
-PRGNAM="ImageJ"
-VERSION="1.52"
-HOMEPAGE="http://rsb.info.nih.gov/ij/"
-DOWNLOAD="http://wsr.imagej.net/distros/cross-platform/ij152.zip"
-MD5SUM="422df5b3c331d436b6a76a4bcc510065"
-DOWNLOAD_x86_64=""
-MD5SUM_x86_64=""
-REQUIRES="jdk"
-MAINTAINER="Petar Petrov"
-EMAIL="slackalaxy@gmail.com"
diff --git a/academic/ImageJ/README b/academic/ImageJ/README
deleted file mode 100644
index 75120f2ee0..0000000000
--- a/academic/ImageJ/README
+++ /dev/null
@@ -1,32 +0,0 @@
-ImageJ is a Java image processing program inspired by NIH Image for
-the Macintosh. It can display, edit, analyze, process, save and print
-8-bit, 16-bit and 32-bit images. It can read many image formats
-including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports
-"stacks", a series of images that share a single window. It is multi-
-threaded, so time-consuming operations such as image file reading can
-be performed in parallel with other operations.
-
-ImageJ can calculate area and pixel value statistics of user-defined
-selections. It can measure distances and angles. It can create density
-histograms and line profile plots. It supports standard image
-processing functions such as contrast manipulation, sharpening,
-smoothing, edge detection and median filtering.
-
-ImageJ does geometric transformations such as scaling, rotation and
-flips. Image can be zoomed up to 32:1 and down to 1:32. All analysis
-and processing functions are available at any magnification factor.
-The program supports any number of windows (images) simultaneously,
-limited only by available memory.
-
-Spatial calibration is available to provide real world dimensional
-measurements in units such as millimeters. Density or gray scale
-calibration is also available.
-
-ImageJ was designed with an open architecture that provides
-extensibility via Java plugins. User-written plugins make it possible
-to solve almost any image processing or analysis problem.
-
-NOTE ABOUT PLUGINS:
-If you are looking for additional features, search for ImageJ plugins
-already available at SBo (ij-plugins-*) or check the program website
-for more.
diff --git a/academic/ImageJ/doinst.sh b/academic/ImageJ/doinst.sh
deleted file mode 100644
index 5fb28930db..0000000000
--- a/academic/ImageJ/doinst.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-if [ -x /usr/bin/update-desktop-database ]; then
-  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
-fi
diff --git a/academic/ImageJ/imagej b/academic/ImageJ/imagej
deleted file mode 100644
index 44922f4fd7..0000000000
--- a/academic/ImageJ/imagej
+++ /dev/null
@@ -1,483 +0,0 @@
-#!/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
diff --git a/academic/ImageJ/imagej.desktop b/academic/ImageJ/imagej.desktop
deleted file mode 100644
index bd6bde5fa7..0000000000
--- a/academic/ImageJ/imagej.desktop
+++ /dev/null
@@ -1,8 +0,0 @@
-[Desktop Entry]
-Categories=Education;
-Comment=Scientific image manipulation software
-Exec=imagej
-Icon=imagej
-Name=ImageJ
-StartupNotify=false
-Type=Application
diff --git a/academic/ImageJ/imagej.png b/academic/ImageJ/imagej.png
deleted file mode 100644
index 8041fc114a..0000000000
--- a/academic/ImageJ/imagej.png
+++ /dev/null
diff --git a/academic/ImageJ/slack-desc b/academic/ImageJ/slack-desc
deleted file mode 100644
index eab74d7de4..0000000000
--- a/academic/ImageJ/slack-desc
+++ /dev/null
@@ -1,19 +0,0 @@
-# HOW TO EDIT THIS FILE:
-# The "handy ruler" below makes it easier to edit a package description.
-# Line up the first '|' above the ':' following the base package name, and
-# the '|' on the right side marks the last column you can put a character in.
-# You must make exactly 11 lines for the formatting to be correct.  It's also
-# customary to leave one space after the ':' except on otherwise blank lines.
-
-      |-----handy-ruler------------------------------------------------------|
-ImageJ: ImageJ (Image processing and analysis in Java)
-ImageJ:
-ImageJ: ImageJ is a Java image processing program inspired by NIH Image
-ImageJ: for the Macintosh. It was designed with an open architecture that
-ImageJ: provides extensibility via Java plugins. User-written plugins make
-ImageJ: it possible to solve almost any image processing or analysis
-ImageJ: problem.
-ImageJ:
-ImageJ: Home: http://rsb.info.nih.gov/ij/
-ImageJ:
-ImageJ: