#!/bin/bash
#
################################################
## The script to call to start OpenMIMS. To
## open the plugin with a particular file, pass
## the file name as an argument.
##
################################################

# If symlinks get involved it gets complicated, see:
# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in
# This script assumes that we're in Fiji.app/lib/

SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
  SOURCE="$(readlink "$SOURCE")"
  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"

FIJIPATH=$DIR/..
cd $FIJIPATH
./ImageJ-linux64 --allow-multiple -eval "run('Open MIMS Image', '$@'); run('Install...', 'install=$FIJIPATH/macros/openmims_tools.fiji.ijm');" >&  $FIJIPATH/logs/logfile_$(whoami)_$(hostname)_$$.txt &