From: preecej <preecej@localhost>
Date: Tue, 9 Oct 2012 21:22:04 +0000 (+0000)
Subject: Removing old copy of SIA project. "Annotation" is the correct project.
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=237b28662f8627637a17990fafbaaf31135c955c;p=old-jaiswallab-svn%2F.git

Removing old copy of SIA project. "Annotation" is the correct project.

svn path=/; revision=397
---

diff --git a/image_annotation/._build.xml b/image_annotation/._build.xml
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index 18adcdd..0000000
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diff --git a/image_annotation/.classpath b/image_annotation/.classpath
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index 810f0b6..0000000
--- a/image_annotation/.classpath
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="lib" path="lib/swt-gtk-64.jar"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="plugins1"/>
-	<classpathentry kind="lib" path="lib/istapi-src.jar" sourcepath="/home/lingutln/practice/istapi-src.jar"/>
-	<classpathentry kind="lib" path="lib/istapi.jar"/>
-	<classpathentry kind="lib" path="lib/jface.jar"/>
-	<classpathentry kind="lib" path="resources/ant/lib/ant-deb.jar"/>
-	<classpathentry kind="lib" path="resources/ant/lib/ant-gzip2.jar"/>
-	<classpathentry kind="lib" path="resources/ant/lib/ant-passwd-task.jar"/>
-	<classpathentry kind="lib" path="resources/ant/lib/ant-swt-identify.jar"/>
-	<classpathentry kind="lib" path="resources/ant/lib/jsmoothgen-ant.jar"/>
-	<classpathentry kind="lib" path="resources/ant/lib/standalone-compiler.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry exported="true" kind="lib" path="lib/swt-gtk.jar"/>
-	<classpathentry kind="lib" path="lib/swt-win.jar"/>
-	<classpathentry kind="lib" path="/home/lingutln/workspace/image_annotation/lib/json.jar"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
diff --git a/image_annotation/.project b/image_annotation/.project
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--- a/image_annotation/.project
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>Segmentation</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-	</natures>
-	<linkedResources>
-		<link>
-			<name>plugins1</name>
-			<type>2</type>
-			<location>/home/lingutln/Downloads/ist-source/Interactive Segmentation App/plugins</location>
-		</link>
-	</linkedResources>
-</projectDescription>
diff --git a/image_annotation/.settings/org.eclipse.jdt.core.prefs b/image_annotation/.settings/org.eclipse.jdt.core.prefs
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index b0ea1ab..0000000
--- a/image_annotation/.settings/org.eclipse.jdt.core.prefs
+++ /dev/null
@@ -1,12 +0,0 @@
-#Thu Mar 25 19:16:32 GMT 2010
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.6
-org.eclipse.jdt.core.compiler.debug.lineNumber=generate
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.source=1.6
diff --git a/image_annotation/bin/BPTPlugin.plugin/bptplugin.jar b/image_annotation/bin/BPTPlugin.plugin/bptplugin.jar
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diff --git a/image_annotation/bin/BPTPlugin.plugin/jbpt.dll b/image_annotation/bin/BPTPlugin.plugin/jbpt.dll
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diff --git a/image_annotation/bin/BPTPlugin.plugin/libjbpt.jnilib b/image_annotation/bin/BPTPlugin.plugin/libjbpt.jnilib
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diff --git a/image_annotation/bin/BPTPlugin.plugin/plugin.xml b/image_annotation/bin/BPTPlugin.plugin/plugin.xml
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index 4ae529d..0000000
--- a/image_annotation/bin/BPTPlugin.plugin/plugin.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<plugin>
-	<meta name="name" value="BPT Plugin" />
-	<meta name="description" value="Binary Partition Tree Plugin" />
-	<meta name="vendor" value="Dublin City University" />
-	<meta name="author" value="Kevin McGuinness" />
-	<meta name="email" value="kevin.mcguinness@gmail.com" />
-	<meta name="segmenter" value="ie.dcu.segment.algorithm.BptSegmenter" />	
-	<jar file="bptplugin.jar" />
-</plugin>
diff --git a/image_annotation/bin/IGCPlugin.plugin/igcplugin.jar b/image_annotation/bin/IGCPlugin.plugin/igcplugin.jar
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diff --git a/image_annotation/bin/IGCPlugin.plugin/jigc.dll b/image_annotation/bin/IGCPlugin.plugin/jigc.dll
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diff --git a/image_annotation/bin/IGCPlugin.plugin/libjigc.jnilib b/image_annotation/bin/IGCPlugin.plugin/libjigc.jnilib
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diff --git a/image_annotation/bin/IGCPlugin.plugin/plugin.xml b/image_annotation/bin/IGCPlugin.plugin/plugin.xml
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index 2b7ae2e..0000000
--- a/image_annotation/bin/IGCPlugin.plugin/plugin.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<plugin>
-	<meta name="name" value="IGC Plugin" />
-	<meta name="description" value="Interactive Graph Cuts Plugin" />
-	<meta name="vendor" value="Dublin City University" />
-	<meta name="author" value="Kevin McGuinness" />
-	<meta name="email" value="kevin.mcguinness@gmail.com" />
-	<meta name="segmenter" value="ie.dcu.segment.algorithm.IgcSegmenter" />	
-	<jar file="igcplugin.jar" />
-</plugin>
diff --git a/image_annotation/bin/SIOXPlugin.plugin/plugin.xml b/image_annotation/bin/SIOXPlugin.plugin/plugin.xml
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index 623ad7b..0000000
--- a/image_annotation/bin/SIOXPlugin.plugin/plugin.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<plugin>
-	<meta name="name" value="SIOX Plugin" />
-	<meta name="description" value="Simple Interactive Object Extraction Plugin" />
-	<meta name="vendor" value="Dublin City University" />
-	<meta name="author" value="Kevin McGuinness" />
-	<meta name="email" value="kevin.mcguinness@gmail.com" />
-	<meta name="segmenter" value="ie.dcu.segment.algorithm.SioxSegmenter" />	
-	<jar file="sioxplugin.jar" />
-	<jar file="sioxapi.jar" />
-</plugin>
diff --git a/image_annotation/bin/SIOXPlugin.plugin/sioxapi.jar b/image_annotation/bin/SIOXPlugin.plugin/sioxapi.jar
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diff --git a/image_annotation/bin/SIOXPlugin.plugin/sioxplugin.jar b/image_annotation/bin/SIOXPlugin.plugin/sioxplugin.jar
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diff --git a/image_annotation/bin/SRGPlugin.plugin/jsrg.dll b/image_annotation/bin/SRGPlugin.plugin/jsrg.dll
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diff --git a/image_annotation/bin/SRGPlugin.plugin/libjsrg.jnilib b/image_annotation/bin/SRGPlugin.plugin/libjsrg.jnilib
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diff --git a/image_annotation/bin/SRGPlugin.plugin/plugin.xml b/image_annotation/bin/SRGPlugin.plugin/plugin.xml
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index 4061f98..0000000
--- a/image_annotation/bin/SRGPlugin.plugin/plugin.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<plugin>
-	<meta name="name" value="SRG Plugin" />
-	<meta name="description" value="Seeded Region Growing Plugin" />
-	<meta name="vendor" value="Dublin City University" />
-	<meta name="author" value="Kevin McGuinness" />
-	<meta name="email" value="kevin.mcguinness@gmail.com" />
-	<meta name="segmenter" value="ie.dcu.segment.algorithm.SrgSegmenter" />	
-	<jar file="srgplugin.jar" />
-</plugin>
diff --git a/image_annotation/bin/SRGPlugin.plugin/srgplugin.jar b/image_annotation/bin/SRGPlugin.plugin/srgplugin.jar
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/AppPrefs$1.class b/image_annotation/bin/ie/dcu/apps/ist/AppPrefs$1.class
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/AppPrefs$Keys.class b/image_annotation/bin/ie/dcu/apps/ist/AppPrefs$Keys.class
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/AppPrefs$SupportedTypes.class b/image_annotation/bin/ie/dcu/apps/ist/AppPrefs$SupportedTypes.class
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/export/imagemap/template.html b/image_annotation/bin/ie/dcu/apps/ist/export/imagemap/template.html
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--- a/image_annotation/bin/ie/dcu/apps/ist/export/imagemap/template.html
+++ /dev/null
@@ -1,38 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-	"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html>
-<head>
-    <!-- Generated using the CDVP Interactive Segmentation Tool -->
-    <meta http-equiv="Content-type" 
-          content="text/html; charset=utf-8"/>
-    <meta name="Generator" 
-          content="Interactive Segmentation Tool"/>
-    
-    <title>${page-title}</title>
-    
-    <script type="text/javascript" language="javascript">
-  		
-${preloads}
-  		
-        function rollover(docElem, image) {
-            docElem.src = image.src
-            return true
-        }
-        
-    </script>
-  
-</head>
-<body>
-    <!-- Image -->
-    <img name="${image-name}"
-         src="${image-href}" 
-         usemap="#${map-name}" 
-         alt="${image-alt}"
-         title="${image-alt}"/>
-    
-    <!-- Image map -->
-    <map name="${map-name}" id="${map-name}">
-${contents}
-    </map>
-</body>
-</html>
\ No newline at end of file
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/ColorSelector$ControlListener.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/ColorSelector$ControlListener.class
deleted file mode 100644
index 105547c..0000000
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/ColorSelector.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/ColorSelector.class
deleted file mode 100644
index afad48d..0000000
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/ImageMenuManager.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/ImageMenuManager.class
deleted file mode 100644
index aea558d..0000000
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$1.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$1.class
deleted file mode 100644
index e6d8d99..0000000
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$2.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$2.class
deleted file mode 100644
index 8ef114d..0000000
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$3.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$3.class
deleted file mode 100644
index 42e939d..0000000
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$4.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$4.class
deleted file mode 100644
index cc64dd0..0000000
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$State.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer$State.class
deleted file mode 100644
index d4391c9..0000000
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diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer.class
deleted file mode 100644
index 0fab82f..0000000
Binary files a/image_annotation/bin/ie/dcu/apps/ist/widgets/SwtTimer.class and /dev/null differ
diff --git a/image_annotation/bin/ie/dcu/apps/ist/widgets/Ticker.class b/image_annotation/bin/ie/dcu/apps/ist/widgets/Ticker.class
deleted file mode 100644
index e95c65e..0000000
Binary files a/image_annotation/bin/ie/dcu/apps/ist/widgets/Ticker.class and /dev/null differ
diff --git a/image_annotation/build.xml b/image_annotation/build.xml
deleted file mode 100644
index e6b752a..0000000
--- a/image_annotation/build.xml
+++ /dev/null
@@ -1,402 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- ====================================================================== 
-     Aug 20, 2009 2:11:20 PM                                                        
-
-     istapp
-     The interactive segmentation tool
-                   
-     Kevin McGuinness                                                                
-     ====================================================================== -->
-<project name="istapp" default="default">
-    <description>
-        The interactive segmentation tool
-    </description>
-    
-    <property file="resources/ant/properties" />
-    <property name="src.dir" location="src"/>
-    <property name="build.dir" location="build"/>
-    <property name="lib.dir" location="lib"/>
-    <property name="doc.dir" location="doc"/>
-    <property name="dist.dir" location="dist"/>
-    <property name="bin.jar" value="istapp.jar"/>
-    <property name="src.jar" value="istapp-src.jar"/>
-    <property name="doc.zip" value="istapp-doc.zip"/>
-    <property name="plugins.dir" location="plugins"/>
-    <property name="deb.prefix" value="${build.dir}/packages/debian/usr" />
-
-    <!-- The following four properties are needed by the copy-plugins action -->
-    <property name="bptplugin.dir" location="../BPT Plugin" />
-    <property name="igcplugin.dir" location="../IGC Plugin" />
-    <property name="srgplugin.dir" location="../SRG Plugin" />
-    <property name="sioxplugin.dir" location="../SIOX Plugin" />
-    
-
-    <path id="class.path">
-        <pathelement location="${build.dir}"/>
-        <fileset dir="${lib.dir}" includes="*.jar"/>
-    </path>
-    
-    <!-- Define tasks -->
-    <taskdef name="deb" classpath="resources/ant/lib/ant-deb.jar" 
-        classname="com.googlecode.ant_deb_task.Deb" />
-    <taskdef name="gzip2" classpath="resources/ant/lib/ant-gzip2.jar" 
-        classname="gzip2.GZip2" />
-    <taskdef name="swt_identify" classpath="resources/ant/lib/ant-swt-identify.jar"
-        classname="ie.cdvp.utils.ant.SwtIdentify" />
-    <taskdef name="jsmooth" classpath="resources/ant/lib/jsmoothgen-ant.jar"
-        classname="net.charabia.jsmoothgen.ant.JSmoothGen" />
-    <taskdef name="izpack" classpath="resources/ant/lib/standalone-compiler.jar"
-        classname="com.izforge.izpack.ant.IzPackTask" />
-    
-    <target name="init">
-        <mkdir dir="${build.dir}"/>
-        <mkdir dir="${build.dir}/classes"/>
-        <mkdir dir="${build.dir}/packages"/>
-        <mkdir dir="${build.dir}/temp"/>
-        <mkdir dir="${doc.dir}"/>
-        <mkdir dir="${dist.dir}"/>
-    </target>
-    
-    <target name="clean">
-        <delete dir="${build.dir}/classes" />
-        <delete dir="${build.dir}/packages" />
-        <delete dir="${build.dir}/temp" />
-        <delete dir="${doc.dir}" />
-        <delete dir="${dist.dir}" />
-    </target>
-    
-    <target name="compile" depends="init">
-        <javac srcdir="${src.dir}" 
-            destdir="${build.dir}/classes" 
-            debug="${java.debug}"
-            source="${java.source.version}"
-            target="${java.target.version}">
-            <classpath refid="class.path"/>
-        </javac>
-        <!-- copy resources -->
-        <copy todir="${build.dir}/classes">
-            <fileset dir="${src.dir}">
-                <include name="**/*.html" />
-            </fileset>
-        </copy>
-    </target>
-    
-    <target name="doc" depends="init">
-        <javadoc sourcepath="${src.dir}" 
-            destdir="${doc.dir}/api" 
-            author="true" 
-            version="true" 
-            use="true" 
-            windowtitle="${app.name}" 
-            classpathref="class.path">
-        <link href="http://java.sun.com/javase/6/docs/api/"/>
-        </javadoc>
-    </target>
-    
-    <target name="dist" depends="compile,doc">
-        <!-- class file jar -->
-        <jar destfile="${dist.dir}/${bin.jar}">
-            <fileset dir="${build.dir}/classes">
-                <include name="**/*"/>
-            </fileset>
-        </jar>
-        <!-- source code jar -->
-        <jar destfile="${dist.dir}/${src.jar}">
-            <fileset dir="${src.dir}">
-                <include name="**/*.java"/>
-            </fileset>
-        </jar>
-        <!-- documentation zip -->
-        <zip destfile="${dist.dir}/${doc.zip}">
-            <fileset dir="${doc.dir}">
-                <include name="**/*"/>
-            </fileset>
-        </zip>
-    </target>
-    
-    <target name="copy-plugins">
-        <!-- Copy plugins from the other projects -->
-        <copy todir="${plugins.dir}">
-            <fileset dir="${bptplugin.dir}/dist/"  includes="BPTPlugin.plugin/**/*" />
-            <fileset dir="${igcplugin.dir}/dist/"  includes="IGCPlugin.plugin/**/*" />
-            <fileset dir="${srgplugin.dir}/dist/"  includes="SRGPlugin.plugin/**/*" />
-            <fileset dir="${sioxplugin.dir}/dist/" includes="SIOXPlugin.plugin/**/*" />
-        </copy>
-    </target>
-    
-    <target name="package-mac" depends="dist">
-        <!-- Make the folders -->
-        <mkdir dir="${dist.dir}/${app.name}.app"/>
-        <mkdir dir="${dist.dir}/${app.name}.app/Contents"/>
-        <mkdir dir="${dist.dir}/${app.name}.app/Contents/MacOS"/>
-        <mkdir dir="${dist.dir}/${app.name}.app/Contents/Resources"/>
-        <mkdir dir="${dist.dir}/${app.name}.app/Contents/Resources/Java"/>
-        <mkdir dir="${dist.dir}/${app.name}.app/Contents/Resources/Java/plugins"/>
-        
-        <!-- Copy and filter plist and PkgInfo -->
-        <copy todir="${dist.dir}/${app.name}.app/Contents/" overwrite="true">
-            <fileset dir="resources/plaf/mac/" includes="Info.plist,PkgInfo"/>
-            <filterset>
-                <filter token="name" value="${app.name}"/>
-                <filter token="version" value="${app.version}"/>
-                <filter token="synopsis" value="${app.synopsis}"/>
-                <filter token="icons" value="icon.icns"/>
-                <filter token="exename" value="ist"/>
-            </filterset>
-        </copy>
-        
-        <!-- Copy and filter launch script -->
-        <copy todir="${dist.dir}/${app.name}.app/Contents/MacOS" overwrite="true">
-            <fileset dir="resources/plaf/mac/" includes="ist" />
-            <filterset>
-                <filter token="appmain" value="${app.main}"/>
-            </filterset>
-        </copy>
-        
-        <!-- Copy resources -->
-        <copy todir="${dist.dir}/${app.name}.app/Contents/Resources">
-            <fileset dir="resources/plaf/mac" includes="icon.icns" />
-            <fileset dir="." includes="resources/config/*" />
-            <fileset dir="." includes="resources/icons/*" />
-            <fileset dir="." includes="resources/doc/*" />
-        </copy>
-        
-        <!-- Copy jars -->
-        <copy todir="${dist.dir}/${app.name}.app/Contents/Resources/Java">
-            <fileset dir="dist" includes="${bin.jar}" />
-            <fileset dir="lib" includes="istapi.jar,swt-cocoa-32.jar,swt-cocoa-64.jar,jface.jar" />
-        </copy>
-        
-        <!-- Copy plugins -->
-        <copy todir="${dist.dir}/${app.name}.app/Contents/Resources/Java/plugins">
-            <fileset dir="${plugins.dir}" >
-                <include name="**/*" />
-                <exclude name="**/*.dll" />
-                <exclude name="**/*.so" />
-            </fileset>
-        </copy>
-    
-        <!-- Make executable -->
-        <chmod perm="0755" file="${dist.dir}/${app.name}.app/Contents/MacOS/ist" />
-        
-        <!-- Bundle into a zip file -->
-        <zip destfile="${dist.dir}/${app.package}_${app.version}_mac.zip">
-            <zipfileset dir="${dist.dir}/${app.name}.app" prefix="${app.name}.app">
-                <include name="**/*" />
-                <exclude name="Contents/MacOS/*"/>
-            </zipfileset>
-        
-            <zipfileset dir="${dist.dir}/${app.name}.app" prefix="${app.name}.app" filemode="755">
-                <include name="Contents/MacOS/*" />
-            </zipfileset>
-        </zip>
-    </target>
-    
-    <target name="package-debian" depends="dist">
-        <!-- Create folder structure -->
-        <mkdir dir="${build.dir}/packages/debian/usr/bin" />
-        <mkdir dir="${build.dir}/packages/debian/usr/share/${app.package}" />
-        <mkdir dir="${build.dir}/packages/debian/usr/share/doc/${app.package}" />
-        <mkdir dir="${build.dir}/packages/debian/usr/share/applications" />
-        <mkdir dir="${build.dir}/packages/debian/usr/share/man/man1" />
-        <mkdir dir="${build.dir}/packages/debian/usr/share/icons/hicolor" />
-        
-        <!-- Man page & copyright-->
-          <gzip2 destfile="${build.dir}/packages/debian/usr/share/man/man1/ist.1.gz"
-            src="resources/plaf/debian/ist.1" level="9" filesystem="unix" />
-        <copy todir="${build.dir}/packages/debian/usr/share/doc/${app.package}"
-            file="resources/plaf/debian/copyright" />
-            
-        <!-- Shortcuts & icons -->
-        <copy tofile="${build.dir}/packages/debian/usr/share/applications/${app.package}.desktop"
-            file="resources/plaf/debian/desktop" />
-        <copy todir="${build.dir}/packages/debian/usr/share/icons/hicolor">
-            <fileset dir="resources/icons" includes="icon-*.png" />
-            <regexpmapper from="icon-(.*)\.png" to="\1x\1/apps/${app.package}.png" />
-        </copy>
-            
-        <!-- Binary (launcher) -->
-        <copy tofile="${build.dir}/packages/debian/usr/bin/ist" 
-            file="resources/plaf/debian/ist" overwrite="true">
-            <filterset>
-                <filter token="jars" value="${bin.jar}:istapi.jar:jface.jar:swt.jar"/>
-                <filter token="data" value="/usr/share/${app.package}" />
-                <filter token="main" value="${app.main}" />
-            </filterset>
-        </copy> 
-        
-        <!-- Application data -->
-        <copy todir="${build.dir}/packages/debian/usr/share/${app.package}">
-            <fileset dir="dist" includes="${bin.jar}"/>
-            <fileset dir="lib" includes="istapi.jar,jface.jar" />
-            <fileset dir="." includes="resources/config/**/*" />
-            <fileset dir="." includes="resources/icons/**/*" />
-            <fileset dir="." includes="resources/doc/**/*" />
-            <fileset dir="." >
-                <include name="plugins/**/*" />
-                <exclude name="plugins/**/*.jnilib" />
-                <exclude name="plugins/**/*.dll" />
-            </fileset>
-        </copy>
-         
-        <!-- Build i386 deb -->
-        <deb todir="dist" package="${app.package}" priority="extra"
-            section="graphics" architecture="i386"
-            depends="sun-java5-jre | sun-java6-jre"
-            postinst="resources/plaf/debian/postinst"
-            postrm="resources/plaf/debian/postrm" >
-            
-            <version upstream="${app.version}" debian="1" />
-            <changelog file="resources/plaf/debian/changelog" />
-            <changelog file="resources/plaf/debian/changelog" debian="true" />
-            <maintainer name="${app.author}" email="${app.email}" />
-            
-            <description synopsis="${app.synopsis}">
-             A tool that allows you to interactively extract an object
-             from an image using a variety of scribble based algorithms
-            </description>
-            
-            <tarfileset dir="${build.dir}/packages/debian/" includes="**/*" excludes="usr/bin/*" />
-            <tarfileset dir="${build.dir}/packages/debian/" includes="usr/bin/*" filemode="0755" />
-            <tarfileset file="${lib.dir}/swt-gtk.jar" fullpath="usr/share/${app.package}/swt.jar"/>
-         </deb>
-         
-         <!-- Build amd64 deb -->
-         <deb todir="dist" package="${app.package}" priority="extra"
-             section="graphics" architecture="amd64"
-             depends="sun-java5-jre | sun-java6-jre"
-             postinst="resources/plaf/debian/postinst"
-             postrm="resources/plaf/debian/postrm" >
-
-             <version upstream="${app.version}" debian="1" />
-             <changelog file="resources/plaf/debian/changelog" />
-             <changelog file="resources/plaf/debian/changelog" debian="true" />
-             <maintainer name="${app.author}" email="${app.email}" />
-
-             <description synopsis="${app.synopsis}">
-             A tool that allows you to interactively extract an object
-             from an image using a variety of scribble based algorithms
-             </description>
-
-             <tarfileset dir="${build.dir}/packages/debian/" includes="**/*" excludes="usr/bin/*" />
-             <tarfileset dir="${build.dir}/packages/debian/" includes="usr/bin/*" filemode="0755" />
-             <tarfileset file="${lib.dir}/swt-gtk-64.jar" fullpath="usr/share/${app.package}/swt.jar"/>
-          </deb>
-    </target>
-    
-    <target name="package-linux" depends="dist">
-        <mkdir dir="${build.dir}/packages/linux" />
-        
-        <!-- common stuff -->
-        <copy todir="${build.dir}/packages/linux" >
-            <fileset dir="dist" includes="istapp.jar"/>
-            <fileset dir="lib" includes="istapi.jar"/>
-            <fileset dir="lib" includes="jface.jar"/>
-            <fileset dir="." includes="resources/config/**/*"/>
-            <fileset dir="." includes="resources/icons/**/*"/>
-            <fileset dir="." includes="resources/doc/**/*"/>
-        </copy>
-        
-        <!-- plugins -->
-        <copy todir="${build.dir}/packages/linux" >
-            <fileset dir="." >
-                <include name="plugins/**/*" />
-                <exclude name="plugins/**/*.dll" />
-                <exclude name="plugins/**/*.jnilib" />
-                <exclude name="plugins/**/*.dynlib" />
-            </fileset>
-        </copy>
-        
-        <!-- tar i386 -->
-        <tar destfile="${dist.dir}/${app.package}_${app.version}_linux_i386.tar.gz"
-            compression="gzip">
-            <tarfileset dir="${build.dir}/packages/linux"
-                includes="**/*"
-                prefix="${app.package}_${app.version}"/>
-            <tarfileset dir="${lib.dir}"
-                includes="swt-gtk.jar"
-                fullpath="${app.package}_${app.version}/swt.jar" />
-            <tarfileset file="resources/plaf/linux/ist" 
-                fullpath="${app.package}_${app.version}/ist"
-                filemode="0755"/>
-        </tar>
-        
-        <!-- tar x86_64 -->
-        <tar destfile="${dist.dir}/${app.package}_${app.version}_linux_x86_64.tar.gz"
-            compression="gzip">
-            <tarfileset dir="${build.dir}/packages/linux"
-                includes="**/*"
-                prefix="${app.package}_${app.version}"/>
-            <tarfileset dir="${lib.dir}"
-                includes="swt-gtk-64.jar"
-                fullpath="${app.package}_${app.version}/swt.jar" />
-            <tarfileset file="resources/plaf/linux/ist" 
-                fullpath="${app.package}_${app.version}/ist"
-                filemode="0755"/>
-        </tar>
-    </target>
-    
-    <target name="package-windows" depends="dist">
-     
-        <!-- Make windows package -->
-        <mkdir dir="${build.dir}/packages/windows" />
-        <jsmooth project="resources/plaf/windows/ist.jsmooth"
-            skeletonroot="resources/plaf/windows/skeletons" />
-        <move file="resources/plaf/windows/ist.exe" 
-            todir="${build.dir}/packages/windows" />
-        <copy todir="${build.dir}/packages/windows" >
-            <fileset dir="dist" includes="istapp.jar"/>
-            <fileset dir="lib" includes="istapi.jar"/>
-            <fileset dir="lib" includes="jface.jar"/>
-            <fileset dir="lib" includes="swt-win.jar"/>
-            <fileset dir="." includes="resources/config/**/*"/>
-            <fileset dir="." includes="resources/icons/**/*"/>
-            <fileset dir="." includes="resources/doc/**/*"/>
-        </copy>
-        <copy todir="${build.dir}/packages/windows" >
-            <fileset dir="." >
-                <include name="plugins/**/*" />
-                <exclude name="plugins/**/*.so" />
-                <exclude name="plugins/**/*.jnilib" />
-                <exclude name="plugins/**/*.dynlib" />
-            </fileset>
-        </copy>
-        
-        <!-- Build an installer -->
-        <copy todir="build/temp" 
-            file="resources/plaf/windows/install.xml" overwrite="true">
-            <filterset>
-                <filter token="name" value="${app.name}" />
-                <filter token="version" value="${app.version}" />
-                <filter token="author" value="${app.author}" />
-                <filter token="email" value="${app.email}" />
-                <filter token="website" value="${app.website}" />
-            </filterset>
-        </copy>
-        <izpack input="build/temp/install.xml"
-            output="dist/${app.package}_${app.version}_win32.jar"
-            installerType="standard" basedir="." />
-        <copy todir="build/temp" 
-            file="resources/plaf/windows/installer.jsmooth" overwrite="true">
-            <filterset>
-                <filter token="input" 
-                    value="../../dist/${app.package}_${app.version}_win32.jar" />
-                <filter token="output" 
-                    value="../../dist/${app.package}_${app.version}_win32.exe" />
-                <filter token="icon" 
-                    value="../../resources/plaf/windows/installer.ico" />
-            </filterset>
-        </copy>
-        <jsmooth project="build/temp/installer.jsmooth"
-            skeletonroot="resources/plaf/windows/skeletons" />
-    </target>
-    
-    
-    
-    <target name="package" depends="package-mac,package-linux,package-debian,package-windows">
-    </target>
-    
-    <target name="default" depends="clean,package">
-    </target>
-
-</project>
diff --git a/image_annotation/lib/._swt-cocoa-32.jar b/image_annotation/lib/._swt-cocoa-32.jar
deleted file mode 100644
index aca5ab2..0000000
Binary files a/image_annotation/lib/._swt-cocoa-32.jar and /dev/null differ
diff --git a/image_annotation/lib/._swt-cocoa-64.jar b/image_annotation/lib/._swt-cocoa-64.jar
deleted file mode 100644
index 90875d7..0000000
Binary files a/image_annotation/lib/._swt-cocoa-64.jar and /dev/null differ
diff --git a/image_annotation/lib/.classpath b/image_annotation/lib/.classpath
deleted file mode 100644
index 4027147..0000000
--- a/image_annotation/lib/.classpath
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="lib" path="._swt-cocoa-32.jar"/>
-	<classpathentry kind="lib" path="._swt-cocoa-64.jar"/>
-	<classpathentry kind="lib" path="istapi-src.jar"/>
-	<classpathentry kind="lib" path="istapi.jar"/>
-	<classpathentry kind="lib" path="jface.jar"/>
-	<classpathentry kind="lib" path="swt-cocoa-32.jar"/>
-	<classpathentry kind="lib" path="swt-cocoa-64.jar"/>
-	<classpathentry kind="lib" path="swt-gtk-64.jar"/>
-	<classpathentry kind="lib" path="swt-gtk.jar"/>
-	<classpathentry kind="lib" path="swt-win.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
diff --git a/image_annotation/lib/.project b/image_annotation/lib/.project
deleted file mode 100644
index 9f09891..0000000
--- a/image_annotation/lib/.project
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>TestAnn</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-	</natures>
-</projectDescription>
diff --git a/image_annotation/lib/istapi-doc.zip b/image_annotation/lib/istapi-doc.zip
deleted file mode 100644
index 90a6377..0000000
Binary files a/image_annotation/lib/istapi-doc.zip and /dev/null differ
diff --git a/image_annotation/lib/istapi-src.jar b/image_annotation/lib/istapi-src.jar
deleted file mode 100644
index 63dd31d..0000000
Binary files a/image_annotation/lib/istapi-src.jar and /dev/null differ
diff --git a/image_annotation/lib/istapi.jar b/image_annotation/lib/istapi.jar
deleted file mode 100644
index 4ad357a..0000000
Binary files a/image_annotation/lib/istapi.jar and /dev/null differ
diff --git a/image_annotation/lib/jface.jar b/image_annotation/lib/jface.jar
deleted file mode 100644
index f515a8f..0000000
Binary files a/image_annotation/lib/jface.jar and /dev/null differ
diff --git a/image_annotation/lib/json.jar b/image_annotation/lib/json.jar
deleted file mode 100644
index 82ad5fb..0000000
Binary files a/image_annotation/lib/json.jar and /dev/null differ
diff --git a/image_annotation/lib/swt-cocoa-32.jar b/image_annotation/lib/swt-cocoa-32.jar
deleted file mode 100644
index d42da95..0000000
Binary files a/image_annotation/lib/swt-cocoa-32.jar and /dev/null differ
diff --git a/image_annotation/lib/swt-cocoa-64.jar b/image_annotation/lib/swt-cocoa-64.jar
deleted file mode 100644
index 228da89..0000000
Binary files a/image_annotation/lib/swt-cocoa-64.jar and /dev/null differ
diff --git a/image_annotation/lib/swt-gtk-64.jar b/image_annotation/lib/swt-gtk-64.jar
deleted file mode 100644
index 4ce079f..0000000
Binary files a/image_annotation/lib/swt-gtk-64.jar and /dev/null differ
diff --git a/image_annotation/lib/swt-gtk.jar b/image_annotation/lib/swt-gtk.jar
deleted file mode 100644
index 5c94f6e..0000000
Binary files a/image_annotation/lib/swt-gtk.jar and /dev/null differ
diff --git a/image_annotation/lib/swt-win.jar b/image_annotation/lib/swt-win.jar
deleted file mode 100644
index 5eb6d90..0000000
Binary files a/image_annotation/lib/swt-win.jar and /dev/null differ
diff --git a/image_annotation/plugins/BPTPlugin.plugin/bptplugin.jar b/image_annotation/plugins/BPTPlugin.plugin/bptplugin.jar
deleted file mode 100644
index d4025cf..0000000
Binary files a/image_annotation/plugins/BPTPlugin.plugin/bptplugin.jar and /dev/null differ
diff --git a/image_annotation/plugins/BPTPlugin.plugin/jbpt.dll b/image_annotation/plugins/BPTPlugin.plugin/jbpt.dll
deleted file mode 100644
index d12f777..0000000
Binary files a/image_annotation/plugins/BPTPlugin.plugin/jbpt.dll and /dev/null differ
diff --git a/image_annotation/plugins/BPTPlugin.plugin/libjbpt.jnilib b/image_annotation/plugins/BPTPlugin.plugin/libjbpt.jnilib
deleted file mode 100644
index 77039d7..0000000
Binary files a/image_annotation/plugins/BPTPlugin.plugin/libjbpt.jnilib and /dev/null differ
diff --git a/image_annotation/plugins/BPTPlugin.plugin/plugin.xml b/image_annotation/plugins/BPTPlugin.plugin/plugin.xml
deleted file mode 100644
index 4ae529d..0000000
--- a/image_annotation/plugins/BPTPlugin.plugin/plugin.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<plugin>
-	<meta name="name" value="BPT Plugin" />
-	<meta name="description" value="Binary Partition Tree Plugin" />
-	<meta name="vendor" value="Dublin City University" />
-	<meta name="author" value="Kevin McGuinness" />
-	<meta name="email" value="kevin.mcguinness@gmail.com" />
-	<meta name="segmenter" value="ie.dcu.segment.algorithm.BptSegmenter" />	
-	<jar file="bptplugin.jar" />
-</plugin>
diff --git a/image_annotation/plugins/IGCPlugin.plugin/igcplugin.jar b/image_annotation/plugins/IGCPlugin.plugin/igcplugin.jar
deleted file mode 100644
index c85393b..0000000
Binary files a/image_annotation/plugins/IGCPlugin.plugin/igcplugin.jar and /dev/null differ
diff --git a/image_annotation/plugins/IGCPlugin.plugin/jigc.dll b/image_annotation/plugins/IGCPlugin.plugin/jigc.dll
deleted file mode 100644
index b4ee98c..0000000
Binary files a/image_annotation/plugins/IGCPlugin.plugin/jigc.dll and /dev/null differ
diff --git a/image_annotation/plugins/IGCPlugin.plugin/libjigc.jnilib b/image_annotation/plugins/IGCPlugin.plugin/libjigc.jnilib
deleted file mode 100644
index 6ff9817..0000000
Binary files a/image_annotation/plugins/IGCPlugin.plugin/libjigc.jnilib and /dev/null differ
diff --git a/image_annotation/plugins/IGCPlugin.plugin/plugin.xml b/image_annotation/plugins/IGCPlugin.plugin/plugin.xml
deleted file mode 100644
index 2b7ae2e..0000000
--- a/image_annotation/plugins/IGCPlugin.plugin/plugin.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<plugin>
-	<meta name="name" value="IGC Plugin" />
-	<meta name="description" value="Interactive Graph Cuts Plugin" />
-	<meta name="vendor" value="Dublin City University" />
-	<meta name="author" value="Kevin McGuinness" />
-	<meta name="email" value="kevin.mcguinness@gmail.com" />
-	<meta name="segmenter" value="ie.dcu.segment.algorithm.IgcSegmenter" />	
-	<jar file="igcplugin.jar" />
-</plugin>
diff --git a/image_annotation/plugins/SIOXPlugin.plugin/plugin.xml b/image_annotation/plugins/SIOXPlugin.plugin/plugin.xml
deleted file mode 100644
index 623ad7b..0000000
--- a/image_annotation/plugins/SIOXPlugin.plugin/plugin.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<plugin>
-	<meta name="name" value="SIOX Plugin" />
-	<meta name="description" value="Simple Interactive Object Extraction Plugin" />
-	<meta name="vendor" value="Dublin City University" />
-	<meta name="author" value="Kevin McGuinness" />
-	<meta name="email" value="kevin.mcguinness@gmail.com" />
-	<meta name="segmenter" value="ie.dcu.segment.algorithm.SioxSegmenter" />	
-	<jar file="sioxplugin.jar" />
-	<jar file="sioxapi.jar" />
-</plugin>
diff --git a/image_annotation/plugins/SIOXPlugin.plugin/sioxapi.jar b/image_annotation/plugins/SIOXPlugin.plugin/sioxapi.jar
deleted file mode 100644
index 4c121b2..0000000
Binary files a/image_annotation/plugins/SIOXPlugin.plugin/sioxapi.jar and /dev/null differ
diff --git a/image_annotation/plugins/SIOXPlugin.plugin/sioxplugin.jar b/image_annotation/plugins/SIOXPlugin.plugin/sioxplugin.jar
deleted file mode 100644
index 31f959a..0000000
Binary files a/image_annotation/plugins/SIOXPlugin.plugin/sioxplugin.jar and /dev/null differ
diff --git a/image_annotation/plugins/SRGPlugin.plugin/jsrg.dll b/image_annotation/plugins/SRGPlugin.plugin/jsrg.dll
deleted file mode 100644
index c381fae..0000000
Binary files a/image_annotation/plugins/SRGPlugin.plugin/jsrg.dll and /dev/null differ
diff --git a/image_annotation/plugins/SRGPlugin.plugin/libjsrg.jnilib b/image_annotation/plugins/SRGPlugin.plugin/libjsrg.jnilib
deleted file mode 100644
index 46427e8..0000000
Binary files a/image_annotation/plugins/SRGPlugin.plugin/libjsrg.jnilib and /dev/null differ
diff --git a/image_annotation/plugins/SRGPlugin.plugin/plugin.xml b/image_annotation/plugins/SRGPlugin.plugin/plugin.xml
deleted file mode 100644
index 4061f98..0000000
--- a/image_annotation/plugins/SRGPlugin.plugin/plugin.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<plugin>
-	<meta name="name" value="SRG Plugin" />
-	<meta name="description" value="Seeded Region Growing Plugin" />
-	<meta name="vendor" value="Dublin City University" />
-	<meta name="author" value="Kevin McGuinness" />
-	<meta name="email" value="kevin.mcguinness@gmail.com" />
-	<meta name="segmenter" value="ie.dcu.segment.algorithm.SrgSegmenter" />	
-	<jar file="srgplugin.jar" />
-</plugin>
diff --git a/image_annotation/plugins/SRGPlugin.plugin/srgplugin.jar b/image_annotation/plugins/SRGPlugin.plugin/srgplugin.jar
deleted file mode 100644
index c888c62..0000000
Binary files a/image_annotation/plugins/SRGPlugin.plugin/srgplugin.jar and /dev/null differ
diff --git a/image_annotation/resources/ant/lib/ant-deb.jar b/image_annotation/resources/ant/lib/ant-deb.jar
deleted file mode 100644
index f602bec..0000000
Binary files a/image_annotation/resources/ant/lib/ant-deb.jar and /dev/null differ
diff --git a/image_annotation/resources/ant/lib/ant-gzip2.jar b/image_annotation/resources/ant/lib/ant-gzip2.jar
deleted file mode 100644
index 271f123..0000000
Binary files a/image_annotation/resources/ant/lib/ant-gzip2.jar and /dev/null differ
diff --git a/image_annotation/resources/ant/lib/ant-passwd-task.jar b/image_annotation/resources/ant/lib/ant-passwd-task.jar
deleted file mode 100644
index b4f4b76..0000000
Binary files a/image_annotation/resources/ant/lib/ant-passwd-task.jar and /dev/null differ
diff --git a/image_annotation/resources/ant/lib/ant-swt-identify.jar b/image_annotation/resources/ant/lib/ant-swt-identify.jar
deleted file mode 100644
index daddc1c..0000000
Binary files a/image_annotation/resources/ant/lib/ant-swt-identify.jar and /dev/null differ
diff --git a/image_annotation/resources/ant/lib/jsmoothgen-ant.jar b/image_annotation/resources/ant/lib/jsmoothgen-ant.jar
deleted file mode 100644
index c9e283d..0000000
Binary files a/image_annotation/resources/ant/lib/jsmoothgen-ant.jar and /dev/null differ
diff --git a/image_annotation/resources/ant/lib/standalone-compiler.jar b/image_annotation/resources/ant/lib/standalone-compiler.jar
deleted file mode 100644
index 2762975..0000000
Binary files a/image_annotation/resources/ant/lib/standalone-compiler.jar and /dev/null differ
diff --git a/image_annotation/resources/ant/properties b/image_annotation/resources/ant/properties
deleted file mode 100644
index 38b429c..0000000
--- a/image_annotation/resources/ant/properties
+++ /dev/null
@@ -1,14 +0,0 @@
-app.name=Interactive Segmentation Tool
-app.package=ist
-app.version=1.3.4
-app.author=Kevin McGuinness
-app.email=kevin.mcguinness@eeng.dcu.ie
-app.website=http://kspace.cdvp.dcu.ie/public/interactive-segmentation
-app.synopsis=The CDVP Interactive Segmentation Tool
-app.main=ie.dcu.apps.ist.Main
-
-# Compilation properties
-java.debug=off
-java.source.version=1.5
-java.target.version=1.5
-
diff --git a/image_annotation/resources/config/actions.mac.properties b/image_annotation/resources/config/actions.mac.properties
deleted file mode 100644
index 8a282fa..0000000
--- a/image_annotation/resources/config/actions.mac.properties
+++ /dev/null
@@ -1,108 +0,0 @@
-
-OpenAction.dialog.text=Open an image or saved context
-OpenAction.dialog.filter.exts=*.jpg;*.jpeg;*.png;*.gif;*.bmp;*.ctx
-OpenAction.dialog.filter.text=Image and Context Files
-
-SaveAction.dialog.text=Save Segmentation Context
-SaveAction.dialog.filter.exts=*.ctx
-SaveAction.dialog.filter.text=Segmentation Context Files
-
-ExportViewAction.dialog.text=Export View As Image
-ExportViewAction.dialog.filter.exts=*.jpg;*.jpeg;*.png;*.gif;*.bmp;
-ExportViewAction.dialog.filter.text=Image Files
-
-OpenExperimentAction.dialog.text=Open an experiment file
-OpenExperimentAction.dialog.filter.exts=*.exp
-OpenExperimentAction.dialog.filter.text=Experiment Files
-
-# Actions
-action.OpenAction.text=&Open...@Command+O
-action.OpenAction.image=file:resources/icons/open.png
-action.OpenAction.tooltip=Open image
-
-action.SaveAction.text=&Save@Command+S
-action.SaveAction.image=file:resources/icons/save.png
-action.SaveAction.tooltip=Save segmentation context
-
-action.SaveAsAction.text=S&ave As...@Command+Shift+S
-action.SaveAsAction.image=file:resources/icons/save-as.png
-action.SaveAsAction.tooltip=Save segmentation context as...
-
-action.ExportViewAction.text=&Current View...@Command+Alt+V
-action.ExportViewAction.image=file:resources/icons/image.png
-action.ExportViewAction.tooltip=Export view as image
-
-action.ExportImageMapAction.text=&HTML Image Map...@Command+Alt+H
-action.ExportImageMapAction.image=file:resources/icons/html.png
-action.ExportImageMapAction.tooltip=Export objects as HTML image map
-
-action.ExportTransparentPNGAction.text=Export Transparent &PNG...@Command+Alt+P
-action.ExportTransparentPNGAction.image=file:resources/icons/image.png
-action.ExportTransparentPNGAction.tooltip=Export a PNG of the current segmentation with a transparent background
-
-action.ImportAction.text=&Import...
-action.ImportAction.image=file:resources/icons/import.png
-action.ImportAction.tooltip=Import images
-
-action.PrintAction.text=&Print@Command+P
-action.PrintAction.image=file:resources/icons/print.png
-action.PrintAction.tooltip=Print view
-
-action.ExitAction.text=E&xit@Command+Q
-action.ExitAction.image=file:resources/icons/exit.png
-action.ExitAction.tooltip=Quit the application
-
-action.UndoAction.text=&Undo@Command+Z
-action.UndoAction.image=file:resources/icons/undo.png
-action.UndoAction.tooltip=Undo last markup
-
-action.RedoAction.text=&Redo@Command+Y
-action.RedoAction.image=file:resources/icons/redo.png
-action.RedoAction.tooltip=Redo markup
-
-action.CopyAction.text=&Copy@Command+C
-action.CopyAction.image=file:resources/icons/copy.png
-action.CopyAction.tooltip=Copy view to clipboard as image
-
-action.PreferencesAction.text=&Preferences...@Command+,
-action.PreferencesAction.image=file:resources/icons/preferences.png
-action.PreferencesAction.tooltip=Change application settings
-
-action.AddFilesAction.text=&Add Files...@Command+A
-action.AddFilesAction.image=file:resources/icons/add.png
-action.AddFilesAction.tooltip=Add image files to project
-
-action.RemoveFilesAction.text=&Remove Files@Command+R
-action.RemoveFilesAction.image=file:resources/icons/remove.png
-action.RemoveFilesAction.tooltip=Remove selected image files from project
-
-action.PreviousAction.text=&Previous@Command+[
-action.PreviousAction.image=file:resources/icons/previous.png
-action.PreviousAction.tooltip=Move to previous image in directory
-
-action.NextAction.text=&Next@Command+]
-action.NextAction.image=file:resources/icons/next.png
-action.NextAction.tooltip=Move to next image in directory
-
-action.HelpAction.text=&Help Contents...@Command+F1
-action.HelpAction.image=file:resources/icons/help.png
-action.HelpAction.tooltip=Show application help browser
-action.HelpAction.helpURL=http://kspace.cdvp.dcu.ie/public/interactive-segmentation/doc/help.html
-
-action.AboutAction.text=&About...
-action.AboutAction.image=file:resources/icons/about.png
-action.AboutAction.tooltip=About the application
-action.AboutAction.aboutImage=file:resources/icons/about-box.png
-
-action.OpenExperimentAction.text=Open &Experiment...
-action.OpenExperimentAction.image=file:resources/icons/experiment.png
-action.OpenExperimentAction.tooltip=Open an experiment file and switch to experiment mode
-
-action.ConfigureSegmenterAction.text=&Configure Segmenter...@Command+Shift+C
-action.ConfigureSegmenterAction.image=file:resources/icons/preferences.png
-action.ConfigureSegmenterAction.tooltip=Configure segmenter parameters
-
-action.SelectSegmenterAction.NA=Algorithm not available on this platform
-
-
-
diff --git a/image_annotation/resources/config/actions.properties b/image_annotation/resources/config/actions.properties
deleted file mode 100644
index f2ddcb0..0000000
--- a/image_annotation/resources/config/actions.properties
+++ /dev/null
@@ -1,106 +0,0 @@
-
-OpenAction.dialog.text=Open an image or saved context
-OpenAction.dialog.filter.exts=*.jpg;*.jpeg;*.png;*.gif;*.bmp;*.ctx
-OpenAction.dialog.filter.text=Image and Context Files
-
-SaveAction.dialog.text=Save Segmentation Context
-SaveAction.dialog.filter.exts=*.ctx
-SaveAction.dialog.filter.text=Segmentation Context Files
-
-ExportViewAction.dialog.text=Export View As Image
-ExportViewAction.dialog.filter.exts=*.jpg;*.jpeg;*.png;*.gif;*.bmp;
-ExportViewAction.dialog.filter.text=Image Files
-
-OpenExperimentAction.dialog.text=Open an experiment file
-OpenExperimentAction.dialog.filter.exts=*.exp
-OpenExperimentAction.dialog.filter.text=Experiment Files
-
-# Actions
-action.OpenAction.text=&Open...@Ctrl+O
-action.OpenAction.image=file:resources/icons/open.png
-action.OpenAction.tooltip=Open image
-
-action.SaveAction.text=&Save@Ctrl+S
-action.SaveAction.image=file:resources/icons/save.png
-action.SaveAction.tooltip=Save segmentation context
-
-action.SaveAsAction.text=S&ave As...@Ctrl+Shift+S
-action.SaveAsAction.image=file:resources/icons/save-as.png
-action.SaveAsAction.tooltip=Save segmentation context as...
-
-action.ExportViewAction.text=&Current View...@Ctrl+Shift+V
-action.ExportViewAction.image=file:resources/icons/image.png
-action.ExportViewAction.tooltip=Export view as image
-
-action.ExportImageMapAction.text=&HTML Image Map...@Ctrl+Shift+H
-action.ExportImageMapAction.image=file:resources/icons/html.png
-action.ExportImageMapAction.tooltip=Export objects as HTML image map
-
-action.ExportTransparentPNGAction.text=Export Transparent &PNG...@Ctrl+Shift+P
-action.ExportTransparentPNGAction.image=file:resources/icons/image.png
-action.ExportTransparentPNGAction.tooltip=Export a PNG of the current segmentation with a transparent background
-
-
-action.ImportAction.text=&Import...
-action.ImportAction.image=file:resources/icons/import.png
-action.ImportAction.tooltip=Import images
-
-action.PrintAction.text=&Print@Ctrl+P
-action.PrintAction.image=file:resources/icons/print.png
-action.PrintAction.tooltip=Print view
-
-action.ExitAction.text=E&xit@Ctrl+Q
-action.ExitAction.image=file:resources/icons/exit.png
-action.ExitAction.tooltip=Quit the application
-
-action.UndoAction.text=&Undo@Ctrl+Z
-action.UndoAction.image=file:resources/icons/undo.png
-action.UndoAction.tooltip=Undo last markup
-
-action.RedoAction.text=&Redo@Ctrl+Y
-action.RedoAction.image=file:resources/icons/redo.png
-action.RedoAction.tooltip=Redo markup
-
-action.CopyAction.text=&Copy@Ctrl+C
-action.CopyAction.image=file:resources/icons/copy.png
-action.CopyAction.tooltip=Copy view to clipboard as image
-
-action.PreferencesAction.text=&Preferences...
-action.PreferencesAction.image=file:resources/icons/preferences.png
-action.PreferencesAction.tooltip=Change application settings
-
-action.AddFilesAction.text=&Add Files...@Ctrl+A
-action.AddFilesAction.image=file:resources/icons/add.png
-action.AddFilesAction.tooltip=Add image files to project
-
-action.RemoveFilesAction.text=&Remove Files@Ctrl+R
-action.RemoveFilesAction.image=file:resources/icons/remove.png
-action.RemoveFilesAction.tooltip=Remove selected image files from project
-
-action.PreviousAction.text=&Previous@Ctrl+[
-action.PreviousAction.image=file:resources/icons/previous.png
-action.PreviousAction.tooltip=Move to previous image in directory
-
-action.NextAction.text=&Next@Ctrl+]
-action.NextAction.image=file:resources/icons/next.png
-action.NextAction.tooltip=Move to next image in directory
-
-action.HelpAction.text=&Help Contents...@Ctrl+F1
-action.HelpAction.image=file:resources/icons/help.png
-action.HelpAction.tooltip=Show application help browser
-action.HelpAction.helpURL=http://kspace.cdvp.dcu.ie/public/interactive-segmentation/doc/help.html
-
-action.AboutAction.text=&About...
-action.AboutAction.image=file:resources/icons/about.png
-action.AboutAction.tooltip=About the application
-action.AboutAction.aboutImage=file:resources/icons/about-box.png
-
-action.OpenExperimentAction.text=Open &Experiment...
-action.OpenExperimentAction.image=file:resources/icons/experiment.png
-action.OpenExperimentAction.tooltip=Open an experiment file and switch to experiment mode
-
-action.ConfigureSegmenterAction.text=&Configure Segmenter...@Ctrl+Shift+C
-action.ConfigureSegmenterAction.image=file:resources/icons/preferences.png
-action.ConfigureSegmenterAction.tooltip=Configure segmenter parameters
-
-action.SelectSegmenterAction.NA=Algorithm not available on this platform
diff --git a/image_annotation/resources/config/application.mac.properties b/image_annotation/resources/config/application.mac.properties
deleted file mode 100644
index 096ea68..0000000
--- a/image_annotation/resources/config/application.mac.properties
+++ /dev/null
@@ -1,25 +0,0 @@
-
-AppRecentMenu.icon=file:resources/icons/open-recent.png
-ExportMenu.icon=file:resources/icons/export.png
-
-# Preferences Dialog
-PrefsDialog.title=Preferences
-PrefsDialog.application=Application
-PrefsDialog.status=Status Area
-PrefsDialog.view=View Preferences
-PrefsDialog.experiment=Experiment Mode
-PrefsDialog.general.tab=General
-PrefsDialog.close.text=&Close
-PrefsDialog.reset.text=&Reset
-PrefsDialog.enable-feedback.text=Show position and color in the status area
-PrefsDialog.foreground-color.text=Foreground color for markup
-PrefsDialog.background-color.text=Background color for markup
-PrefsDialog.experiment-embedded.text=Show experiment panel embedded in main window
-PrefsDialog.confirm-exit.text=Confirm exit when application is closed
-
-# Experiment Panel
-ExperimentPanel.description.title=Task Description 
-ExperimentPanel.timeout-message=The time allocated for this task is up!
-ExperimentPanel.experiment-complete-message=The experiment has been completed
-ExperimentPanel.button.text.start=Start
-ExperimentPanel.button.text.finish=Finish
diff --git a/image_annotation/resources/config/application.properties b/image_annotation/resources/config/application.properties
deleted file mode 100644
index d21c608..0000000
--- a/image_annotation/resources/config/application.properties
+++ /dev/null
@@ -1,27 +0,0 @@
-
-AppRecentMenu.icon=file:resources/icons/open-recent.png
-ExportMenu.icon=file:resources/icons/export.png
-
-# Preferences Dialog
-PrefsDialog.title=Preferences
-PrefsDialog.application=Application
-PrefsDialog.status=Status Area
-PrefsDialog.view=View Preferences
-PrefsDialog.experiment=Experiment Mode
-PrefsDialog.general.tab=General
-PrefsDialog.close.text=&Close
-PrefsDialog.close.icon=file:resources/icons/close.png
-PrefsDialog.reset.text=&Reset
-PrefsDialog.reset.icon=file:resources/icons/reset.png
-PrefsDialog.enable-feedback.text=Show position and color in the status area
-PrefsDialog.foreground-color.text=Foreground color for markup
-PrefsDialog.background-color.text=Background color for markup
-PrefsDialog.experiment-embedded.text=Show experiment panel embedded in main window
-PrefsDialog.confirm-exit.text=Confirm exit when application is closed
-
-# Experiment Panel
-ExperimentPanel.description.title=Task Description 
-ExperimentPanel.timeout-message=The time allocated for this task is up!
-ExperimentPanel.experiment-complete-message=The experiment has been completed
-ExperimentPanel.button.text.start=Start
-ExperimentPanel.button.text.finish=Finish
diff --git a/image_annotation/resources/config/view.properties b/image_annotation/resources/config/view.properties
deleted file mode 100644
index 73be3a2..0000000
--- a/image_annotation/resources/config/view.properties
+++ /dev/null
@@ -1,49 +0,0 @@
-SegmentationView.Action.Foreground.text=Markup Foreground
-SegmentationView.Action.Foreground.tooltip=Markup Foreground Pixels
-SegmentationView.Action.Foreground.image=file:resources/icons/foreground.png
-SegmentationView.Action.Background.text=Markup Background
-SegmentationView.Action.Background.tooltip=Markup Background Pixels
-SegmentationView.Action.Background.image=file:resources/icons/background.png
-SegmentationView.Action.ZoomIn.text=Zoom In
-SegmentationView.Action.ZoomIn.tooltip=Zoom In
-SegmentationView.Action.ZoomIn.image=file:resources/icons/zoom-in.png
-SegmentationView.Action.ZoomOut.text=Zoom Out
-SegmentationView.Action.ZoomOut.tooltip=Zoom Out
-SegmentationView.Action.ZoomOut.image=file:resources/icons/zoom-out.png
-SegmentationView.Action.ZoomOriginal.text=Zoom Original
-SegmentationView.Action.ZoomOriginal.tooltip=Zoom to Original Size
-SegmentationView.Action.ZoomOriginal.image=file:resources/icons/zoom-original.png
-SegmentationView.Action.ZoomBestFit.text=Zoom Best Fit
-SegmentationView.Action.ZoomBestFit.tooltip=Zoom to Best Fit
-SegmentationView.Action.ZoomBestFit.image=file:resources/icons/zoom-best-fit.png
-SegmentationView.Action.Repaint.text=Refresh
-SegmentationView.Action.Repaint.tooltip=Refresh and repaint view
-SegmentationView.Action.Repaint.image=file:resources/icons/refresh.png
-SegmentationView.Action.Undo.text=&Undo@Ctrl+Z
-SegmentationView.Action.Undo.tooltip=Undo last markup
-SegmentationView.Action.Undo.image=file:resources/icons/undo.png
-SegmentationView.Action.Redo.text=&Redo@Ctrl+Y
-SegmentationView.Action.Redo.tooltip=Redo markup
-SegmentationView.Action.Redo.image=file:resources/icons/redo.png
-SegmentationView.Action.Clear.text=&Clear@Ctrl+DELETE
-SegmentationView.Action.Clear.tooltip=Clear all markup
-SegmentationView.Action.Clear.image=file:resources/icons/clear.png
-SegmentationView.Action.SetBrushSize.text=Set &Brush@Ctrl+B
-SegmentationView.Action.SetBrushSize.tooltip=Set the markup brush size
-SegmentationView.Action.SetBrushSize.image=file:resources/icons/brush.png
-SegmentationView.Action.AutoApply.text=Auto Segment@Ctrl+Shift+A
-SegmentationView.Action.AutoApply.tooltip=Toggle auto segment
-SegmentationView.Action.AutoApply.image=file:resources/icons/auto.png
-SegmentationView.Action.Apply.text=Segment@Ctrl+Shift+S
-SegmentationView.Action.Apply.tooltip=Apply new markup now
-SegmentationView.Action.Apply.image=file:resources/icons/apply.png
-SegmentationView.Action.SetPainter.text=View :
-SegmentationView.Action.SetPainter.tooltip=Select how to view the image/segmentation.
-SegmentationView.Action.SetPainter.image=
-SegmentationView.Action.SegmenterOptions.text=Configure Segmenter@Ctrl+Shift+C
-SegmentationView.Action.SegmenterOptions.tooltip=Configure the segmenter
-SegmentationView.Action.SegmenterOptions.image=file:resources/icons/preferences.png
-SegmentationView.Action.SetLabel.text=Annotate :
-SegmentationView.Action.SetLabel.tooltip=Annotate the segmented piece.
-SegmentationView.Action.SetLabel.image=
-
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-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
-<html><head><meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>Interactive Segmentation Tool - User Guide</title><style type="text/css">
-.guicommand {
-  font-family: "Courier New",Courier,monospace;
-  font-weight: normal;
-  color: #990100;
-}
-.guishortcut {
-  font-family: "Courier New",Courier,monospace;
-  color: #666666;
-  font-style: italic;
-}
-.section {
-  font-weight: bold;
-  color: #404040;
-}
-.all {
-  margin: 0px;
-  padding: 10px 15px 50px;
-  background-color: white;
-}
-body {
-  margin: 0px 10px;
-  padding: 0px;
-  border-right-width: 1px;
-  border-left-width: 1px;
-  font-family: Arial,Helvetica,sans-serif;
-  border-right-style: dotted;
-  border-left-style: dotted;
-  background-color: #eff0ea;
-}
-h1 {
-  margin: 0px;
-  border-bottom-style: solid;
-  border-bottom-width: 1px;
-  padding-top: 10px;
-  padding-bottom: 15px;
-  text-align: center;
-  color: #404040;
-}
-h2 {
-  text-align: center;
-  color: #404040;
-}
-h3 {
-  color: #404040;
-}
-li {
-  padding-bottom: 10px;
-}
-.footer {
-  font-size: x-small;
-  text-align: center;
-}
-
-</style></head>
-<body>
-<div class="all">
-<h1>Interactive Segmentation Tool</h1>
-<h2>User Guide</h2>
-<h3>Usage</h3>
-In this section I will outline how to perform typical operations using
-the tool, such as opening images, extracting objects and exporting
-segmentation masks.<br>
-<br>
-<span class="section">Open an Image</span>&nbsp;<br>
-To open an image, select <span class="guicommand">File-&gt;Open</span><span class="guishortcut"></span>. Recently open files can
-be accessed using the <span class="guicommand">File-&gt;Open
-Recent</span> menu. Alternatively, an image file can be dragged
-from your file system and dropped into the application to open it.
-Currently images of type JPEG, PNG, GIF, and BMP are supported.<br>
-<br>
-<span class="section">Select a Segmenter</span><br>
-There are several different segmenters available in the tool. These can
-be selected from the <span class="guicommand">Tools</span>
-menu<span class="guicommand"></span>. To select one,
-click on it.<br>
-<br>
-<span class="section">Segmenting the Image&nbsp;</span><br class="section">
-Once you have an image open and a segmenter selected, you can segment
-the image by drawing scribbles on the image. First, move the mouse over
-the object you want to extract. Left click and drag inside the object
-to draw some scribbles inside the object. Now, move the mouse outside
-the object to some background pixels. Using the right mouse button,
-scribble outside the object to select some background. If using Mac
-OSX, or if you do not have a right mouse button (Graphics Tablet etc),
-you can use <span style="font-family: monospace;">Ctrl</span>
-and click instead of right click.<br>
-<br>
-The image will be segmented and the foreground will be brightened and
-the background darkened. If you are not happy with the segmentation,
-you can add more foreground and background scribbles.<br>
-<br>
-<span class="section">Undo, Redo and Clear</span><br>
-If you make a mistake, it can be undone by selecting <span class="guicommand">Edit-&gt;Undo</span><span style="font-weight: bold;"><span style="font-weight: bold;"></span> </span>or
-clicking the undo <img style="width: 16px; height: 16px;" alt="Undo Button" src="icons/undo.png"> button in the
-toolbar. To redo, select <span class="guicommand">Edit-&gt;Redo&nbsp;</span><span style="font-weight: bold;"></span>or click the
-redo&nbsp;<img style="width: 16px; height: 16px;" alt="Redo Button" src="icons/redo.png"> button. To
-remove all forground and background markup, click on the clear&nbsp;<img style="width: 16px; height: 16px;" alt="Clear Button" src="icons/reset.png"> button in the toolbar.<br>
-<br>
-<span class="section">Zooming</span><br>
-To get a closer look at&nbsp;the image, the toolbar can also be
-used to zoom-in on the image. To zoom-in by 10% use the <img style="width: 16px; height: 16px;" alt="Zoom In" src="icons/zoom-in.png"> button. To zoom-out by 10% use
-the&nbsp;<img style="width: 16px; height: 16px;" alt="Zoom Out" src="icons/zoom-out.png"> button. To
-zoom the image such that it fits into the window without needing
-scrollbars, use the <img style="width: 16px; height: 16px;" alt="Zoom Best Fit" src="icons/zoom-best-fit.png">
-button. To restore the image to its original size use the <img style="width: 16px; height: 16px;" alt="Zoom Original" src="icons/zoom-original.png"> button.<br>
-<br>
-<span class="section">Brush Size</span><br>
-To change the brush size, use the <img style="width: 16px; height: 16px;" alt="Paintbrush" src="icons/brush.png"> button to show the brush size
-chooser. It is often useful to use a bigger brush to make markings more
-visible or to quickly mark up more pixels.<br>
-<br>
-<span class="section">Views</span><br>
-It is sometimes useful to view the segmentation results in different
-ways. The default selected view is called "Combined" and shows the
-image, it's segmentation highlighted and the scribbles all overlayed on
-the same image. By using the drop down menu, you can select a different
-view:<br>
-<ul>
-<li><span style="font-style: italic;">Combined</span>:
-Shows the image with foreground areas brightened and background areas
-darkened. The foreground and background scribbles are overlayed.</li>
-<li><span style="font-style: italic;">Original:</span>
-Shows the original image, without any segmentation or scribbles
-overlayed.</li>
-<li><span style="font-style: italic;">Markup:</span>
-Shows only the foreground and background markup (scribbles).</li>
-<li><span style="font-style: italic;">Mask:</span>
-Shows the segmentation mask. That is, an image such that the foreground
-area is completely white and the background area completely black.</li>
-<li><span style="font-style: italic;">Foreground
-Only:</span> Removes all background elements and displays only
-the foreground object.</li>
-<li><span style="font-style: italic;">Outline
-Overlayed: </span>Displays and outline of the object overlayed
-onto the original image.</li>
-</ul>
-<strong>Note:</strong><span style="font-weight: bold;">
-</span>Only the combined view displays the foreground and
-background markup (scribbles). So if you are wondering where the
-scribbles disappeared to, select the combined view to make them visible.<br>
-<br class="section">
-<span class="section">Saving and Exporting</span><br>
-To save an work in progress segmentation, select <span class="guicommand">File-&gt;Save</span> or <span class="guicommand">File-&gt;Save As</span>. This
-will save the current segmentation and markup as a context file (<span style="font-family: monospace;">.ctx</span>). When
-finished segmenting an image, you may want to export the view as an
-image. To export the current view select <span class="guicommand">File-&gt;Export</span>.
-For example, if you wanted to save the segmentation mask, select the
-mask view and then <span class="guicommand">File-&gt;Export</span>.
-<br>
-<br class="section">
-<span class="section">Configuring a Segmenter</span><br>
-Some segmenters have parameters and options that can are configurable.
-To configure the selected segmenter, select <span class="guicommand">Tools-&gt;Configure
-Segmenter</span>, or click the <img style="width: 16px; height: 16px;" alt="Configure" src="icons/configure.png"> button in the toolbar.<br>
-<br class="section">
-<span class="section">Navigating Directories of Images</span><br>
-To quickly jump to the next or previous image in the current directory
-(the one containing the open image), use the <span class="guicommand">Go-&gt;Next</span> and <span class="guicommand">Go-&gt;Previous</span> menu
-items.<br>
-<br>
-<span class="section">Experiments</span><br class="section">
-Experiment files can be opened using the <span class="guicommand">Tools-&gt;Open
-Experiment</span> menu item.<br><br><br>
-<div class="footer">Kevin McGuinness 2008
-</div>
-</div>
-</body></html>
\ No newline at end of file
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-ist (1.3.4-1) stable; urgency=low
-
-  * Support for Mac OS X leopard (64 bit JVM)
-  
-  * Fixed bug in transparent PNG export on Windows platforms
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Thur, 27 Mar 2010 19:10:00 +0000
-
-ist (1.3.3-1) stable; urgency=low
-
-  * Updated API documentation
-
-  * Larger dialog for segmenter options
-
-  * Linux plugin builds now use GCC-4.1 for better compatibility
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Wed, 7 Oct 2009 19:00:00 +0000
-
-ist (1.3.2-1) stable; urgency=low
-
-  * Moved more components to the API layer. This includes painters and the image
-    control. This allows other apps to share core components.
-    
-  * Added export transparent PNG option
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Wed, 7 Oct 2009 18:00:00 +0000
-
-ist (1.3.1-1) stable; urgency=low
-
-  * Updated export HTML feature to export XHTML
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Wed, 2 Sep 2009 18:00:00 +0000
-
-ist (1.3.0-1) stable; urgency=low
-
-  * Major restructuring of application to ease plugin development
-  
-  * New version of SWT
-  
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Mon, 24 Aug 2009 18:00:00 +0000
-
-ist (1.2.5-1) stable; urgency=low
-
-  * Added code for automated evaluation
-  
-  * Update man page and run templates
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Mon, 9 Mar 2009 16:21:00 +0000
-
-ist (1.2.4-1) stable; urgency=medium
-
-  * Fixed erratic behavior of SIOX segmenter
-  
-  * Added a lot of code for automated evaluation
-  
-  * Added option to force segmenters to retain all markup pixels in mask.
-  
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Fri, 23 Jan 2009 18:00:00 +0000
- 
-ist (1.2.3-1) stable; urgency=medium
-
-  * Fixed redo bug (redo was calling undo)
-  
-  * Segmentation context does not create an Image unless asked to now. This
-    prevents it initializing the swt Display object unless it needs to, allowing
-    console applications that use the core segmentation stuff to be created
-    without initializing the Display.
-  
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Thu, 8 Jan 2009 15:00:00 +0000
-
-ist (1.2.2-1) stable; urgency=low
-
-  * Fixed application name in menu bar on OS X
-  
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 6 Jan 2009 15:00:00 +0000
-
-ist (1.2.1-1) stable; urgency=low
-
-  * Use command key instead of ctrl key for shortcuts on Mac OSX
-  
-  * Zip file for app bundle on OS X: it's better supported than tar.gz
-  
-  * Modified about box to display SWT version
-  
-  * Added standard Command+, binding for preferences on Mac
-  
-  * Use small icons in menus on all platforms
-  
-  * Removed icons in preference dialog buttons on Mac OS
-  
-  * Improved and included several new icons
-  
-  * Fixed visual bug on linux: horizontal separators didn't look right in
-    the export dialog.
-  
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Wed, 17 Dec 2008 17:00:00 +0000
-
-ist (1.2.0-1) stable; urgency=low
-  
-  * New feature: export to HTML image maps integrated. Supports exporting 
-    polygons and rectangles for now. Can export several rollover effects using 
-    the javascript image swapping technique.
-    
-  * Fixed bug on Mac OS X: application did not always exit properly
-  
-  * Open browser window to show the HTML page when export completes
-  
-  * Option to turn on or off the open browser window behavior
-  
-  * Best practices: use var for global image preloads.
-    
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 16 Dec 2008 21:37:00 +0000
-
-ist (1.1.0-1) stable; urgency=low
-  
-  * Several new features are planned for introduction, so the version number
-    has been incremented to 1.1
-  
-  * Changed context file format. This is now stored as a zip archive including 
-    the image, mask and annotations, so that it is more "self-contained". The
-    new file format is NOT compatible with the old one.
-    
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 29 Feb 2008 12:25:00 +0000
-
-ist (1.0.6-1) stable; urgency=low
-
-  * Added startup check for gdiplus.dll for platforms where it's needed but not 
-    installed by default. Program will now show a useful message and exit gracefully
-    instead of spewing stack traces on the console and behaving oddly.
-    
-  * Fixed bug that caused the auto-apply toggle button to be always disabled
-    after first image load.
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 28 Feb 2008 10:36:00 +0000
-
-ist (1.0.5-1) stable; urgency=medium
-
-  * Fixed bug that caused the brush control (and some other toolbar buttons) to be
-    disabled after an experiment was cancelled.
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 12 Feb 2008 13:25:00 +0000
- 
-ist (1.0.4-1) stable; urgency=low
-
-  * Updated the integrated help file (help.html)
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 28 Jan 2008 16:40:00 +0000
-
-ist (1.0.3-1) stable; urgency=low
-
-  * MacOSX PowerPC now supported
-
-  * Mostly non-functional changes on Linux, refactoring and the like
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 25 Jan 2008 16:08:00 +0000
-
-ist (1.0.2-1) stable; urgency=low
-
-  * Application icon added
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 16 Jan 2008 19:43:00 +0000
-
-ist (1.0.1-1) stable; urgency=low
-
-  * Created debian package
-  
-  * Support added for 64 bit linux
-
- -- Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>  Tue, 15 Jan 2008 19:43:00 +0000
diff --git a/image_annotation/resources/plaf/debian/copyright b/image_annotation/resources/plaf/debian/copyright
deleted file mode 100644
index 32da294..0000000
--- a/image_annotation/resources/plaf/debian/copyright
+++ /dev/null
@@ -1,10 +0,0 @@
-ist
-
-Copyright: Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>
-           Center for Digital Video Processing
-           Dublin City University
-
-2008-01-14
-
-The home page of ist is at: 
-https://www.kspace.cdvp.dcu.ie/public/interactive-segmentation
diff --git a/image_annotation/resources/plaf/debian/desktop b/image_annotation/resources/plaf/debian/desktop
deleted file mode 100644
index 718ced1..0000000
--- a/image_annotation/resources/plaf/debian/desktop
+++ /dev/null
@@ -1,10 +0,0 @@
-# freedesktop.org desktop entry
-[Desktop Entry]
-Version=1.0
-Type=Application
-Name=Interactive Segmentation Tool
-Comment=Interactively extract objects from images using various algorithms
-Icon=ist
-Exec=ist
-Terminal=false
-Categories=GTK;Graphics
diff --git a/image_annotation/resources/plaf/debian/ist b/image_annotation/resources/plaf/debian/ist
deleted file mode 100644
index d1e385d..0000000
--- a/image_annotation/resources/plaf/debian/ist
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/sh
-
-# Setup
-data=@data@
-main=@main@
-jars=@jars@
-
-# Change directory
-cd "${data}"
-
-# This is needed for the browser widget on linux
-if [ -z "${MOZILLA_FIVE_HOME}" ]; then
-	# Check if common locations exist
-	if [ -d "/usr/lib/firefox" ]; then
-		export MOZILLA_FIVE_HOME=/usr/lib/firefox
-	elif [ -d "/usr/lib/mozilla-firefox" ]; then
-		export MOZILLA_FIVE_HOME=/usr/lib/mozilla-firefox
-	elif [ -d "/usr/lib/mozilla" ]; then
-		export MOZILLA_FIVE_HOME=/usr/lib/mozilla
-	fi
-fi
-
-# Set library path
-if [ -n "${MOZILLA_FIVE_HOME}" ]; then
-	export LD_LIBRARY_PATH=${MOZILLA_FIVE_HOME}:${LD_LIBRARY_PATH}
-fi
-
-# Launch
-if [ -n "${JAVA_HOME}" ]; then
-	${JAVA_HOME}/bin/java -classpath "${jars}" ${main} $*
-else
-	java -classpath "${jars}" ${main} $*
-fi
-
-cd "$OLDPWD"
-
diff --git a/image_annotation/resources/plaf/debian/ist.1 b/image_annotation/resources/plaf/debian/ist.1
deleted file mode 100644
index 29faaf6..0000000
--- a/image_annotation/resources/plaf/debian/ist.1
+++ /dev/null
@@ -1,29 +0,0 @@
-.TH "ist" "1" "1.3.3" "Kevin McGuinness" "Graphics"
-.SH "NAME"
-.LP 
-ist \- Interactive Segmentation Tool
-.SH "SYNTAX"
-.LP 
-ist [options]
-
-.SH "DESCRIPTION"
-.LP 
-Launches the interactive segmentation tool graphical user interface
-
-.SH "ENVIRONMENT VARIABLES"
-.LP 
-.TP 
-\fBMOZILLA_FIVE_HOME\fP
-Specifies the location of the mozilla 5 browser 
-(firefox etc.). This is usually something like 
-/usr/lib/firefox
-
-.SH "EXAMPLES"
-.LP 
-To run this program the standard way type:
-.LP 
-$ ist
-
-.SH "AUTHORS"
-.LP 
-Kevin McGuinness <kevin.mcguinness@eeng.dcu.ie>
diff --git a/image_annotation/resources/plaf/debian/postinst b/image_annotation/resources/plaf/debian/postinst
deleted file mode 100644
index fb29bea..0000000
--- a/image_annotation/resources/plaf/debian/postinst
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-sudo update-desktop-database
-sudo gtk-update-icon-cache /usr/share/icons/hicolor
diff --git a/image_annotation/resources/plaf/debian/postrm b/image_annotation/resources/plaf/debian/postrm
deleted file mode 100644
index fb29bea..0000000
--- a/image_annotation/resources/plaf/debian/postrm
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-sudo update-desktop-database
-sudo gtk-update-icon-cache /usr/share/icons/hicolor
diff --git a/image_annotation/resources/plaf/linux/ist b/image_annotation/resources/plaf/linux/ist
deleted file mode 100644
index 1f45a3a..0000000
--- a/image_annotation/resources/plaf/linux/ist
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/sh
-
-jars=istapp.jar:istapi.jar:swt.jar:jface.jar
-main=ie.dcu.apps.ist.Main
-
-# Change directory
-cd "`dirname "$0"`"
-
-# This is needed for the SWT browser widget on linux
-if [ -z "${MOZILLA_FIVE_HOME}" ]; then
-
-	# Check if common locations exist
-	if [ -d "/usr/lib/firefox" ]; then
-		export MOZILLA_FIVE_HOME=/usr/lib/firefox
-	elif [ -d "/usr/lib/mozilla-firefox" ]; then
-		export MOZILLA_FIVE_HOME=/usr/lib/mozilla-firefox
-	elif [ -d "/usr/lib/mozilla" ]; then
-		export MOZILLA_FIVE_HOME=/usr/lib/mozilla
-	fi
-	
-fi
-
-# Set library path
-if [ -n "${MOZILLA_FIVE_HOME}" ]; then
-	export LD_LIBRARY_PATH=${MOZILLA_FIVE_HOME}:${LD_LIBRARY_PATH}
-fi
-
-if [ -n "${JAVA_HOME}" ]; then
-	${JAVA_HOME}/bin/java -classpath "${jars}"  ${main} $*
-else
-	java -classpath "${jars}" ${main} $*
-fi
-
-cd "$OLDPWD"
diff --git a/image_annotation/resources/plaf/mac/Info.plist b/image_annotation/resources/plaf/mac/Info.plist
deleted file mode 100644
index 0fbcac6..0000000
--- a/image_annotation/resources/plaf/mac/Info.plist
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN"
-                       "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
-<plist version="1.0">
-  <dict>
-    <key>CFBundleName</key>
-    <string>@name@</string>
-    <key>CFBundleShortVersionString</key>
-    <string>@version@</string>
-    <key>CFBundleGetInfoString</key>
-    <string>@synopsis@ (v@version@)</string>
-    <key>CFBundleAllowMixedLocalizations</key>
-    <string>false</string>
-    <key>CFBundleInfoDictionaryVersion</key>
-    <string>6.0</string>
-    <key>CFBundleExecutable</key>
-    <string>@exename@</string>
-    <key>CFBundleDevelopmentRegion</key>
-    <string>English</string>
-    <key>CFBundlePackageType</key>
-    <string>APPL</string>
-    <key>CFBundleSignature</key>
-    <string>????</string>
-    <key>CFBundleIconFile</key>
-    <string>@icons@</string>
-  </dict>
-</plist>
diff --git a/image_annotation/resources/plaf/mac/PkgInfo b/image_annotation/resources/plaf/mac/PkgInfo
deleted file mode 100644
index 6f749b0..0000000
--- a/image_annotation/resources/plaf/mac/PkgInfo
+++ /dev/null
@@ -1 +0,0 @@
-APPL????
diff --git a/image_annotation/resources/plaf/mac/icon.icns b/image_annotation/resources/plaf/mac/icon.icns
deleted file mode 100644
index ae867d3..0000000
Binary files a/image_annotation/resources/plaf/mac/icon.icns and /dev/null differ
diff --git a/image_annotation/resources/plaf/mac/ist b/image_annotation/resources/plaf/mac/ist
deleted file mode 100644
index 07663d1..0000000
--- a/image_annotation/resources/plaf/mac/ist
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/sh
-
-# What kinda mac are we on
-CPU=`uname -p`
-
-# Absolute path to where the app was launched from
-APP_PACKAGE="`dirname "$0"`/../.."
-APP_PACKAGE="`cd "${APP_PACKAGE}"; pwd`"
-
-# Locations of resources, jars, and libs
-LIB_DIR="Libraries/${CPU}"
-
-# Move to the resource directory
-cd "${APP_PACKAGE}/Contents/Resources"
-
-# Establish whether we should use the 32 bit or 64 bit cocoa library
-SWT_LIBNAME=swt-cocoa-32.jar
-java -version 2>&1 | grep "64-Bit" > /dev/null
-if [ "$?" -eq "0" ]; then
-	SWT_LIBNAME=swt-cocoa-64.jar
-fi
-
-echo "SWT Library: ${SWT_LIBNAME}"
-
-# Launch app
-java \
-  -XstartOnFirstThread \
-  -classpath "Java/istapp.jar:Java/istapi.jar:Java/jface.jar:Java/${SWT_LIBNAME}" \
-  -Dorg.eclipse.swt.internal.carbon.noFocusRing \
-  -Dorg.eclipse.swt.internal.carbon.smallFonts \
-  @appmain@ $*
-
-# Go back to the old working directory
-cd "${OLDPWD}"
diff --git a/image_annotation/resources/plaf/windows/application.ico b/image_annotation/resources/plaf/windows/application.ico
deleted file mode 100644
index ae1ac33..0000000
Binary files a/image_annotation/resources/plaf/windows/application.ico and /dev/null differ
diff --git a/image_annotation/resources/plaf/windows/install.xml b/image_annotation/resources/plaf/windows/install.xml
deleted file mode 100644
index 23cb85e..0000000
--- a/image_annotation/resources/plaf/windows/install.xml
+++ /dev/null
@@ -1,56 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1" standalone="yes" ?>
-
-<!-- 
-    IzPack install file for the Interactive Segmentation Tool
--->
-
-<installation version="1.0">
-
-    <!-- The info section. -->
-    <info>
-        <appname>@name@</appname>
-        <appversion>@version@</appversion>
-        <authors>
-            <author name="@author@" email="@email@"/>
-        </authors>
-        <url>@website@</url>
-        <javaversion>1.5</javaversion>
-    </info>
-
-    <!-- The gui preferences indication. -->
-    <guiprefs width="640" height="480" resizable="no"/>
-
-    <!-- The locale section. -->
-    <locale>
-        <langpack iso3="eng"/>
-    </locale>
-
-    <!-- The resources section. -->
-    <resources>
-        <res src="resources/plaf/windows/shortcuts.xml" id="shortcutSpec.xml"/>
-    </resources>
-
-    <!-- Shell-link for windows. -->
-    <native type="izpack" name="ShellLink.dll" />
-
-    <!-- The panels section. -->
-    <panels>
-        <panel classname="HelloPanel"/>
-        <panel classname="TargetPanel"/> 
-        <panel classname="PacksPanel"/>
-        <panel classname="InstallPanel"/>
-        <panel classname="ShortcutPanel"/>
-        <panel classname="FinishPanel"/>
-    </panels>
-
-    <!-- The packs section. -->
-    <packs>
-        <pack name="Base" required="yes">
-            <description> Base installation files </description>
-            <fileset dir="build/packages/windows" targetdir="${INSTALL_PATH}" >
-                <include name="**/*" />
-            </fileset>
-        </pack>
-    </packs>
-    
-</installation>
diff --git a/image_annotation/resources/plaf/windows/installer.ico b/image_annotation/resources/plaf/windows/installer.ico
deleted file mode 100644
index 66d530f..0000000
Binary files a/image_annotation/resources/plaf/windows/installer.ico and /dev/null differ
diff --git a/image_annotation/resources/plaf/windows/installer.jsmooth b/image_annotation/resources/plaf/windows/installer.jsmooth
deleted file mode 100644
index 823d035..0000000
--- a/image_annotation/resources/plaf/windows/installer.jsmooth
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="ISO-8859-1"?>
-<jsmoothproject>
-    <JVMSearchPath>registry</JVMSearchPath>
-    <JVMSearchPath>javahome</JVMSearchPath>
-    <JVMSearchPath>jrepath</JVMSearchPath>
-    <JVMSearchPath>jdkpath</JVMSearchPath>
-    <JVMSearchPath>exepath</JVMSearchPath>
-    <JVMSearchPath>jview</JVMSearchPath>
-    <jarLocation>@input@</jarLocation>
-    <iconLocation>@icon@</iconLocation>
-    <currentDirectory>${EXECUTABLEPATH}</currentDirectory>
-    <embeddedJar>true</embeddedJar>
-    <executableName>@output@</executableName>
-    <initialMemoryHeap>-1</initialMemoryHeap>
-    <mainClassName>com.izforge.izpack.installer.Installer</mainClassName>
-    <maximumMemoryHeap>-1</maximumMemoryHeap>
-    <maximumVersion></maximumVersion>
-    <minimumVersion>1.5</minimumVersion>
-    <skeletonName>Windowed Wrapper</skeletonName>
-    <skeletonProperties>
-        <key>Message</key>
-        <value>Java has not been found on your computer.
-        Do you want to download it?</value>
-    </skeletonProperties>
-    <skeletonProperties>
-        <key>Debug</key>
-        <value>0</value>
-    </skeletonProperties>
-</jsmoothproject>
diff --git a/image_annotation/resources/plaf/windows/ist.jsmooth b/image_annotation/resources/plaf/windows/ist.jsmooth
deleted file mode 100644
index 52388f9..0000000
--- a/image_annotation/resources/plaf/windows/ist.jsmooth
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="ISO-8859-1"?>
-<jsmoothproject>
-    <JVMSearchPath>registry</JVMSearchPath>
-    <JVMSearchPath>javahome</JVMSearchPath>
-    <JVMSearchPath>jrepath</JVMSearchPath>
-    <JVMSearchPath>jdkpath</JVMSearchPath>
-    <JVMSearchPath>exepath</JVMSearchPath>
-    <JVMSearchPath>jview</JVMSearchPath>
-    <classPath>istapp.jar</classPath>
-    <classPath>istapi.jar</classPath>
-    <classPath>swt-win.jar</classPath>
-    <classPath>jface.jar</classPath>
-    <currentDirectory>${EXECUTABLEPATH}</currentDirectory>
-    <embeddedJar>false</embeddedJar>
-    <executableName>ist.exe</executableName>
-    <iconLocation>application.ico</iconLocation>
-    <initialMemoryHeap>-1</initialMemoryHeap>
-    <mainClassName>ie.dcu.apps.ist.Main</mainClassName>
-    <maximumMemoryHeap>-1</maximumMemoryHeap>
-    <minimumVersion>1.5.0</minimumVersion>
-    <skeletonName>Windowed Wrapper</skeletonName>
-    <skeletonProperties>
-        <key>Message</key>
-        <value>This program needs Java to run.
-        Please download it at http://www.java.com</value>
-    </skeletonProperties>
-    <skeletonProperties>
-        <key>Debug</key>
-        <value>0</value>
-    </skeletonProperties>
-</jsmoothproject>
diff --git a/image_annotation/resources/plaf/windows/shortcuts.xml b/image_annotation/resources/plaf/windows/shortcuts.xml
deleted file mode 100644
index d34c867..0000000
--- a/image_annotation/resources/plaf/windows/shortcuts.xml
+++ /dev/null
@@ -1,36 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
-<shortcuts>
-	<skipIfNotSupported/>
-	<programGroup defaultName="IST" location="applications"/>
-	
-	<shortcut
-		name="Interactive Segmentation Tool"
-		target="$INSTALL_PATH\ist.exe"
-		workingDirectory="$INSTALL_PATH"
-		description="Launch the Interactive Segmentation Tool"
-		initialState="normal"
-		programGroup="yes"
-		desktop="yes"
-		applications="no"
-		startMenu="no"
-		startup="no"
-	>
-		<createForPack name="Base"/>
-	</shortcut>
-
-	<shortcut
-		name="Uninstall"
-		target="${JAVA_HOME}\bin\java.exe"
-		commandLine="-jar &quot;$INSTALL_PATH/Uninstaller/uninstaller.jar&quot;"
-		description="Uninstall Interactive Segmentation Tool"
-		initialState="noShow"
-		programGroup="yes"
-		desktop="no"
-		applications="no"
-		startMenu="no"
-		startup="no"
-	>
-		<createForPack name="Base"/>
-	</shortcut>
-
-</shortcuts>
diff --git a/image_annotation/resources/plaf/windows/skeletons/windowed-wrapper/description.skel b/image_annotation/resources/plaf/windows/skeletons/windowed-wrapper/description.skel
deleted file mode 100644
index 52acb08..0000000
--- a/image_annotation/resources/plaf/windows/skeletons/windowed-wrapper/description.skel
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="ISO-8859-1"?>
-<jsmoothskeleton>
-<debug>false</debug>
-<description>SKEL_SIMPLEWRAPPER_DESCRIPTION</description>
-<executableName>jwrap.exe</executableName>
-<resourceCategory>JAVA</resourceCategory>
-<resourceJarId>102</resourceJarId>
-<resourcePropsId>103</resourcePropsId>
-<shortName>Windowed Wrapper</shortName>
-<skeletonProperties>
-<description>SKEL_SIMPLEWRAPPER_PROPERTY_MESSAGE_DESCRIPTION</description>
-<idName>Message</idName>
-<label>SKEL_SIMPLEWRAPPER_PROPERTY_MESSAGE_LABEL</label>
-<type>textarea</type>
-<value>Java has not been found on your computer. Do you want to download it?</value>
-</skeletonProperties>
-<skeletonProperties>
-<description>SKEL_SIMPLEWRAPPER_PROPERTY_URL_DESCRIPTION</description>
-<idName>URL</idName>
-<label>SKEL_SIMPLEWRAPPER_PROPERTY_URL_LABEL</label>
-<type>string</type>
-<value>http://www.java.com</value>
-</skeletonProperties>
-<skeletonProperties>
-<description>SKEL_GENERIC_PROPERTY_SINGLEPROCESS_DESCRIPTION</description>
-<idName>SingleProcess</idName>
-<label>SKEL_GENERIC_PROPERTY_SINGLEPROCESS_LABEL</label>
-<type>boolean</type>
-<value>0</value>
-</skeletonProperties>
-<skeletonProperties>
-<description>SKEL_GENERIC_SINGLEINSTANCE_DESCRIPTION</description>
-<idName>SingleInstance</idName>
-<label>SKEL_GENERIC_SINGLEINSTANCE</label>
-<type>boolean</type>
-<value>0</value>
-</skeletonProperties>
-<skeletonProperties>
-<description>SKEL_GENERIC_JNISMOOTH_DESCRIPTION</description>
-<idName>JniSmooth</idName>
-<label>SKEL_GENERIC_JNISMOOTH</label>
-<type>boolean</type>
-<value>0</value>
-</skeletonProperties>
-<skeletonProperties>
-<description>SKEL_GENERIC_PROPERTY_DEBUG_DESCRIPTION</description>
-<idName>Debug</idName>
-<label>SKEL_GENERIC_PROPERTY_DEBUG_LABEL</label>
-<type>boolean</type>
-<value>0</value>
-</skeletonProperties>
-</jsmoothskeleton>
diff --git a/image_annotation/resources/plaf/windows/skeletons/windowed-wrapper/jwrap.exe b/image_annotation/resources/plaf/windows/skeletons/windowed-wrapper/jwrap.exe
deleted file mode 100755
index 436402d..0000000
Binary files a/image_annotation/resources/plaf/windows/skeletons/windowed-wrapper/jwrap.exe and /dev/null differ
diff --git a/image_annotation/src/ie/dcu/apps/ist/AppPrefs.java b/image_annotation/src/ie/dcu/apps/ist/AppPrefs.java
deleted file mode 100644
index fabc554..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/AppPrefs.java
+++ /dev/null
@@ -1,259 +0,0 @@
-package ie.dcu.apps.ist;
-
-import ie.dcu.swt.SwtUtils;
-
-import java.util.*;
-import java.util.logging.Logger;
-import java.util.prefs.*;
-
-import org.eclipse.swt.graphics.RGB;
-import org.eclipse.swt.widgets.Display;
-
-/**
- * Manages application preferences
- * 
- * @author Kevin McGuinness
- */
-public class AppPrefs {
-	
-	public interface Keys {
-		public static final String ENABLE_FEEDBACK = "enable-feedback";
-		public static final String FOREGROUND_COLOR = "foreground-color";
-		public static final String BACKGROUND_COLOR = "background-color";
-		public static final String EXPERIMENT_EMBEDDED = "experiment-embedded";
-		public static final String CONFIRM_EXIT = "confirm-exit";
-	}
-	
-	public interface SupportedTypes {
-		public static final Class<Integer> INTEGER = Integer.class;
-		public static final Class<Double>  DOUBLE  = Double.class;
-		public static final Class<Float>   FLOAT   = Float.class;
-		public static final Class<Short>   SHORT   = Short.class;
-		public static final Class<Byte>    BYTE    = Byte.class;
-		public static final Class<Long>    LONG    = Long.class;
-		public static final Class<String>  STRING  = String.class;
-		public static final Class<Boolean> BOOLEAN = Boolean.class;
-		public static final Class<RGB>     RGB     = RGB.class;
-	}
-	
-	
-	private final Logger log;
-	private final Preferences prefs;
-	private final List<PreferenceChangeListener> listeners;
-
-	
-	public AppPrefs() {
-		this.log = Logger.getLogger(getClass().getName());
-		this.prefs = Preferences.userRoot().node(Application.APP_ID);
-		this.listeners = new LinkedList<PreferenceChangeListener>();
-		
-		addSwtThreadAdaptionListener();
-	}
-	
-	
-	private void addSwtThreadAdaptionListener() {
-		prefs.addPreferenceChangeListener(new PreferenceChangeListener() {
-			public void preferenceChange(PreferenceChangeEvent evt) {
-				firePreferenceChangedSynced(evt);
-			}
-		});
-	}
-
-
-	private void firePreferenceChangedSynced(final PreferenceChangeEvent evt) {
-			
-		// Delegate to event SWT event dispatching thread
-		Display.getDefault().syncExec(new Runnable() {
-			public void run() {
-				firePreferenceChanged(evt);	
-			}
-		});
-	
-	}
-
-
-	private void firePreferenceChanged(PreferenceChangeEvent evt) {
-		for (PreferenceChangeListener listener : listeners) {
-			listener.preferenceChange(evt);
-		}
-	}
-
-
-	public void sync() {
-		try {
-			prefs.sync();
-		} catch (BackingStoreException e) {
-			log.warning("Error syncing preferences: " + e.getMessage());
-		}
-	}
-	
-	
-	public void flush() {
-		try {
-			prefs.flush();
-		} catch (BackingStoreException e) {
-			log.warning("Error writing preferences: " + e.getMessage());
-		}
-	}
-	
-
-	public void clear() {
-		try {
-			prefs.clear();
-		} catch (BackingStoreException e) {
-			log.warning("Error clearing preferences: " + e.getMessage());
-		}
-	}
-
-
-	public String[] keys() {
-		try {
-			return prefs.keys();
-		} catch (BackingStoreException e) {
-			log.warning("Error retrieving preference keys: " + e.getMessage());
-		}
-		return new String[0];
-	}
-
-
-	public void remove(String key) {
-		prefs.remove(key);
-	}
-
-
-	public <T> T get(Class<T> clazz, String key, T def) {
-		String value =  (def != null) ? 
-				get(key, def.toString()) : get(key, null);
-		
-		return decode(clazz, value, def);
-	}
-	
-
-	public <T> void put(Class<T> clazz, String key, T value) {
-		prefs.put(key, encode(clazz, value));
-	}
-	
-	
-	public void put(String key, String value) {
-		prefs.put(key, value);
-	}
-	
-	
-	public String get(String key, String def) {
-		return prefs.get(key, def);
-	}
-	
-	
-	public void addPreferenceChangeListener(PreferenceChangeListener pcl) {
-		listeners.add(pcl);
-	}
-
-
-	public void removePreferenceChangeListener(PreferenceChangeListener pcl) {
-		listeners.remove(pcl);
-	}
-
-
-	public <T> String encode(Class<T> clazz, T value) {
-		if (clazz.equals(RGB.class)) {
-			return encodeRGB((RGB) value);
-		} else if (value != null) {
-			return String.valueOf(value);
-		} else {
-			return null;
-		}
-	}
-	
-	
-	public <T> T decode(Class<T> clazz, String str, T def) {
-		if (str == null) {
-			return def;
-		}	else if (isNumeric(clazz)) {
-			return clazz.cast(decodeNumeric(clazz, str, def));
-		} else if (isString(clazz)) {
-			return clazz.cast(str);
-		} else if (isBoolean(clazz)) {
-			return clazz.cast(decodeBoolean(str, (Boolean) def));
-		} else if (clazz.equals(RGB.class)) {
-			return clazz.cast(decodeRGB(str, (RGB) def));
-		} else {
-			log.warning("Unable to decode class: " + clazz.getName());
-		}
-		
-		return def;
-	}
-	
-	
-	private boolean isString(Class<?> clazz) {
-		return clazz.equals(String.class);
-	}
-	
-	
-	private boolean isBoolean(Class<?> clazz) {
-		return clazz.equals(Boolean.class);
-	}
-	
-	
-	
-	private boolean isNumeric(Class<?> clazz) {
-		return 
-			clazz.equals(Integer.class) ||
-			clazz.equals(Double.class) ||
-			clazz.equals(Float.class) ||
-			clazz.equals(Short.class) ||
-			clazz.equals(Byte.class) ||
-			clazz.equals(Long.class);      
-	}
-	
-	
-	private RGB decodeRGB(String str, RGB def) {
-		if (str.startsWith("#")) {
-			try {
-				int hex = Integer.parseInt(str.substring(1), 16);
-				return SwtUtils.int2rgb(hex);
-			} catch (NumberFormatException e) {
-				log.warning("Not a valid color: " + str);
-			}
-		}
-		return def;
-	}
-	
-	
-	private String encodeRGB(RGB rgb) {
-		return String.format("#%06x", SwtUtils.rgb2int(rgb));
-	}
-	
-	
-	private boolean decodeBoolean(String str, boolean def) {
-		return str.equalsIgnoreCase("true") ||
-			(str.equalsIgnoreCase("false") ? false : def);
-	}
-	
-	
-	private <T> T decodeNumeric(Class<T> clazz, String s, T def) {
-		try {
-			if (clazz.equals(Integer.class)) {
-				return clazz.cast(Integer.parseInt(s));
-				
-			} else if (clazz.equals(Double.class)) {
-				return clazz.cast(Double.parseDouble(s));
-			
-			} else if (clazz.equals(Float.class)) {
-				return clazz.cast(Float.parseFloat(s));
-			
-			} else if (clazz.equals(Short.class)) {
-				return clazz.cast(Short.parseShort(s));
-			
-			} else if (clazz.equals(Byte.class)) {
-				return clazz.cast(Byte.parseByte(s));
-			
-			} else if (clazz.equals(Long.class)) {
-				return clazz.cast(Long.parseLong(s));
-			
-			}  
-		} catch (NumberFormatException ex) {
-			log.warning("Invalid numeric value in preferences: " + s);
-		}
-		return def;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/AppPrefsManager.java b/image_annotation/src/ie/dcu/apps/ist/AppPrefsManager.java
deleted file mode 100644
index e41ea3b..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/AppPrefsManager.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package ie.dcu.apps.ist;
-
-import static ie.dcu.segment.annotate.AnnotationType.*;
-import static ie.dcu.apps.ist.AppPrefs.Keys.*;
-import static ie.dcu.apps.ist.AppPrefs.SupportedTypes.*;
-import ie.dcu.segment.annotate.*;
-import ie.dcu.apps.ist.AppPrefs.*;
-
-import java.util.prefs.*;
-
-import org.eclipse.jface.resource.*;
-import org.eclipse.swt.graphics.*;
-
-/**
- * Manages updating various components when preferences change.
- * 
- * @author Kevin McGuinness
- */
-class AppPrefsManager implements PreferenceChangeListener {
-	
-	private final AppWindow window;
-	private final ColorRegistry colorRegistry;
-	private final AppPrefs prefs;
-	
-
-	public AppPrefsManager(AppWindow window) {
-		this.window = window;
-		this.colorRegistry = JFaceResources.getColorRegistry();
-		this.prefs = loadPreferences();
-	}
-	
-	
-	private AppPrefs loadPreferences() {
-		AppPrefs prefs = new AppPrefs();
-		prefs.addPreferenceChangeListener(this);
-		return prefs;
-	}
-	
-	
-	public AppPrefs getPrefs() {
-		return prefs;
-	}
-	
-	
-	public void update() {
-		updateFeedbackEnabled();
-		updateBackgroundColor();
-		updateForegroundColor();
-		updateExperimentEmbedded();
-	}
-	
-	
-	public void updateExperimentEmbedded() {
-		boolean on = prefs.get(BOOLEAN, Keys.EXPERIMENT_EMBEDDED, false);
-		window.setExperimentModeEmbedded(on);
-	}
-	
-	
-	public void updateFeedbackEnabled() {
-		boolean on = prefs.get(BOOLEAN, Keys.ENABLE_FEEDBACK, true);
-		window.setEnableFeedback(on);
-	}
-	
-	
-	public void updateForegroundColor() {
-		RGB color = prefs.get(RGB, Keys.FOREGROUND_COLOR, DEFAULT_FOREGROUND);
-		colorRegistry.put(AnnotationType.Foreground.key, color);
-		window.getView().repaint();
-	}
-	
-	
-	public void updateBackgroundColor() {
-		RGB color = prefs.get(RGB, Keys.BACKGROUND_COLOR, DEFAULT_BACKGROUND);
-		colorRegistry.put(AnnotationType.Background.key, color);
-		window.getView().repaint();
-	}
-	
-
-	public void preferenceChange(PreferenceChangeEvent evt) {
-		String pref = evt.getKey();
-		
-		if (pref.equals(ENABLE_FEEDBACK)) {
-			updateFeedbackEnabled();
-		
-		} else if (pref.equals(FOREGROUND_COLOR)) {
-			updateForegroundColor();
-		
-		} else if (pref.equals(BACKGROUND_COLOR)) {
-			updateBackgroundColor();
-			
-		} else if (pref.equals(EXPERIMENT_EMBEDDED)) {
-			updateExperimentEmbedded();
-		}
-
-	}
-
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/AppRecentFiles.java b/image_annotation/src/ie/dcu/apps/ist/AppRecentFiles.java
deleted file mode 100644
index c2b7b31..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/AppRecentFiles.java
+++ /dev/null
@@ -1,93 +0,0 @@
-package ie.dcu.apps.ist;
-
-import ie.dcu.apps.ist.recent.*;
-
-import java.io.*;
-
-/**
- * Manages applications recent files list.
- * 
- * @author Kevin McGuinness
- */
-public class AppRecentFiles extends RecentFiles {
-	public static final String APP_SETTINGS_PATH = ".ist";
-	public static final String HISTORY_FILE_NAME = ".history";
-
-	private static AppRecentFiles history;
-	
-	
-	private AppRecentFiles(File store) {
-		super(store);
-	}
-	
-	
-	public static AppRecentFiles getInstance() {
-		if (history == null) {
-			history = create();
-		}
-		return history;
-	}
-	
-	
-	private static AppRecentFiles create() {
-		AppRecentFiles history = null;
-		try {
-			history = new AppRecentFiles(getHistoryFile());
-			history.load();
-		} catch (IOException e) {
-			getLogger().warning("Unable to create history file: " + e);
-		}
-		
-		return history;
-	}
-	
-	
-	@Override
-	public void load() {
-		try {
-			super.load();
-		} catch (IOException e) {
-			getLogger().warning("Error loading recent documents list: " + e);
-		}
-	}
-
-	@Override
-	public void store() {
-		try {
-			super.store();
-		} catch (IOException e) {
-			getLogger().warning("Error storing recent documents list: " + e);
-		}
-	}
-
-
-	private static File getHistoryFile() throws IOException {
-		File file = new File(getSettingsDirectory(), HISTORY_FILE_NAME);
-		if (file.exists()) {
-			// Check we can write
-			if (file.canWrite()) {
-				return file;
-			}
-		} else {
-			return file;
-		}
-		
-		throw new IOException("History file is unwritable");
-	}
-
-
-	private static File getSettingsDirectory() throws IOException {
-		String home = System.getProperty("user.home");
-		File settings = new File(home, APP_SETTINGS_PATH);
-		
-		if (!settings.exists()) {
-			if (settings.mkdirs()) {
-				return settings;
-			}
-		} else {
-			return settings;
-		}
-		
-		throw new IOException("Unable to create application settings directory");
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/AppRecentMenu.java b/image_annotation/src/ie/dcu/apps/ist/AppRecentMenu.java
deleted file mode 100644
index 84fe0cb..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/AppRecentMenu.java
+++ /dev/null
@@ -1,113 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist;
-
-import ie.dcu.apps.ist.actions.ActionManager;
-import ie.dcu.apps.ist.actions.HoverMenuManager;
-import ie.dcu.apps.ist.actions.OpenAction;
-import ie.dcu.apps.ist.actions.OpenRecentAction;
-
-import java.io.File;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.Properties;
-
-import org.eclipse.jface.action.Action;
-import org.eclipse.jface.action.IAction;
-import org.eclipse.jface.action.IMenuListener;
-import org.eclipse.jface.action.IMenuManager;
-import org.eclipse.jface.util.IPropertyChangeListener;
-import org.eclipse.jface.util.PropertyChangeEvent;
-import org.eclipse.swt.widgets.Menu;
-import org.eclipse.swt.widgets.MenuItem;
-
-/**
- * Recent files menu.
- * 
- * @author Kevin McGuinness
- */
-class AppRecentMenu extends HoverMenuManager {
-	private final AppRecentFiles history;
-	private final EmptyAction empty;
-	private final AppWindow window;
-	private IAction action;
-	
-	public AppRecentMenu(AppWindow window, IMenuManager parent) {
-		super("Open &Recent");
-		
-		this.window = window;
-		setParent(parent);
-		history = AppRecentFiles.getInstance();
-		add(empty = new EmptyAction());
-		addMenuListener(menuListener);
-	
-		ActionManager actions = window.getActions();
-		if (actions != null) {
-			OpenAction openAction = actions.get(OpenAction.class);
-			openAction.addPropertyChangeListener(actionListener);
-			action = openAction;
-		}
-		
-		try {
-			Properties props = window.getProperties();
-			String icon = props.getProperty("AppRecentMenu.icon", 
-				"file:icons/open-recent.png");
-			setImageURL(new URL(icon));
-		} catch (MalformedURLException e) {
-			// Ignore
-		}
-	}	
-	
-	@Override
-	public void fill(Menu parent, int index) {
-		super.fill(parent, index);
-		MenuItem item = getMenuItem();
-		if (item != null) {
-			item.setEnabled(action.isEnabled());
-		}
-	}
-
-
-	private void buildMenu() {
-		removeAll();
-		
-		if (history.empty()) {
-			add(empty);
-		} else {
-			for (File file : history) {
-				add(new OpenRecentAction(window.getActions(), file));
-			}
-		}
-		
-		update(false);
-	}
-	
-	
-	private final class EmptyAction extends Action {
-		public EmptyAction() {
-			setText("No Recent Files");
-			setEnabled(false);
-		}
-	};
-	
-	
-	private final IMenuListener menuListener = new IMenuListener() {
-		public void menuAboutToShow(IMenuManager manager) {
-			buildMenu();
-		}
-	};
-
-	
-	private final IPropertyChangeListener actionListener 
-		= new IPropertyChangeListener() {
-
-		public void propertyChange(PropertyChangeEvent event) {
-			MenuItem item = getMenuItem();
-			if (item != null) {
-				item.setEnabled(action.isEnabled());
-			}
-		}
-	};
-	
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/AppStatus.java b/image_annotation/src/ie/dcu/apps/ist/AppStatus.java
deleted file mode 100644
index b888e21..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/AppStatus.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package ie.dcu.apps.ist;
-
-import java.net.*;
-
-import org.eclipse.jface.resource.*;
-import org.eclipse.swt.graphics.*;
-
-/**
- * Application status bar message type.
- * 
- * @author Kevin McGuinness
- */
-public enum AppStatus {
-	Information, Warning, Error;
-	
-	public Image getIcon() {
-		String key = key();
-		Image image = JFaceResources.getImage(key);
-		if (image == null) {
-			ImageRegistry registry = JFaceResources.getImageRegistry();
-			ImageDescriptor descriptor = createImageDescriptor();
-			registry.put(key, descriptor);
-			image = registry.get(key);
-		}
-		return image;
-	}
-	
-	private ImageDescriptor createImageDescriptor() {
-		try {
-			return ImageDescriptor.createFromURL(new URL(key()));
-		} catch (MalformedURLException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	private String key() {
-		switch (this) {
-		case Information:
-			return "file:resources/icons/dialog-information.png";
-		case Warning:
-			return "file:resources/icons/dialog-warning.png";
-		default:
-			return "file:resources/icons/dialog-error.png";
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/AppWindow.java b/image_annotation/src/ie/dcu/apps/ist/AppWindow.java
deleted file mode 100644
index 5f32b24..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/AppWindow.java
+++ /dev/null
@@ -1,725 +0,0 @@
-package ie.dcu.apps.ist;
-
-import ie.dcu.apps.ist.actions.*;
-import ie.dcu.apps.ist.event.*;
-import ie.dcu.apps.ist.exp.Experiment;
-import ie.dcu.apps.ist.views.*;
-import ie.dcu.segment.*;
-import ie.dcu.segment.annotate.*;
-import ie.dcu.swt.*;
-import ie.dcu.swt.event.*;
-import ie.dcu.swt.layout.LayoutFactory;
-import ie.dcu.util.*;
-
-import java.io.*;
-import java.net.*;
-import java.util.Properties;
-import java.util.logging.*;
-
-import org.eclipse.jface.action.*;
-import org.eclipse.jface.resource.*;
-import org.eclipse.jface.window.ApplicationWindow;
-import org.eclipse.swt.*;
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.layout.GridData;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Main interactive segmentation tool application window.
- * 
- * @author Kevin McGuinness
- */
-public class AppWindow extends ApplicationWindow implements FileDropListener {
-	private static final Logger log = Logger.getLogger("AppWindow");
-
-	private final Properties props;
-
-	private AppPrefsManager prefsManager;
-	private ActionManager actions;
-	private Composite content;
-	private SegmentationView view;
-	private Shell shell;
-	private ImageObserver observer;
-	private Experiment experiment;
-	private ExperimentPanel experimentPanel;
-	private boolean experimentModeEmbedded;
-
-
-	public AppWindow() {
-		super(null);
-
-		props = loadProperties();
-
-		addMenuBar();
-		addStatusLine();
-	}
-	
-	
-	@Override
-	protected boolean canHandleShellCloseEvent() {
-		if (!ExitAction.confirmExit(this)) {
-			return false; 
-		}
-		return super.canHandleShellCloseEvent();
-	}
-
-
-	private Properties loadProperties() {
-		try {
-			return Application.loadProperties(getPropertiesFile());
-		} catch (IOException e) {
-			log.severe("Unable to load properties file " + e.getMessage());
-			throw new RuntimeException(e);
-		}
-	}
-	
-	private String getPropertiesFile() {
-		return OsUtils.isMacOS() ? "application.mac" : "application";
-	}
-
-
-	public void updateWindowTitle() {
-		String title;
-		if (hasContext()) {
-			String file = getContext().getFile().getName();
-			title = String.format("%s [%s]", Application.APP_NAME, file);
-			
-		} else {
-			title = Application.APP_NAME;
-		}
-		
-		if (isExperimentMode()) {
-			title += " - Experiment Mode";
-		}
-		
-		getShell().setText(title);
-	}
-
-
-	private SegmentationView createView(Composite parent) {
-
-		// Load props
-		Properties props;
-		try {
-			props = Application.loadProperties("view"); 
-		} catch (IOException e) {
-			log.severe("Error loading view properties " + e.getLocalizedMessage());
-			throw new RuntimeException(e);
-		}
-
-		// Create view
-		SegmentationView view = new SegmentationView(props, parent, 0);
-
-		boolean blocksOnFork = false;
-		
-		// Set runnable context 
-		view.setRunnableContext(this, blocksOnFork);
-
-		// Add observer
-		observer = new ImageObserver(view);
-
-		// Return new view
-		return view;
-	}
-
-
-	private static ImageDescriptor createImageDescriptor(String url) {
-		try {
-			return ImageDescriptor.createFromURL(new URL(url));
-		} catch (MalformedURLException e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-
-	private void updateEnabledActions() {
-		ActionManager a = getActions();
-		boolean ctxAvailable = hasContext();
-		boolean experimentMode = isExperimentMode();
-		
-		a.setEnabled(OpenAction.class, !experimentMode);
-		a.setEnabled(PreferencesAction.class, !experimentMode);
-		a.setEnabled(SaveAction.class, ctxAvailable && !experimentMode);
-		a.setEnabled(SaveAsAction.class, ctxAvailable && !experimentMode);
-		a.setEnabled(ExportViewAction.class, ctxAvailable && !experimentMode);
-		a.setEnabled(ExportTransparentPNGAction.class, ctxAvailable && !experimentMode);
-		a.setEnabled(PrintAction.class, ctxAvailable && !experimentMode);
-		a.setEnabled(CopyAction.class, ctxAvailable && !experimentMode);
-		a.setEnabled(UndoAction.class, ctxAvailable && view.canUndo());
-		a.setEnabled(RedoAction.class, ctxAvailable && view.canRedo());
-		a.setEnabled(NextAction.class, ctxAvailable && !experimentMode);
-		a.setEnabled(PreviousAction.class, ctxAvailable && !experimentMode);
-		a.setEnabled(OpenExperimentAction.class, !experimentMode);
-		
-		updateExportImageMapAction();
-		
-		if (experimentMode) {
-			
-			boolean changeSelection = false;
-			
-			// Enable experiment segmenters
-			for (SelectSegmenterAction s : a.getSegmentationActions()) {
-				Segmenter segmenter = s.getSegmenter();
-				boolean enabled = experiment.using(segmenter);
-				s.setEnabled(enabled);
-				
-				if (!s.isEnabled() && s.isChecked()) {
-					// The selected segmenter has been disabled,
-					// we need to select a different one
-					changeSelection = true;
-					s.setChecked(false);
-				}
-			}
-			
-			if (changeSelection) {
-				// Select the first available segmenter
-				for (SelectSegmenterAction s : a.getSegmentationActions()) {
-					if (experiment.using(s.getSegmenter())) {
-						s.setChecked(true);
-						s.run();
-						break;
-					}
-				}
-			}
-			
-		} else {
-			// Enable all select segmenter actions
-			for (SelectSegmenterAction s : a.getSegmentationActions()) {
-				s.setEnabled(true);
-			}
-		}
-	}
-	
-	private void updateExportImageMapAction() {
-		ActionManager a = getActions();
-		SegmentationContext ctx = getContext();
-		
-		if (ctx != null && !isExperimentMode()) {
-			AnnotationManager am = ctx.getAnnotations();
-			boolean hasObject = am.hasForegroundAnnotation() 
-				&& am.hasBackgroundAnnotation();
-			a.setEnabled(ExportImageMapAction.class, hasObject);
-		
-		} else {
-			a.setEnabled(ExportImageMapAction.class, false);
-		}
-	}
-	
-	
-	private void updateUndoRedoActions() {
-		ActionManager a = getActions();
-		boolean ctxAvailable = hasContext();
-		a.setEnabled(UndoAction.class, ctxAvailable && view.canUndo());
-		a.setEnabled(RedoAction.class, ctxAvailable && view.canRedo());
-	}
-
-
-	@Override
-	protected void configureShell(Shell shell) {
-		this.shell = shell;
-		super.configureShell(shell);
-		updateWindowTitle();
-		loadIcons(shell);
-		shell.setSize(800, 600);
-		SwtUtils.center(shell);
-	}
-	
-	
-	private void loadIcons(Shell shell) {
-		final String[] icons = { 
-				"resources/icons/icon-16.png",
-				"resources/icons/icon-24.png",
-				"resources/icons/icon-32.png",
-				"resources/icons/icon-48.png"
-		};
-		
-		Image[] images = new Image[icons.length];
-		Display display = shell.getDisplay();
-		
-		try {
-			int i = 0;
-			for (String file : icons) {
-				images[i++] = new Image(display, file);
-			}
-			
-			shell.setImages(images);
-	
-		} catch (SWTException e) {
-			log.warning("Error loading application window icons: " 
-				+ e.getLocalizedMessage());
-		}
-	}
-
-
-	@Override
-	protected Control createContents(Composite parent) {
-		content = new Composite(parent, SWT.NONE);
-
-		content.setLayout(LayoutFactory.createGridLayout(0, 0, 2, false));
-
-		view = createView(content);
-		view.setLayoutData(LayoutFactory.createGridData());
-		view.addContextChangeListener(contextListener);
-		
-		SwtUtils.createFileDropTarget(view, this);
-
-		// Done creating contents
-		getPrefsManager().update();
-		updateEnabledActions();
-
-		return content;
-	}
-
-
-	@Override
-	protected boolean showTopSeperator() {
-		return false;
-	}
-
-
-	@Override
-	protected MenuManager createMenuManager() {
-		MenuManager bar = new MenuManager();
-
-		ActionManager actions = getActions();
-
-		MenuManager file = addMenu(bar, "&File");
-		file.add(actions.get(OpenAction.class));
-		
-		file.add(new AppRecentMenu(this, file));
-		
-		file.add(new Separator());
-		file.add(actions.get(SaveAction.class));
-		file.add(actions.get(SaveAsAction.class));
-		file.add(new Separator());
-		
-		// Export menu ->
-		MenuManager exportMenu = addMenu(file, "&Export", 
-			props.getProperty("ExportMenu.icon"));
-		
-		exportMenu.add(actions.get(ExportViewAction.class));
-		exportMenu.add(actions.get(ExportImageMapAction.class));
-		exportMenu.add(actions.get(ExportTransparentPNGAction.class));
-		
-		file.add(new Separator());
-		file.add(actions.get(PrintAction.class));
-		file.add(new Separator());
-		file.add(actions.get(ExitAction.class));
-
-		MenuManager edit = addMenu(bar, "&Edit");
-
-		edit.add(actions.get(UndoAction.class));
-		edit.add(actions.get(RedoAction.class));
-		edit.add(new Separator());
-		edit.add(actions.get(CopyAction.class));
-		edit.add(new Separator());
-		edit.add(actions.get(PreferencesAction.class));
-
-		MenuManager tools = addMenu(bar, "&Tools");
-		tools.add(actions.get(OpenExperimentAction.class));
-		tools.add(new Separator());
-		
-		for (SelectSegmenterAction a : actions.getSegmentationActions()) {
-			tools.add(a);
-		}
-		
-		tools.add(new Separator());
-		tools.add(actions.get(ConfigureSegmenterAction.class));
-		
-		MenuManager go = addMenu(bar, "&Go");
-		go.add(actions.get(NextAction.class));
-		go.add(actions.get(PreviousAction.class));
-		
-		
-		MenuManager help = addMenu(bar, "&Help");
-
-		help.add(actions.get(HelpAction.class));
-		help.add(actions.get(AboutAction.class));
-		
-		if (OsUtils.isMacOSX()) {
-			// Enhance the UI on the Mac
-			IAction aboutAction = actions.get(AboutAction.class);
-			IAction prefAction = actions.get(PreferencesAction.class);
-			Listener quitListener = new Listener() {
-				public void handleEvent(Event evt) {
-					getActions().get(ExitAction.class).runWithEvent(evt);
-				}
-			};
-			CocoaUIEnhancer enhancer = new CocoaUIEnhancer(Application.APP_NAME);
-			enhancer.hookApplicationMenu(Display.getDefault(), 
-				quitListener, aboutAction, prefAction);
-		}
-
-		return bar;
-	}
-
-
-	protected static MenuManager addMenu(MenuManager parent, String text) {
-		MenuManager menu = new HoverMenuManager(text);
-		parent.add(menu);
-		return menu;
-	}
-	
-	protected static MenuManager addMenu(MenuManager parent, 
-			String text, String image) {
-		
-		MenuManager menu;
-		try {
-			menu = new HoverMenuManager(text, image != null ? 
-				new URL(image) : null);
-		} catch (MalformedURLException e) {
-			log.log(Level.WARNING, "Malformed URL", e);
-			menu = new HoverMenuManager(text);
-		}
-		
-		parent.add(menu);
-		return menu;
-	}
-	
-	
-	
-	public void setExperiment(Experiment ex) {
-		if (experiment != ex) {
-			experiment = ex;
-			setContext(null);
-			
-			if (ex == null) {
-				
-				if (experimentPanel != null) {
-					experimentPanel.dispose();
-					experimentPanel = null;
-					content.layout();
-				}
-			} else {
-			
-				if (experimentModeEmbedded) {
-					experimentPanel = new ExperimentPanel(this, content, SWT.NONE);
-					GridData data = new GridData(SWT.FILL, SWT.FILL, false, true);
-					data.widthHint = 180;
-					data.verticalIndent = 5;
-					experimentPanel.setLayoutData(data);
-					content.layout();
-					
-				} else {
-					ExperimentPanel.open(this);
-				}
-			}
-			updateEnabledActions();
-			updateWindowTitle();
-		}
-	}
-	
-	
-	public Experiment getExperiment() {
-		return experiment;
-	}
-
-
-	public boolean isExperimentMode() {
-		return experiment != null;
-	}
-
-
-	public void setExperimentModeEmbedded(boolean on) {
-		this.experimentModeEmbedded = on;
-	}
-
-
-	public AppPrefs getPrefs() {
-		return getPrefsManager().getPrefs();
-	}
-
-
-	AppPrefsManager getPrefsManager() {
-		if (prefsManager == null) {
-			prefsManager = new AppPrefsManager(this);
-		}
-		return prefsManager;
-	}
-
-
-	public Properties getProperties() {
-		return props;
-	}
-
-
-	public ActionManager getActions() {
-		if (actions == null) {
-			actions = new ActionManager(this);
-		}
-		return actions;
-	}
-
-
-	public Shell getShell() {
-		Shell shell = super.getShell();
-		if (shell == null) {
-			return this.shell;
-		}
-		return shell;
-	}
-
-
-	public SegmentationView getView() {
-		return view;
-	}
-
-
-	public SegmentationContext getContext() {
-		if (view != null) {
-			return view.getContext();
-		}
-		return null;
-	}
-
-
-	public File getContextFile() {
-		if (hasContextFile()) {
-			return getContext().getFile();
-		}
-		return null;
-	}
-
-
-	public Image getIcon(String url) {
-		Image image = JFaceResources.getImage(url);
-		if (image == null) {
-			ImageRegistry registry = JFaceResources.getImageRegistry();
-			ImageDescriptor descriptor = createImageDescriptor(url);
-			registry.put(url, descriptor);
-			image = registry.get(url);
-		}
-		return image;
-	}
-
-
-	public boolean hasContext() {
-		if (view != null) {
-			return view.getContext() != null;
-		}
-		return false;
-	}
-
-
-	public boolean hasContextFile() {
-		return getContext() != null ? getContext().hasContextFile() : false;
-	}
-
-
-	public void setEnableFeedback(boolean on) {
-		if (observer != null) {
-			observer.setEnabled(on);
-		}
-	}
-
-
-	public void setContext(SegmentationContext ctx) {
-		if (ctx != null) {
-			// Set a segmenter if one has not been set
-			if (!view.hasSegmenter()) {
-				SegmenterRegistry registry = SegmenterRegistry.getInstance();
-				view.setSegmenter(registry.getDefault());
-			}
-		}
-	
-		// Set context
-		view.setContext(ctx);
-		updateWindowTitle();
-	}
-
-
-	public void status(String message) {
-		setStatus(message);
-	}
-
-
-	public void status(String format, Object... args) {
-		setStatus(String.format(format, args));
-	}
-
-
-	public void status(Image image, String format, Object... args) {
-		StatusLineManager manager = getStatusLineManager();
-		if (manager != null) {
-			manager.setMessage(image, String.format(format, args));
-		}
-	}
-
-
-	public void status(AppStatus s, String format, Object... args) {
-		if (format == null) {
-			setStatus(null);
-
-		} else {
-			StatusLineManager manager = getStatusLineManager();
-			if (manager != null) {
-				if (s == AppStatus.Error) {
-					manager.setErrorMessage(s.getIcon(), String.format(format, args));
-				} else {
-					manager.setMessage(s.getIcon(), String.format(format, args));
-				}
-			}
-		}
-	}
-
-
-	public void drop(FileDropEvent evt) {
-		System.out.println("drop received");
-		for (File f : evt.files()) {
-			if (isAcceptable(f)) {
-				getActions().get(OpenAction.class).open(f);
-				break;
-			}
-		}
-	}
-
-
-	public boolean isAcceptable(File file) {
-		String ext = FileUtils.getExtension(file);
-		return (ext.equals(".ctx") || SwtUtils.getImageFormat(file) != -1);
-	}
-
-	
-	private void handleContextChanged(ContextChangedEvent evt) {
-		
-		// Remove listener from old context
-		if (evt.oldContext != null) {
-			evt.oldContext.removeAnnotationListener(annotationListener);
-		}
-		
-		// Add listener to new context
-		if (evt.newContext != null) {
-			evt.newContext.addAnnotationListener(annotationListener);
-		}
-		
-		// Update application state
-		updateEnabledActions();
-	}
-	
-	
-	private void handleAnnotationPerformed(AnnotationEvent e) {
-		
-		// Update state of undo and redo menu items
-		updateUndoRedoActions();
-		updateExportImageMapAction();
-	}
-	
-	
-	private final ContextChangeListener contextListener = new ContextChangeListener() {
-		public void contextChanged(ContextChangedEvent evt) {
-			handleContextChanged(evt);
-		}
-	};
-	
-	
-	private final AnnotationListener annotationListener = new AnnotationAdapter() {
-		public void annotationsChanged(AnnotationEvent e) {
-			handleAnnotationPerformed(e);
-		}		
-	};
-	
-	
-	private class ImageObserver implements MouseMoveListener, ContextChangeListener {
-		private static final String MONOSPACE_FONT = "Monospace";
-
-		private final ImageControl ctrl;
-		private ImageData image;
-		private boolean inside;
-		private boolean enabled;
-
-
-		public ImageObserver(SegmentationView view) {
-			view.addContextChangeListener(this);
-			view.getCanvas().addMouseMoveListener(this);
-			ctrl = view.getImageControl();
-			contextChanged(view.getContext());
-			FontDescriptor fd = FontDescriptor.createFrom(MONOSPACE_FONT, 8, SWT.NORMAL);
-			JFaceResources.getFontRegistry().put(MONOSPACE_FONT, fd.getFontData());
-		}
-
-
-		public void setEnabled(boolean enabled) {
-			if (this.enabled != enabled) {
-				status(null);
-				Font font = JFaceResources.getDefaultFont();
-				getStatusLineManager().getControl().setFont(font);
-				this.inside = false;
-				this.enabled = enabled;
-			}
-		}
-
-
-		public boolean isEnabled() {
-			return enabled;
-		}
-
-
-		public void mouseMove(MouseEvent e) {
-			if (isEnabled()) {
-				Point pt = getImagePoint(e);
-				if (pt != null) {
-					inside(pt, getColor(pt));
-				} else {
-					outside();
-				}
-			}
-		}
-
-
-		private void outside() {
-			if (inside) {
-				status(null);
-				Font font = JFaceResources.getDefaultFont();
-				getStatusLineManager().getControl().setFont(font);
-				inside = false;
-			}
-		}
-
-
-		private final Point getImagePoint(MouseEvent e) {
-			if (image != null) {
-				Point pt = new Point(e.x, e.y);
-				if (ctrl.imageContains(pt)) {
-					return ctrl.canvasToImage(pt);
-				}
-			}
-			return null;
-		}
-
-
-		private final RGB getColor(Point pt) {
-				
-			int pixel = image.getPixel(pt.x, pt.y);
-			return image.palette.getRGB(pixel);
-		}
-
-
-		private void inside(Point pt, RGB c) {
-			if (!inside) {
-				Font font = JFaceResources.getFont(MONOSPACE_FONT);
-				getStatusLineManager().getControl().setFont(font);
-			}
-
-			status(AppStatus.Information, 
-					"Location [%4d,%4d] Color [%3d,%3d,%3d]",
-					pt.x, pt.y, c.red, c.green, c.blue);
-			
-			inside = true;
-		}
-
-
-		public void contextChanged(ContextChangedEvent evt) {
-			contextChanged(evt.newContext);
-		}
-
-
-		public void contextChanged(SegmentationContext ctx) {
-			if (ctx != null) {
-				image = ctx.getImageData();
-			} else {
-				image = null;
-			}
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/Application.java b/image_annotation/src/ie/dcu/apps/ist/Application.java
deleted file mode 100644
index bbd3b38..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/Application.java
+++ /dev/null
@@ -1,110 +0,0 @@
-package ie.dcu.apps.ist;
-
-import ie.dcu.util.*;
-
-import java.io.*;
-import java.net.*;
-import java.security.*;
-import java.util.*;
-
-import static ie.dcu.util.FileUtils.pathJoin;
-import static ie.dcu.util.OsUtils.*;
-
-/**
- * Base application. Contains information strings and methods to load
- * application wide resources.
- * 
- * @author Kevin McGuinness
- */
-public class Application {
-	public static final String APP_ID   = "ist";
-	public static final String APP_NAME = "Interactive Segmentation and Annotation Tool";
-	public static final String APP_VERSION  = "1.3.4";
-	public static final String APP_RESOURCE_DIR = "resources";
-	
-	/**
-	 * Default locations to look for plugins
-	 */
-	public static final String[] DEFAULT_PLUGIN_SEARCH_PATH 
-		= defaultPluginSearchPath();
-	
-	/**
-	 * Loads a properties file from the application resource area
-	 * (resources/config)
-	 * 
-	 * @param name
-	 *        The properties file name. ".properties" will be appended if
-	 *        necessary.
-	 * @return A Properties object
-	 * @throws IOException
-	 *         If there is an error creating the Properties object.
-	 */
-	public static Properties loadProperties(String name) throws IOException {
-		if (!name.endsWith(".properties")) {
-			name = name + ".properties";
-		}
-		
-		String path = FileUtils.pathJoin(APP_RESOURCE_DIR, "config", name);
-		File file = new File(path);
-		System.out.println("Path:" + file);
-		return PropsUtils.load(file);
-	}
-	
-	/**
-	 * Returns the users plugins folder
-	 */
-	public static String userPluginsFolder() {
-		return pathJoin(userHome(), ".ist", "plugins");
-	}
-	
-	/**
-	 * Returns the applications base folder
-	 */
-	public static String applicationFolder() {
-		String apphome = System.getenv("IST_HOME");
-		if (apphome != null) {
-			File file = new File(apphome);
-			if  (file.isDirectory()) {
-				return file.getAbsolutePath();
-			}
-		} 
-		
-		ProtectionDomain domain = Application.class.getProtectionDomain();
-		CodeSource source = domain.getCodeSource();
-		URL location = source.getLocation();
-		String path = location.getPath();
-		try {
-			
-			path = URLDecoder.decode(path, "UTF-8");
-			if (isWindows()) {
-				path = path.substring(1);
-			}
-				
-			path = new File(path).getParent();
-		} catch (UnsupportedEncodingException e) {
-			path = System.getProperty("user.dir");
-		}
-			
-		return path;
-	}
-	
-	public static String applicationPluginsFolder() {
-		return pathJoin(applicationFolder(), "plugins");
-	}
-	
-	public static String osxPluginSearchPath() {
-		return pathJoin(userHome(), "Library", 
-			"Application Support", APP_NAME, "Plugins");
-	}
-	
-	private static String[] defaultPluginSearchPath() {
-		ArrayList<String> paths = new ArrayList<String>();
-		paths.add(userPluginsFolder());
-		if (isMacOSX()) {
-			paths.add(osxPluginSearchPath());
-		}
-		paths.add(applicationPluginsFolder());
-		return paths.toArray(new String[paths.size()]);
-	}
-	
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/EvaluatorRegistry.java b/image_annotation/src/ie/dcu/apps/ist/EvaluatorRegistry.java
deleted file mode 100644
index d7bc7b4..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/EvaluatorRegistry.java
+++ /dev/null
@@ -1,70 +0,0 @@
-package ie.dcu.apps.ist;
-
-import ie.dcu.eval.*;
-
-import java.util.*;
-
-public class EvaluatorRegistry {
-	private static EvaluatorRegistry instance;
-	private final Set<Evaluator> evaluators;
-	
-	private EvaluatorRegistry() {
-		evaluators = new LinkedHashSet<Evaluator>();
-		init();
-	}
-	
-	
-	private void init() {
-		add(new ConfusionMatrixEvaluator());
-		add(new BoundaryAccuracyEvaluator());
-	}
-	
-	
-	public static EvaluatorRegistry getInstance() {
-		if (instance == null) {
-			instance = new EvaluatorRegistry();
-		}
-		return instance;
-	}
-	
-	
-	public Evaluator find(String name) {
-		for (Evaluator e : evaluators) {
-			
-			// Check name
-			String ename = e.getName();
-			if (ename.equals(name)) {
-				return e;
-			}
-			
-			// Check class name
-			String cname = e.getClass().getName();
-			if (cname.equals(name)) {
-				return e;
-			}
-			
-			// Check simple name
-			String sname = e.getClass().getSimpleName();
-			if (sname.equals(name)) {
-				return e;
-			}
-		}
-		
-		return null;
-	}
-	
-	
-	public void add(Evaluator evaluator) {
-		evaluators.add(evaluator);
-	}
-	
-	
-	public Set<Evaluator> evaluators() {
-		return Collections.unmodifiableSet(evaluators);
-	}
-
-
-	public Iterator<Evaluator> iterator() {
-		return evaluators.iterator();
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/Main.java b/image_annotation/src/ie/dcu/apps/ist/Main.java
deleted file mode 100644
index d878efd..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/Main.java
+++ /dev/null
@@ -1,119 +0,0 @@
-package ie.dcu.apps.ist;
-
-import ie.dcu.plugin.*;
-import ie.dcu.segment.Segmenter;
-
-import java.util.logging.Logger;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.graphics.Rectangle;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Application launcher.
- * 
- * @author Kevin McGuinness
- */
-public class Main {
-	public static final Logger log = Logger.getLogger("Main");
-	
-	/**
-	 * Message to show when GDI+ is not installed.
-	 */
-	private static final String NO_GDIPLUS = 
-		"Unable to load required library: GDI+ (gdiplus.dll)\n\n" +
-		"The GDI+ library needs to be installed before this program " +
-		"can be used on this platform. See the note at the end of " +
-		"the download page for further details.";
-		
-	
-	public static void main(String[] args) {
-		System.out.print(Application.DEFAULT_PLUGIN_SEARCH_PATH);
-		for (String s: Application.DEFAULT_PLUGIN_SEARCH_PATH) {
-			System.out.println(s);
-		}
-
-		Display.setAppName(Application.APP_NAME);
-		check();
-		loadPlugins();
-		AppWindow window = new AppWindow();
-		window.setBlockOnOpen(true);
-		window.open();
-		System.exit(0);
-	}
-	
-	private static void loadPlugins() {
-		PluginManager manager = new PluginManager();
-		for (String path : Application.DEFAULT_PLUGIN_SEARCH_PATH) {
-			manager.searchPath().add(path);
-		}
-		manager.loadPlugins();
-		for (Plugin plugin : manager.plugins()) {
-			String classname = plugin.getMetadata("segmenter");
-			if (classname != null) {
-				loadSegmenterPlugin(plugin, classname);
-			}
-		}
-	}
-
-	private static void loadSegmenterPlugin(Plugin plugin, String classname) {
-		try {
-			Segmenter segmenter = (Segmenter) 
-				plugin.loadObject(classname);
-			
-			SegmenterRegistry.getInstance().add(segmenter);
-			
-		} catch (PluginException e) {
-			log.severe("Unable to load plugin: " + e);
-		}
-	}
-
-	public static boolean contains(String[] args, String argument) {
-		for (String arg : args) {
-			while (arg.startsWith("-")) {
-				arg = arg.substring(1);
-			}
-			
-			if (arg.equals(argument)) {
-				return true;
-			}
-		}
-		return false;
-	}
-	
-	private static void check() {
-		// Check for potential missing GDI+ on Win2K, NT, ME 98
-		String os = System.getProperty("os.name");
-		if (os.equals("Windows 2000") ||
-			os.equals("Windows NT") ||
-			os.equals("Windows ME") ||
-			os.equals("Windows 98")) 
-		{
-			try {
-				System.loadLibrary("gdiplus");
-			} catch (RuntimeException e) {
-				exit(NO_GDIPLUS);
-			}
-		}
-	}
-	
-	static void exit(String message) {
-		Display display = Display.getDefault();
-		Rectangle rect = display.getBounds();
-		
-		Shell shell = display.getActiveShell();
-		if (shell == null) {
-			shell = new Shell(display, SWT.NO_TRIM);
-			shell.setBounds(rect.width/2, rect.height/2, 0, 0);
-			shell.open();
-			shell.setText("Error");
-		}
-		
-		MessageBox box = new MessageBox(shell, SWT.ICON_ERROR);
-		box.setText("Error");
-		box.setMessage(message);
-		box.open();
-		display.dispose();
-		System.exit(1);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/PainterRegistry.java b/image_annotation/src/ie/dcu/apps/ist/PainterRegistry.java
deleted file mode 100644
index 7b437b0..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/PainterRegistry.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package ie.dcu.apps.ist;
-
-import ie.dcu.segment.painters.*;
-
-import java.util.*;
-
-public class PainterRegistry {
-	private final LinkedHashMap<String, SegmentationPainter> painters;
-
-	public PainterRegistry() {
-		painters = new LinkedHashMap<String, SegmentationPainter>();
-		init();
-	}
-	
-	
-	private void init() {
-		add(new CombinedPainter());
-		add(new OriginalPainter());
-		add(new MarkupPainter());
-		add(new MaskPainter());
-		add(new ForegroundOnlyPainter());
-		add(new OutlineOverlayPainter());
-	}
-	
-	
-	public void add(SegmentationPainter painter) {
-		painters.put(painter.getName(), painter);
-	}
-	
-	
-	public SegmentationPainter get(String painter) {
-		return painters.get(painter);
-	}
-	
-	
-	public Collection<SegmentationPainter> values() {
-		return painters.values();
-	}
-	
-	
-	public void dispose() {
-		for (SegmentationPainter p : values()) {
-			p.dispose();
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/SegmenterRegistry.java b/image_annotation/src/ie/dcu/apps/ist/SegmenterRegistry.java
deleted file mode 100644
index f3fec09..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/SegmenterRegistry.java
+++ /dev/null
@@ -1,107 +0,0 @@
-package ie.dcu.apps.ist;
-
-import ie.dcu.segment.*;
-
-import java.util.*;
-
-/**
- * Registry for segmenters.
- * 
- * @author Kevin McGuinness
- */
-public class SegmenterRegistry implements Iterable<Segmenter> {
-	private static final String DEFAULT_SEGMENTER_NAME = "IgcSegmenter";
-	private static SegmenterRegistry instance;
-	private final Set<Segmenter> segmenters;
-	
-	private SegmenterRegistry() {
-		segmenters = new LinkedHashSet<Segmenter>();
-		init();
-	}
-	
-	
-	private void init() {
-		// OutlineSegmenter is not very useful
-		// add(new OutlineSegmenter());
-		
-		// Geodesic Active Contours is too sensitive to parameters
-		// for general use on natural images.
-		// add(new SeededGacSegmenter());
-		
-		//add(new SrgSegmenter());
-		//add(new IgcSegmenter());
-		//add(new BptSegmenter());
-		//add(new SioxSegmenter());
-		//add(new SpatiogramSegmenter());
-	}
-
-
-	public static SegmenterRegistry getInstance() {
-		if (instance == null) {
-			instance = new SegmenterRegistry();
-		}
-		return instance;
-	}
-	
-	
-	public Segmenter find(String name) {
-		for (Segmenter s : segmenters) {
-			
-			// Check name
-			String ename = s.getName();
-			if (ename.equals(name)) {
-				return s;
-			}
-			
-			// Check class name
-			String cname = s.getClass().getName();
-			if (cname.equals(name)) {
-				return s;
-			}
-			
-			// Check simple name
-			String sname = s.getClass().getSimpleName();
-			if (sname.equals(name)) {
-				return s;
-			}
-		}
-		
-		return null;
-	}
-	
-	
-	public boolean isDefault(Segmenter s) {
-		if (s != null) {
-			if (segmenters.size() == 1 && segmenters.contains(s)) {
-				return true;
-			}
-			return s.getClass().getSimpleName().equals(DEFAULT_SEGMENTER_NAME);
-		}
-		return false;
-	}
-	
-	
-	public Segmenter getDefault() {
-		for (Segmenter s : segmenters) {
-			if (isDefault(s)) {
-				return s;
-			}
-		}
-		return null;
-	}
-	
-	
-	public void add(Segmenter segmenter) {
-		segmenters.add(segmenter);
-	}
-	
-	
-	public Set<Segmenter> segmenters() {
-		return Collections.unmodifiableSet(segmenters);
-	}
-
-
-	public Iterator<Segmenter> iterator() {
-		return segmenters.iterator();
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/AboutAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/AboutAction.java
deleted file mode 100644
index be5d61f..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/AboutAction.java
+++ /dev/null
@@ -1,109 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.Application;
-import ie.dcu.swt.layout.LayoutFactory;
-
-import org.eclipse.jface.dialogs.*;
-import org.eclipse.jface.dialogs.Dialog;
-import org.eclipse.jface.resource.JFaceResources;
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.widgets.*;
-
-
-/**
- * Show an about dialog.
- * 
- * @author Kevin McGuinness
- */
-public class AboutAction extends AppAction {
-	
-	private AboutBox dialog;
-	
-	public AboutAction(ActionManager m) {
-		super(m);
-	}
-
-	
-	@Override 
-	public void run() { 
-		if (dialog == null) {
-			dialog = new AboutBox();
-		}
-		dialog.open();
-	}
-	
-	
-	private class AboutBox extends Dialog {
-		
-		private static final String MESSAGE = 
-			"   Kevin McGuinness <a href=\"mailto:kevin.mcguinness@eeng.dcu.ie\">" +
-			"kevin.mcguinness@eeng.dcu.ie</a>\n" +
-			"   Center for Digital Video Processing\n" +
-			"   Dublin City University.\n" +
-			"   <a href=\"http://www.cdvp.dcu.ie\">http://www.cdvp.dcu.ie</a>";
-		
-		
-		private Composite composite;
-		
-
-		protected AboutBox() {
-			super(window);
-		}
-		
-
-		@Override
-		protected Control createDialogArea(Composite parent) {
-			composite = new Composite(parent, SWT.NONE);
-			composite.setLayout(LayoutFactory.createGridLayout(5, 5));
-			
-			String image = string("aboutImage");
-			addImage(image);
-			addLabel(String.format("Version %s", Application.APP_VERSION), SWT.CENTER);
-			addLabel(" SWT Version " + swtVersionString(), SWT.CENTER);
-			addLabel(" Developed By:", SWT.LEFT);
-			addLink(MESSAGE);
-		
-			return composite;
-		}
-		
-		private String swtVersionString() {
-			return String.format("%d (%s)", SWT.getVersion(), SWT.getPlatform());
-		}
-	
-		
-		@Override
-		protected void createButtonsForButtonBar(Composite parent) {
-			createButton(parent, 
-					IDialogConstants.OK_ID, IDialogConstants.OK_LABEL, true);
-		}
-
-
-		@Override
-		protected void configureShell(Shell shell) {
-			super.configureShell(shell);
-			shell.setText("About");
-		}
-		
-		
-		private void addLink(String string) {
-			Link link = new Link(composite, 0);
-			link.setText(string);
-			link.setLayoutData(LayoutFactory.createGridData());
-		}
-
-		
-		private void addLabel(String text, int alignment) {
-			Label label = new Label(composite, 0);
-			label.setText(text);
-			label.setAlignment(alignment);
-			label.setLayoutData(LayoutFactory.createGridData());
-			label.setFont(JFaceResources.getBannerFont());
-		}
-		
-		private void addImage(String url) {
-			Label label = new Label(composite, 0);
-			label.setImage(window.getIcon(url));
-			label.setLayoutData(LayoutFactory.createGridData());
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/ActionManager.java b/image_annotation/src/ie/dcu/apps/ist/actions/ActionManager.java
deleted file mode 100644
index b1897f8..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/ActionManager.java
+++ /dev/null
@@ -1,133 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.*;
-import ie.dcu.segment.Segmenter;
-import ie.dcu.util.OsUtils;
-
-import java.io.IOException;
-import java.util.*;
-import java.util.logging.Logger;
-
-/**
- * Manages application actions.
- * 
- * @author Kevin McGuinness
- */
-public class ActionManager {
-	private static final Logger log = Logger.getLogger("ActionManager");
-	
-	private final AppWindow window;
-	private final Map<String, AppAction> actions;
-	private ArrayList<SelectSegmenterAction> segmenterActions;
-	private Properties props;
-	
-	
-	public ActionManager(AppWindow window) {
-		
-		this.window = window;
-		this.actions = new HashMap<String, AppAction>();
-		
-		try {
-			this.props = Application.loadProperties(getPropertiesFile());
-		} catch (IOException e) {
-			log.severe("Error loading action properties: " + 
-					e.getLocalizedMessage());
-			throw new RuntimeException(e);
-		}
-		
-		init();
-	}
-	
-	
-	private String getPropertiesFile() {
-		return OsUtils.isMacOS() ? "actions.mac" : "actions";
-	}
-	
-	
-	Properties getProperties() {
-		return props;
-	}
-	
-	
-	AppWindow getWindow() {
-		return window;
-	}
-	
-
-	public void init() {
-		add(new OpenAction(this));
-		add(new SaveAction(this));
-		add(new SaveAsAction(this));
-		add(new AboutAction(this));
-		add(new CopyAction(this));
-		add(new ExitAction(this));
-		add(new ExportViewAction(this));
-		add(new ExportImageMapAction(this));
-		add(new ExportTransparentPNGAction(this));
-		add(new HelpAction(this));
-		add(new PreferencesAction(this));
-		add(new PrintAction(this));
-		add(new RedoAction(this));
-		add(new UndoAction(this));
-		add(new NextAction(this));
-		add(new PreviousAction(this));
-		add(new OpenExperimentAction(this));
-		add(new ConfigureSegmenterAction(this));
-		
-		// Add select segmenter actions
-		SegmenterRegistry registry = SegmenterRegistry.getInstance();
-		for (Segmenter s : registry) {
-			add(new SelectSegmenterAction(this, registry, s));
-		}
-	}
-	
-	
-	public void add(AppAction action) {
-		actions.put(action.id(), action);
-	}
-	
-	
-	public <T extends AppAction> T get(Class<T> clazz) {
-		return clazz.cast(actions.get(id(clazz)));
-	} 
-	
-	
-	public <T extends AppAction> T get(Class<T> clazz, String id) {
-		return clazz.cast(actions.get(id));
-	}
-	
-	
-	public void setEnabled(String id, boolean enabled) {
-		AppAction action = actions.get(id);
-		if (action != null) {
-			action.setEnabled(enabled);
-		}
-	}
-	
-	
-	public <T extends AppAction> void setEnabled(Class<T> clazz, boolean enabled) {
-		AppAction action = get(clazz);
-		if (action != null) {
-			action.setEnabled(enabled);
-		}
-	}
-	
-	
-	public Collection<SelectSegmenterAction> getSegmentationActions() {
-		if (segmenterActions == null) {
-			segmenterActions = new ArrayList<SelectSegmenterAction>();
-			for (AppAction a : actions.values()) {
-				if (a instanceof SelectSegmenterAction) {
-					segmenterActions.add((SelectSegmenterAction) a);
-				}
-			}
-		}
-		
-		return Collections.unmodifiableCollection(segmenterActions);
-	}
-	
-	
-	private String id(Class<?> clazz) {
-		return clazz.getName();
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/AppAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/AppAction.java
deleted file mode 100644
index a5a11a8..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/AppAction.java
+++ /dev/null
@@ -1,122 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import java.util.logging.*;
-
-import org.eclipse.jface.dialogs.*;
-import org.eclipse.swt.graphics.*;
-
-import ie.dcu.apps.ist.*;
-
-/**
- * Root class for all application actions.
- * 
- * @author Kevin McGuinness
- */
-public class AppAction extends ConfiguredAction {
-	
-	// Make easier for subclasses to set status
-	protected static final AppStatus Information = AppStatus.Information;
-	protected static final AppStatus Warning = AppStatus.Warning;
-	protected static final AppStatus Error = AppStatus.Error;
-	
-	// Logger
-	protected final Logger log = Logger.getLogger(getClass().getSimpleName());
-	
-	// Window
-	protected final AppWindow window;
-	
-	// Action manager
-	protected final ActionManager manager;
-	
-
-	public AppAction(ActionManager m) {
-		super(m.getProperties());
-		manager = m;
-		window = m.getWindow();
-	}
-	
-	
-	public AppAction(ActionManager m, int style) {
-		super(m.getProperties(), style);
-		manager = m;
-		window = m.getWindow();
-	}
-	
-	
-	@Override
-	public void arm() {
-		super.arm();
-		status(AppStatus.Information, getDescription());
-	}
-
-
-	@Override
-	public void disarm() {
-		super.disarm();
-		window.setStatus(null);
-	}
-
-
-	public String id() {
-		return getClass().getName();
-	}
-	
-	
-	protected Image icon(String key) {
-		String prop = string(key);
-		if (prop != null) {
-			return window.getIcon(prop);
-		}
-		return null;
-	}
-
-
-	protected void error(String message) {
-		MessageDialog.openError(window.getShell(), "Error", message);
-	}
-
-
-	protected void error(String format, Object... args) {
-		error(String.format(format, args));
-	}
-
-
-	protected void warning(String message) {
-		MessageDialog.openWarning(window.getShell(), "Warning", message);
-	}
-
-
-	protected void warning(String format, Object... args) {
-		warning(String.format(format, args));
-	}
-
-
-	protected void info(String message) {
-		MessageDialog.openInformation(window.getShell(), "Information", message);
-	}
-
-
-	protected void info(String format, Object... args) {
-		info(String.format(format, args));
-	}
-
-
-	protected void log(Level level, String message, Throwable th) {
-		log.log(level, message, th);
-	}
-
-
-	protected String property(String key) {
-		return properties.getProperty(key);
-	}
-
-
-	protected void status(AppStatus s, String format, Object... args) {
-		window.status(s, format, args);
-	}
-
-
-	protected void status(String format, Object... args) {
-		status(Information, format, args);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/ConfigureSegmenterAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/ConfigureSegmenterAction.java
deleted file mode 100644
index 5221928..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/ConfigureSegmenterAction.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.views.SegmentationView;
-
-/**
- * Show the configure segmenter dialog.
- * 
- * @author Kevin McGuinness
- */
-public class ConfigureSegmenterAction extends AppAction {
-
-	public ConfigureSegmenterAction(ActionManager m) {
-		super(m);
-	}
-
-	
-	@Override 
-	public void run() { 
-		SegmentationView view = window.getView();
-		if (view.canShowOptions()) {
-			view.showSegmenterOptions();
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/ConfiguredAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/ConfiguredAction.java
deleted file mode 100644
index 24a33f0..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/ConfiguredAction.java
+++ /dev/null
@@ -1,169 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import java.net.*;
-import java.util.*;
-import java.util.logging.*;
-
-import org.eclipse.jface.action.*;
-import org.eclipse.jface.resource.*;
-
-/**
- * Hover Action configured from a properties file.
- * 
- * @author Kevin McGuinness
- */
-public class ConfiguredAction extends HoverAction {
-	private static final Logger log = Logger.getLogger("ConfiguredAction");
-	
-	protected final Properties properties;
-	private final String id;
-	
-	
-	public ConfiguredAction(Properties properties) {
-		this(properties, null, AS_PUSH_BUTTON);
-	}
-	
-	
-	public ConfiguredAction(Properties properties, int style) {
-		this(properties, null, style);
-	}
-	
-	
-	public ConfiguredAction(Properties properties, String id, int style) {
-		super(null, style);
-		
-		assert (properties != null);
-		this.properties = properties;
-		
-		if (id != null) {
-			this.id = id;
-		} else {
-			this.id = getClass().getSimpleName();
-		}
-		
-		configure();
-	}
-
-	
-	private void configure() {
-		
-		// Set id
-		setId(id);
-
-		// Set text
-		setText(string("text"));
-		
-		// Set description
-		String description;
-		if ((description = string("description")) != null) {
-			setDescription(description);
-		}
-		
-		// Set tooltip
-		String tooltip;
-		if ((tooltip = string("tooltip")) != null) {
-			setToolTipText(tooltip);
-		}
-		
-		// Set accelerator
-		Integer keycode;
-		if ((keycode = accelerator("accelerator")) != null) {
-			setAccelerator(keycode);
-		}
-	
-		// Set images
-		ImageDescriptor im;
-		
-		if ((im = image("image")) != null) {
-			setImageDescriptor(im);
-		}
-		
-		if ((im = image("hoverImage")) != null) {
-			setHoverImageDescriptor(im);
-		}
-		
-		if ((im = image("disabledImage")) != null) {
-			setDisabledImageDescriptor(im);
-		}
-		
-		// Set status
-		Boolean status;
-		
-		if ((status = bool("checked") != null)) {
-			setChecked(status);
-		}
-		
-		if ((status = bool("enabled") != null)) {
-			setEnabled(status);
-		}
-	}
-	
-	
-	protected final Integer accelerator(String key) {
-		String value = string(key);
-		
-		if (value == null) {
-			return null;
-		}
-		
-		int code = Action.convertAccelerator(value);
-		
-		if (code == 0) {
-			log.warning("No accelerator: " + value);
-			return null;
-		}
-		
-		if (code == -1) {
-			log.warning("Not a valid accelerator keycode: " + value);
-			return null;
-		}
-		
-		return code;
-	}
-	
-	
-	protected final Boolean bool(String key) {
-		String value = string(key);
-		
-		if (value == null) {
-			return null;
-		}
-		
-		if (value.trim().equals("true")) {
-			return true;
-		} else if (value.trim().equals("false")) {
-			return false;
-		} else {
-			log.warning("Not a boolean value: " + value);
-			return null;
-		}
-	}
-	
-	
-	protected final ImageDescriptor image(String key) {
-		String url = string(key);
-		
-		if (url == null) {
-			return null;
-		}
-		
-		try {
-			return ImageDescriptor.createFromURL(new URL(url));
-			
-		} catch (MalformedURLException e) {
-			log.warning("Invalid URL for image " + url);
-			return null;
-		}
-	}
-	
-	
-	protected final String string(String key) {
-		return properties.getProperty(key(key));
-	}
-	
-	
-	protected final String key(String name) {
-		return String.format("action.%s.%s", id, name);
-	}
-
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/CopyAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/CopyAction.java
deleted file mode 100644
index 1e7eb65..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/CopyAction.java
+++ /dev/null
@@ -1,100 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.views.SegmentationView;
-import ie.dcu.segment.SegmentationContext;
-import ie.dcu.segment.painters.SegmentationPainter;
-import ie.dcu.swt.*;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.*;
-import java.awt.image.BufferedImage;
-
-import org.eclipse.swt.graphics.Image;
-import org.eclipse.swt.widgets.Display;
-
-/**
- * Copy view to clipboard.
- * 
- * @author Kevin McGuinness
- */
-public class CopyAction extends AppAction {
-	
-	public CopyAction(ActionManager m) {
-		super(m);
-	}
-
-	@Override 
-	public void run() { 
-		
-		if (window.hasContext()) {
-			copy();
-		}
-	}
-
-	
-	private void copy() {
-		setClipboard(paintContext());
-		status("View copied to clipboard as image");
-	}
-	
-	
-	private static BufferedImage convert(Image image) {
-		BufferedImage im = ImageConverter.convert(image.getImageData());
-		image.dispose();
-		return im;
-	}
-
-
-	public void setClipboard(Image image) {
-		ImageSelection selection = new ImageSelection(convert(image));
-		Clipboard clip = Toolkit.getDefaultToolkit().getSystemClipboard();
-		clip.setContents(selection, null);
-	}
-	
-	
-	
-	private Image paintContext() {
-		SegmentationView view = window.getView();
-		SegmentationContext ctx = window.getContext();
-		SegmentationPainter painter = view.getPainter();
-		ObservableImage im = createCompatibleImage(ctx);
-		painter.paint(ctx, im);
-		return im.getImage();
-	}
-	
-	
-	private ObservableImage createCompatibleImage(SegmentationContext ctx) {
-		Image im = new Image(Display.getCurrent(), ctx.getBounds());
-		return new ObservableImage(im);
-	}
-	
-	
-	private static class ImageSelection implements Transferable {
-		private BufferedImage image;
-
-		
-		public ImageSelection(BufferedImage image) {
-			this.image = image;
-		}
-
-
-		public DataFlavor[] getTransferDataFlavors() {
-			return new DataFlavor[] { DataFlavor.imageFlavor };
-		}
-
-
-		public boolean isDataFlavorSupported(DataFlavor flavor) {
-			return DataFlavor.imageFlavor.equals(flavor);
-		}
-
-
-		public Object getTransferData(DataFlavor flavor) 
-			throws UnsupportedFlavorException
-		{
-			if (!DataFlavor.imageFlavor.equals(flavor)) {
-				throw new UnsupportedFlavorException(flavor);
-			}
-			return image;
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/ExitAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/ExitAction.java
deleted file mode 100644
index e6ee5c2..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/ExitAction.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.*;
-
-import org.eclipse.jface.dialogs.MessageDialog;
-
-/**
- * Terminate the application.
- * 
- * @author Kevin McGuinness
- */
-public class ExitAction extends AppAction {
-	public ExitAction(ActionManager m) {
-		super(m);
-	}
-
-	@Override 
-	public void run() {
-		if (confirmExit(window)) {
-			window.close();
-			System.exit(0);
-		}
-	}
-	
-	public static boolean confirmExit(AppWindow window) {
-		boolean confirm = window.getPrefs().get(
-				Boolean.class, AppPrefs.Keys.CONFIRM_EXIT, true);
-		
-		if (confirm) {
-			return MessageDialog.openConfirm(
-					window.getShell(), "Confirm", 
-					"Really exit the application?");
-		}
-		
-		return true;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/ExportImageMapAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/ExportImageMapAction.java
deleted file mode 100644
index 3efe020..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/ExportImageMapAction.java
+++ /dev/null
@@ -1,89 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.dialogs.ExportDialog;
-import ie.dcu.apps.ist.export.imagemap.*;
-import ie.dcu.apps.ist.views.*;
-import ie.dcu.segment.*;
-import ie.dcu.swt.ImageConverter;
-
-import java.awt.image.BufferedImage;
-import java.io.*;
-import java.util.logging.Level;
-
-import org.eclipse.swt.program.Program;
-
-/**
- * Export segmentation results as HTML image maps
- * 
- * @author Kevin McGuinness
- */
-public class ExportImageMapAction extends AppAction{
-
-	public ExportImageMapAction(ActionManager m) {
-		super(m);
-	}
-
-	@Override 
-	public void run() { 
-		
-		if (window.hasContext()) {
-			
-			// Get options from user
-			ExportDialog dialog = new ExportDialog(window.getShell());
-			ExportDialog.Result result = dialog.open();
-			
-			if (result != null) {
-				
-				// Grab image and mask
-				SegmentationContext ctx = window.getContext();
-				SegmentationMask mask = ctx.getMask();
-				BufferedImage image = ImageConverter.convert(ctx.getImageData());
-				
-				// Setup exporter
-				Exporter exporter = new Exporter(image, mask);
-				exporter.setEffect(result.effect);
-				exporter.setHtmlFile(result.html);
-				exporter.setImageFile(result.image);
-				exporter.setObjectLink(result.link);
-				exporter.setExportShape(result.shape);
-				exporter.setObjectDescription(result.description);
-				String label = SegmentationView.comboLabel.getText();
-	        	if(label.indexOf('{') != -1)
-	        	{
-	        		label = label.substring(0,label.indexOf('{')-1);
-	        	}
-	           	exporter.setTitle(label);
-				
-				// Export
-				try {
-					exporter.export(result.folder);
-				} catch (IOException e) {
-					handleError(e);
-					return;
-				} catch (ExportException e) {
-					handleError(e);
-					return;
-				} 
-				// for opening the image after saving as ImageMap
-				if (result.open) {
-					File file = new File(result.folder, result.html);
-					Program program = Program.findProgram(".html");
-					if (program != null) {
-						program.execute(file.getAbsolutePath());
-					}
-				}
-			}
-		}
-	}
-	
-	private void handleError(Exception e) {
-		log(Level.WARNING, "Error exporting view as HTML image map", e);
-		
-		// Show error dialog
-		error("Error exporting view as HTML image map: %s",  
-				e.getLocalizedMessage());
-		
-		// Set status message
-		status(Error, "Error exporting view as HTML image map");
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/ExportTransparentPNGAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/ExportTransparentPNGAction.java
deleted file mode 100644
index 1315e33..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/ExportTransparentPNGAction.java
+++ /dev/null
@@ -1,148 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.segment.*;
-import ie.dcu.swt.SwtUtils;
-import ie.dcu.util.FileUtils;
-
-import java.io.*;
-import java.util.logging.Level;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.widgets.FileDialog;
-
-public class ExportTransparentPNGAction extends AppAction {
-	
-private static final String DEFAULT_SUFFIX = ".png";
-	
-	private FileDialog dialog;
-	private String directory;
-
-	public ExportTransparentPNGAction(ActionManager m) {
-		super(m);
-	}
-	
-	@Override 
-	public void run() { 
-		if (window.hasContext()) {
-			File file = getFile();
-			if (file != null) {
-				directory = file.getParent();
-				export(file);
-			}
-		}		
-	}
-
-
-	private void export(File file) {
-		ImageData im = createSemiTransparentImage();
-		try {
-			SwtUtils.saveImage(im, file);
-		} catch (IOException e) {
-			handleError(file, e);
-		}
-	}
-	
-	
-	private ImageData createSemiTransparentImage() {
-		SegmentationContext ctx = window.getContext();
-		ImageData image = ctx.getImageData();
-		SegmentationMask mask = ctx.getMask();
-		ImageData result = new ImageData(image.width, image.height, 32, image.palette);
-		
-		int[] pixels = new int[image.width];
-		byte[] alphas = new byte[image.width];
-		
-		for (int y = 0; y < image.height; y++) {
-			image.getPixels(0, y, image.width, pixels, 0);
-			
-			int offset = y * mask.cols;
-			for (int i = 0; i < mask.cols; i++) {
-				if (mask.values[i+offset] == SegmentationMask.BACKGROUND) {
-					alphas[i] = (byte) 0x00;
-				} else {
-					alphas[i] = (byte) 0xff;
-				}
-			}
-			
-			result.setPixels(0, y, image.width, pixels, 0);
-			result.setAlphas(0, y, image.width, alphas, 0);
-		}
-		
-		return result;
-	}
-
-	
-	private void handleError(File file, IOException e) {
-		// Log
-		log(Level.WARNING, "Error exporting view as image", e);
-		
-		// Show error dialog
-		error("Error exporting view as image %s: %s", 
-				file.getName(), e.getLocalizedMessage()
-		);
-		
-		// Set status message
-		status(Error, "Error exporting view as image %s", file.getName());
-	}
-
-	
-	private File getFile() {
-		createExportDialog();
-		
-		String path = dialog.open();
-		if (path != null) {
-			return checkFile(path);
-		}
-		
-		return null;
-	}
-	
-	
-	private File checkFile(String path) {
-		File file = new File(path);
-
-		if (SwtUtils.getImageFormat(file) != -1) {
-			return file;
-		} 
-		
-		// Unknown file extension, so assume jpg
-		return new File(FileUtils.replaceExtension(path, DEFAULT_SUFFIX));
-	}
-
-	
-	private void createExportDialog() {
-		if (dialog == null) {
-			dialog = new FileDialog(window.getShell(), SWT.SAVE | SWT.SHEET);
-			dialog.setText("Export Transparent PNG");
-			dialog.setFilterExtensions(new String[]{"*.png"});
-			dialog.setFilterNames(new String[]{"PNG Images"});
-		}
-		
-		dialog.setFileName(getFileName());
-		
-		String dir = getDirectory();
-		if (dir != null) {
-			// Unfortunately this is buggy on SWT/GTK and
-			// the filter path isin't always set :'-(
-			dialog.setFilterPath(dir);
-		}
-	}
-	
-	private String getFileName() {
-		File file = window.getContext().getFile();
-		return FileUtils.replaceExtension(file.getName(), DEFAULT_SUFFIX);
-	}
-	
-	
-	private String getDirectory() {
-		if (directory == null) {
-			File folder = window.getContext().getFolder();
-			directory = (folder != null) ? 
-					directory = folder.getAbsolutePath() : null;
-		}
-		
-		return directory;
-	}
-	
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/ExportViewAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/ExportViewAction.java
deleted file mode 100644
index a6ca7b5..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/ExportViewAction.java
+++ /dev/null
@@ -1,162 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-
-import ie.dcu.apps.ist.views.SegmentationView;
-import ie.dcu.segment.SegmentationContext;
-import ie.dcu.segment.painters.SegmentationPainter;
-import ie.dcu.swt.*;
-import ie.dcu.util.FileUtils;
-
-import java.io.*;
-import java.util.logging.Level;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.graphics.Image;
-import org.eclipse.swt.widgets.*;
-
-
-/**
- * Export current view as image.
- * 
- * @author Kevin McGuinness
- */
-public class ExportViewAction extends AppAction {
-	
-	private static final String DEFAULT_SUFFIX = ".png";
-	
-	private FileDialog dialog;
-	private String directory;
-	
-	public ExportViewAction(ActionManager m) {
-		super(m);
-	}
-
-	@Override 
-	public void run() { 
-		if (window.hasContext()) {
-			File file = getFile();
-			if (file != null) {
-				directory = file.getParent();
-				export(file);
-			}
-		}		
-	}
-
-
-	private void export(File file) {
-		Image im = paintContext();
-		
-		try {
-			SwtUtils.saveImage(im, file);
-			status("View successfully exported as %s", file.getName());
-			
-		} catch (IOException e) {
-		
-			handleError(file, e);
-			
-		} finally {
-			
-			im.dispose();
-		}
-	}
-
-	
-	private void handleError(File file, IOException e) {
-		// Log
-		log(Level.WARNING, "Error exporting view as image", e);
-		
-		// Show error dialog
-		error("Error exporting view as image %s: %s", 
-				file.getName(), e.getLocalizedMessage()
-		);
-		
-		// Set status message
-		status(Error, "Error exporting view as image %s", file.getName());
-	}
-
-	
-	private File getFile() {
-		createExportDialog();
-		
-		String path = dialog.open();
-		if (path != null) {
-			return checkFile(path);
-		}
-		
-		return null;
-	}
-	
-	
-	private File checkFile(String path) {
-		File file = new File(path);
-
-		if (SwtUtils.getImageFormat(file) != -1) {
-			return file;
-		} 
-		
-		// Unknown file extension, so assume jpg
-		return new File(FileUtils.replaceExtension(path, DEFAULT_SUFFIX));
-	}
-
-	
-	private void createExportDialog() {
-		if (dialog == null) {
-			dialog = new FileDialog(window.getShell(), SWT.SAVE | SWT.SHEET);
-			dialog.setText(property("ExportViewAction.dialog.text"));
-			dialog.setFilterExtensions(getFilters());
-			dialog.setFilterNames(getFilterNames());
-		}
-		
-		dialog.setFileName(getFileName());
-		
-		String dir = getDirectory();
-		if (dir != null) {
-			// Unfortunately this is buggy on SWT/GTK and
-			// the filter path isin't always set :'-(
-			dialog.setFilterPath(dir);
-		}
-	}
-	
-	private String getFileName() {
-		File file = window.getContext().getFile();
-		return FileUtils.replaceExtension(file.getName(), DEFAULT_SUFFIX);
-	}
-	
-	
-	private String getDirectory() {
-		if (directory == null) {
-			File folder = window.getContext().getFolder();
-			directory = (folder != null) ? 
-					directory = folder.getAbsolutePath() : null;
-		}
-		
-		return directory;
-	}
-	
-	
-	
-	private String[] getFilters() {
-		return new String[] { property("ExportViewAction.dialog.filter.exts") };
-	}
-	
-	
-	private String[] getFilterNames() {
-		return new String[] { property("ExportViewAction.dialog.filter.text") };
-	}
-	
-	
-	private Image paintContext() {
-		SegmentationView view = window.getView();
-		SegmentationContext ctx = window.getContext();
-		SegmentationPainter painter = view.getPainter();
-		ObservableImage im = createCompatibleImage(ctx);
-		painter.paint(ctx, im);
-		return im.getImage();
-	}
-	
-	
-	private ObservableImage createCompatibleImage(SegmentationContext ctx) {
-		Image im = new Image(Display.getCurrent(), ctx.getBounds());
-		return new ObservableImage(im);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/HelpAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/HelpAction.java
deleted file mode 100644
index 6905dd6..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/HelpAction.java
+++ /dev/null
@@ -1,126 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.swt.layout.LayoutFactory;
-
-import org.eclipse.swt.*;
-import org.eclipse.swt.browser.Browser;
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.layout.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Show a help dialog.
- * 
- * @author Kevin McGuinness
- */
-public class HelpAction extends AppAction {
-	
-	private HelpBox dialog;
-	
-	
-	public HelpAction(ActionManager m) {
-		super(m);
-	}
-
-	
-	@Override 
-	public void run() { 
-		if (dialog == null) {
-			dialog = new HelpBox();
-		}
-		
-		if (dialog.available()) {
-			dialog.open();
-		} else {
-			info("Help browser unavailable on this system");
-		}
-	}
-	
-	
-	/**
-	 * Help dialog box, just wraps a browser.
-	 */
-	private class HelpBox {
-		private Shell shell;
-		private Composite content;
-		private Browser browser;
-		
-		
-		public HelpBox() {
-			createShell();
-			createContent();
-		}
-
-
-		private void createShell() {
-			shell = new Shell(window.getShell(), SWT.SHELL_TRIM);
-			
-			// Prevent the shell from disposing on close
-			shell.addShellListener(new ShellAdapter() {
-				public void shellClosed(ShellEvent evt) {
-					evt.doit = false;
-					close();
-				}
-			});
-			
-			// Use a fill layout
-			shell.setLayout(new GridLayout());
-			
-			// Set size and title
-			shell.setSize(640, 480);
-			shell.setText("Help");
-		}
-
-
-		private void createContent() {
-			// Create content pane
-			content = new Composite(shell, SWT.BORDER);
-			content.setLayout(new FillLayout());
-			content.setLayoutData(LayoutFactory.createGridData());
-			
-			// Add browser widget
-			try {
-				browser = new Browser(content, SWT.NONE);
-			} catch (SWTError e) {
-				
-				// Log warning and return
-				log.warning("Browser unavailable: " + e.getMessage());
-				browser = null;
-				return;
-			}
-			
-			// Go to help home page
-			home();
-		}
-
-
-		public void home() {
-			String urlString = string("helpURL");
-			if (urlString != null) {
-				go(urlString);
-			} else {
-				browser.setText("Help file is unavailable");
-			}
-		}
-		
-		
-		public void go(String url) {
-			browser.setUrl(url);
-		}
-				
-		
-		public boolean available() {
-			return browser != null;
-		}
-		
-		
-		public void open() {
-			shell.setVisible(true);
-		}
-		
-		
-		public void close() {
-			shell.setVisible(false);
-		}
-	}	
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/HoverAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/HoverAction.java
deleted file mode 100644
index cf933bc..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/HoverAction.java
+++ /dev/null
@@ -1,88 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import org.eclipse.jface.action.*;
-import org.eclipse.jface.resource.*;
-
-/**
- * Default implementation of {@link IHoverAction}. 
- * 
- * @author Kevin McGuinness
- */
-public class HoverAction extends Action implements IHoverAction {
-	private boolean armed = false;
-	
-	/**
-	 * Creates a new action with no text and no image. Configure the action later
-	 * using the set methods.
-	 */
-	public HoverAction() {
-		super();
-	}
-
-
-	/**
-	 * Creates a new action with the given text and no image.
-	 * 
-	 * @param text
-	 *          the string used as the text for the action, or <code>null</code>
-	 *          if there is no text
-	 */
-	public HoverAction(String text) {
-		super(text);
-	}
-
-
-	/**
-	 * Creates a new action with the given text and image.
-	 * 
-	 * @param text
-	 *          the action's text, or <code>null</code> if there is no text
-	 * @param image
-	 *          the action's image, or <code>null</code> if there is no image
-	 */
-	public HoverAction(String text, ImageDescriptor image) {
-		super(text, image);
-	}
-
-
-	/**
-	 * Creates a new action with the given text and style.
-	 * 
-	 * @param text
-	 *            the action's text, or <code>null</code> if there is no text.
-	 * @param style
-	 *            one of 
-	 *            <code>AS_PUSH_BUTTON</code>,
-	 *            <code>AS_CHECK_BOX</code>, 
-	 *            <code>AS_DROP_DOWN_MENU</code>,
-	 *            <code>AS_RADIO_BUTTON</code>, and
-	 *            <code>AS_UNSPECIFIED</code>.
-	 */
-	public HoverAction(String text, int style) {
-		super(text, style);
-	}
-
-
-	/**
-	 * Sets the armed property to <code>true</code>.
-	 */
-	public void arm() {
-		armed = true;
-	}
-
-
-	/**
-	 * Sets the armed property to <code>false</code>.
-	 */
-	public void disarm() {
-		armed = false;
-	}
-
-
-	/**
-	 * Returns <code>true</code> if armed.
-	 */
-	public boolean isArmed() {
-		return armed;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/HoverMenuManager.java b/image_annotation/src/ie/dcu/apps/ist/actions/HoverMenuManager.java
deleted file mode 100644
index d3b051a..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/HoverMenuManager.java
+++ /dev/null
@@ -1,149 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.widgets.ImageMenuManager;
-
-import java.net.URL;
-import java.util.*;
-
-import org.eclipse.jface.action.*;
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Menu Manager that notifies instances of IHoverAction when they are armed and
- * disarmed.
- * 
- * @author Kevin McGuinness
- */
-public class HoverMenuManager extends ImageMenuManager  {
-	
-	/**
-	 * Stores items that have hover listeners added to them. 
-	 */
-	private final Set<MenuItem> hoverItems = new HashSet<MenuItem>();
-	
-	
-	/**
-	 * Create hover menu manager.
-	 */
-	public HoverMenuManager() {
-		init();
-	}
-
-	
-	/**
-	 * Create hover menu manager with id and text.
-	 * 
-	 * @param text
-	 *          the text for the menu, or <code>null</code> if none.
-	 * @param imageURL
-	 *          the menu image url, or <code>null</code>.
-	 */
-	public HoverMenuManager(String text, URL imageURL) {
-		super(text, imageURL);
-		init();
-	}
-
-
-  /**
-	 * Create hover menu manager text.
-	 * 
-	 * @param text
-	 *          the text for the menu, or <code>null</code> if none.
-	 */
-	public HoverMenuManager(String text) {
-		super(text);
-		init();
-	}
-
-	
-	private void init() {
-		addMenuListener(menuListener);
-	}
-
-
-	private void addHoverListeners() {
-		Menu menu = getMenu();
-		for (MenuItem item : menu.getItems()) {
-			addHoverListener(item);
-		}
-	}
-	
-
-	private void addHoverListener(MenuItem item) {
-		IHoverAction action = getHoverAction(item);
-		if (action != null) {
-			addHoverListener(item, action);
-		}
-	}
-
-	
-	private void addHoverListener(MenuItem item, IHoverAction action) {
-		if (!hoverItems.contains(item)) {
-			item.addArmListener(new HoverListener(action));
-			hoverItems.add(item);
-		}
-	}
-	
-	
-	private void disarmAll() {
-		Menu menu = getMenu();
-		for (MenuItem item : menu.getItems()) {
-			disarm(item);
-		}
-	}
-	
-	
-	private void disarm(MenuItem item) {
-		IHoverAction action = getHoverAction(item);
-		if (action != null) {
-			disarm(action);
-		}
-	}
-
-
-	private void disarm(IHoverAction action) {
-		if (action.isArmed()) {
-			action.disarm();
-		}
-	}
-	
-	
-	private IHoverAction getHoverAction(MenuItem item) {
-		Object data = item.getData();
-		if (data instanceof ActionContributionItem) {
-			IAction action = ((ActionContributionItem) data).getAction();
-			
-			if (action instanceof IHoverAction) {
-				return (IHoverAction) action;
-			}
-		}
-		return null;
-	}
-
-
-	private IMenuListener menuListener = new IMenuListener2() {
-		public void menuAboutToShow(IMenuManager manager) {
-			addHoverListeners();
-		}
-
-		public void menuAboutToHide(IMenuManager manager) {
-			disarmAll();
-		}		
-	};
-	
-	
-	private final class HoverListener implements ArmListener {
-		private final IHoverAction action;
-
-		public HoverListener(IHoverAction action) {
-			this.action = action;
-		}
-
-		
-		public void widgetArmed(ArmEvent e) {
-			disarmAll();
-			action.arm();
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/IHoverAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/IHoverAction.java
deleted file mode 100644
index cac72be..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/IHoverAction.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import org.eclipse.jface.action.*;
-
-/**
- * Extension of IAction that supports arming when the mouse hovers over the
- * item. This may be useful for displaying descriptions of menu items in the
- * status bar, for example. To use hover actions the {@link HoverMenuManager}
- * must be used.
- * 
- * @author Kevin McGuinness
- */
-public interface IHoverAction extends IAction {
-	
-	
-	/**
-	 * Executed when the action is hovered/armed.
-	 */
-	public void arm();
-	
-	
-	/**
-	 * Executed when the action is de-hovered/disarmed.
-	 */
-	public void disarm();
-	
-	
-	/**
-	 * Query if the action is armed.
-	 * 
-	 * @return <code>true</code> if armed.
-	 */
-	public boolean isArmed();
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/NextAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/NextAction.java
deleted file mode 100644
index 900618b..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/NextAction.java
+++ /dev/null
@@ -1,122 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.actions;
-
-import java.io.*;
-import java.util.*;
-
-/**
- * Jump to the next image in the directory
- * 
- * @author Kevin McGuinness
- */
-public class NextAction extends AppAction {
-	// Supported file extensions
-	static final String EXTENSIONS = "jpg;jpeg;png;gif;bmp;ctx";
-	
-	private final java.io.FileFilter imageFilter;
-
-	
-	public NextAction(ActionManager m) {
-		super(m);
-		
-		// Create an image file filter
-		imageFilter = new SimpleFileFilter(EXTENSIONS);
-	}
-
-	
-	@Override 
-	public void run() {
-		if (window.hasContext()) {
-			// Get currently opened file
-			File file = window.getContext().getFile();
-			
-			// Find the one after & open it
-			File next = findNext(file);
-			if (next != null) {
-				manager.get(OpenAction.class).open(next);
-			}
-		}
-	}
-	
-	
-	private File findNext(File file) {
-		File dir = file.getParentFile();
-		
-		if (dir != null) {
-			
-			// List the images
-			File[] files = dir.listFiles(imageFilter);
-			
-			// Need at least one
-			if (files.length > 1) {
-				
-				// Search for ourself...
-				for (int i = 0; i < files.length; i++) {
-					
-					if (files[i].equals(file)) {
-						
-						// Use next file (wrap back to first)
-						return files[(i+1)%files.length];
-					}
-				}
-			}
-		}
-		
-		return null;
-	}
-	
-}
-
-class SimpleFileFilter implements java.io.FileFilter {
-	
-	/**
-	 * Holds the list of extensions. It is expected it will be quite
-	 * short, so we use an ArrayList.
-	 */
-	private final ArrayList<String> extensions;
-	
-	
-	/**
-	 * Construct a simple file extension filter based on a semicolon separated
-	 * list of file extensions.
-	 * 
-	 * @param extensions
-	 *          A list of file extensions (ex. jpeg;jpg;png)
-	 */
-	public SimpleFileFilter(String extensions) {
-		String[] exts = extensions.split(";");
-		this.extensions = new ArrayList<String>(exts.length);
-		
-		for (String s : exts) {
-			if ((s = s.trim()).length() != 0) {
-				if (s.startsWith("*")) {
-					s = s.substring(1);
-				}
-				
-				if (!s.startsWith(".")) {
-					s = "." + s;
-				}
-				
-				this.extensions.add(s);
-			}
-		}
-	}
-	
-
-	public boolean accept(File pathname) {
-		if (pathname.isFile()) {
-			String name = pathname.getName();
-			
-			// List of extensions should be fairly short..
-			for (String ext : extensions) {
-				if (name.endsWith(ext)) {
-					return true;
-				}
-			}
-		}
-		
-		return false;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/OpenAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/OpenAction.java
deleted file mode 100644
index 823f176..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/OpenAction.java
+++ /dev/null
@@ -1,110 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.*;
-import ie.dcu.segment.SegmentationContext;
-
-import java.io.*;
-
-import org.eclipse.swt.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Open an image or segmentation context.
- * 
- * @author Kevin McGuinness
- */
-public class OpenAction extends AppAction {
-
-	private FileDialog dialog;
-	
-	public OpenAction(ActionManager m) {
-		super(m);
-	}
-	
-
-	@Override
-	public void run() {
-		File file = getFile();
-		if (file != null) {
-			open(file);
-		}
-	}
-	
-
-	public boolean open(File file) {
-		String name = file.getName();
-		try {
-			if (SegmentationContext.isContextFile(file)) {
-			
-				// Load context
-				window.setContext(SegmentationContext.load(file));
-				status("Opened segmentation context %s successfully", name);
-			} else {
-			
-				// Create context
-				window.setContext(SegmentationContext.create(file));
-				status("Opened image file %s successfully", name);
-			}
-			
-			// Save history
-			AppRecentFiles.getInstance().add(file);
-			
-			// Ok
-			return true;
-			
-		} catch (IOException e) {
-			
-			handleError(file, e);
-			status(Warning, "Proplem opening file %s", name);
-		
-			return false;
-		}
-	}
-
-
-	private void handleError(File file, IOException e) {
-
-		// Get appropriate message
-		String message = e.getCause() == null ? e.getLocalizedMessage() :
-			e.getCause().getLocalizedMessage();
-		
-		// Log warning
-		log.warning(String.format(
-				"Unable to open %s\n Problem: %s", file, message
-		));
-
-		// Show warning dialog
-		warning("Unable to open %s:\n%s", file.getName(), message);
-	}
-
-
-	private void createOpenDialog() {
-		// Create dialog if necessary
-		if (dialog == null) {
-			dialog = new FileDialog(window.getShell(), SWT.OPEN | SWT.SHEET);
-			dialog.setText(property("OpenAction.dialog.text"));
-			dialog.setFilterExtensions(getFilters());
-			dialog.setFilterNames(getFilterNames());
-		}
-	}
-	
-	private String[] getFilters() {
-		return new String[] { property("OpenAction.dialog.filter.exts") };
-	}
-	
-	private String[] getFilterNames() {
-		return new String[] { property("OpenAction.dialog.filter.text") };
-	}
-	
-	
-	private File getFile() {
-		createOpenDialog();
-		
-		String path = dialog.open();
-		if (path != null) {
-			return new File(path);
-		}
-		
-		return null;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/OpenExperimentAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/OpenExperimentAction.java
deleted file mode 100644
index 2e27dd4..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/OpenExperimentAction.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.exp.*;
-
-import java.io.*;
-
-import org.eclipse.swt.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Open an experiment file and switch to experiment mode.
- * 
- * @author Kevin McGuinness
- */
-public class OpenExperimentAction extends AppAction {
-	
-	private FileDialog dialog;
-	
-
-	public OpenExperimentAction(ActionManager m) {
-		super(m);
-	}
-
-	
-	@Override
-	public void run() {
-		File file = getFile();
-		if (file != null) {
-			open(file);
-		}
-	}
-	
-	
-	private void open(File file) {
-		try {
-			Experiment ex = ExperimentFactory.getInstance().load(file);
-			window.setExperiment(ex);
-			
-		} catch (IOException ex) {
-			handleError(file, ex);
-		} catch (FormatException ex) {
-			handleError(file, ex);
-		}
-	}
-	
-	
-	private void handleError(File file, Exception ex) {
-		// Get appropriate message
-		String mesg = ex.getMessage();
-		
-		// Log warning
-		log.warning(String.format(
-				"Unable to open experiment file %s\n Problem: %s", file, mesg
-		));
-
-		// Show warning dialog
-		warning("Unable to open experiment file %s:\n%s", file.getName(), mesg);
-	}
-
-
-	private File getFile() {
-		createOpenDialog();
-		
-		String path = dialog.open();
-		if (path != null) {
-			return new File(path);
-		}
-		
-		return null;
-	}
-	
-	
-	private void createOpenDialog() {
-		// Create dialog if necessary
-		if (dialog == null) {
-			dialog = new FileDialog(window.getShell(), SWT.OPEN | SWT.SHEET);
-			dialog.setText(property("OpenExperimentAction.dialog.text"));
-			dialog.setFilterExtensions(getFilters());
-			dialog.setFilterNames(getFilterNames());
-		}
-	}
-	
-	private String[] getFilters() {
-		return new String[] { 
-				property("OpenExperimentAction.dialog.filter.exts") 
-		};
-	}
-	
-	private String[] getFilterNames() {
-		return new String[] { 
-				property("OpenExperimentAction.dialog.filter.text") 
-		};
-	}
-	
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/OpenRecentAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/OpenRecentAction.java
deleted file mode 100644
index 299117e..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/OpenRecentAction.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import java.io.*;
-
-/**
- * Action to open a recent file.
- * 
- * @author Kevin McGuinness
- */
-public class OpenRecentAction extends AppAction {
-	private final File file;
-
-	public OpenRecentAction(ActionManager m, File file) {
-		super(m);
-		this.file = file;
-		setText(file.getName());
-		String path = file.getAbsolutePath();
-		setToolTipText(path);
-		setDescription(String.format("Open file %s", path));
-	}
-	
-	public void run() {
-		manager.get(OpenAction.class).open(file);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/PreferencesAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/PreferencesAction.java
deleted file mode 100644
index 1ccfc38..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/PreferencesAction.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.dialogs.*;
-
-/**
- * Show preferences dialog box.
- * 
- * @author Kevin McGuinness
- */
-public class PreferencesAction extends AppAction {
-	private PrefsDialog dialog;
-	
-	public PreferencesAction(ActionManager m) {
-		super(m);
-	}
-
-	
-	public void run() { 
-		if (dialog == null) {
-			dialog = new PrefsDialog(window);
-		}
-		dialog.open();
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/PreviousAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/PreviousAction.java
deleted file mode 100644
index 4bfb907..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/PreviousAction.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.actions;
-
-import java.io.*;
-
-/**
- * Jump to previous file in current directory.
- * 
- * @author Kevin McGuinness
- */
-public class PreviousAction extends AppAction {
-	private final java.io.FileFilter imageFilter;
-
-
-	public PreviousAction(ActionManager m) {
-		super(m);
-		
-		// Create an image file filter
-		imageFilter = new SimpleFileFilter(NextAction.EXTENSIONS);
-	}
-	
-	
-	@Override 
-	public void run() {
-		if (window.hasContext()) {
-			// Get currently opened file
-			File file = window.getContext().getFile();
-			
-			// Find the one before & open it
-			File next = findPrevious(file);
-			if (next != null) {
-				manager.get(OpenAction.class).open(next);
-			}
-		}
-	}
-	
-
-	
-	private File findPrevious(File file) {
-		File dir = file.getParentFile();
-		
-		if (dir != null) {
-			
-			// List the images
-			File[] files = dir.listFiles(imageFilter);
-			
-			// Need at least one
-			if (files.length > 1) {
-				
-				// Search for ourself...
-				for (int i = 0; i < files.length; i++) {
-					
-					if (files[i].equals(file)) {
-						
-						// Use previous file (wrap back to last)
-						return files[(i > 0) ? i - 1 : files.length - 1];
-					}
-				}
-			}
-		}
-		
-		return null;
-	}
-
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/PrintAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/PrintAction.java
deleted file mode 100644
index 3645631..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/PrintAction.java
+++ /dev/null
@@ -1,107 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-
-import ie.dcu.apps.ist.views.SegmentationView;
-import ie.dcu.segment.SegmentationContext;
-import ie.dcu.segment.painters.SegmentationPainter;
-import ie.dcu.swt.ObservableImage;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.printing.*;
-import org.eclipse.swt.widgets.Display;
-
-/**
- * Send current view to printer.
- * 
- * @author Kevin McGuinness
- */
-public class PrintAction extends AppAction {
-	
-	private static final String JOB_NAME = "Interactive Segmentation Tool";
-	private PrintDialog dialog;
-	
-	public PrintAction(ActionManager m) {
-		super(m);
-	}
-
-	@Override 
-	public void run() { 
-		if (window.hasContext()) {
-			status("Printing...");
-			PrinterData data = getPrintData();
-			if (data != null) {
-				print(data);
-				status("Printing complete");
-			} else {
-				status(null);
-			}
-		}
-	}
-	
-	
-	private PrinterData getPrintData() {
-		createPrintDialog();
-		return dialog.open();
-	}
-
-
-	private void print(PrinterData data) {
-		Printer printer = new Printer(data);
-		try {
-			print(printer);
-			
-		} finally {
-			printer.dispose();
-		}
-	}
-
-
-	private void print(Printer printer) {
-		if (printer.startJob(JOB_NAME)) {
-			if (printer.startPage()) {
-				GC gc = new GC(printer);
-				try {
-					paint(gc, printer);
-				} finally {
-					gc.dispose();
-				}
-				printer.endPage();
-			}
-			printer.endJob();
-		}
-	}
-
-	
-	private void paint(GC gc, Printer printer) {
-		Image im = paintContext();
-		try {
-			gc.drawImage(im, 30, 30);
-		} finally {
-			im.dispose();
-		}
-	}
-	
-
-	private void createPrintDialog() {
-		if (dialog == null) {
-			dialog = new PrintDialog(window.getShell(), SWT.SHEET);
-		}
-	}
-	
-	
-	private Image paintContext() {
-		SegmentationView view = window.getView();
-		SegmentationContext ctx = window.getContext();
-		SegmentationPainter painter = view.getPainter();
-		ObservableImage im = createCompatibleImage(ctx);
-		painter.paint(ctx, im);
-		return im.getImage();
-	}
-	
-	
-	private ObservableImage createCompatibleImage(SegmentationContext ctx) {
-		Image im = new Image(Display.getCurrent(), ctx.getBounds());
-		return new ObservableImage(im);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/RedoAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/RedoAction.java
deleted file mode 100644
index 4e84880..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/RedoAction.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.views.SegmentationView;
-
-
-/**
- * Redo last annotation action.
- * 
- * @author Kevin McGuinness
- */
-public class RedoAction extends AppAction {
-	public RedoAction(ActionManager m) {
-		super(m);
-	}
-
-	@Override 
-	public void run() {
-		SegmentationView view = window.getView();
-		if (view.canRedo()) {
-			view.redo();
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/SaveAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/SaveAction.java
deleted file mode 100644
index e652d28..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/SaveAction.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import java.io.*;
-import java.util.logging.*;
-
-import org.eclipse.swt.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Save segmentation context.
- * 
- * @author Kevin McGuinness
- */
-public class SaveAction extends AppAction {
-	
-	private FileDialog dialog;
-
-	public SaveAction(ActionManager m) {
-		super(m);
-	}
-
-	
-	@Override
-	public void run() {
-		
-		if (window.hasContext()) {
-			
-			File file;
-			if (window.hasContextFile()) {
-				file = window.getContextFile();
-			} else {
-				file = getFile();
-			}
-			
-			if (file != null) {
-				save(file);
-			}
-		}
-	}
-	
-
-	private void createSaveDialog() {
-		if (dialog == null) {
-			dialog = new FileDialog(window.getShell(), SWT.SAVE | SWT.SHEET);
-			dialog.setText(property("SaveAction.dialog.text"));
-			dialog.setFilterExtensions(getFilters());
-			dialog.setFilterNames(getFilterNames());
-			
-			String dir = getDirectory();
-			if (dir != null) {
-				dialog.setFilterPath(dir);
-			}
-		}
-		
-		dialog.setFileName(getFileName());
-	}
-	
-	
-	private String getDirectory() {
-		File folder = window.getContext().getFolder();
-		if (folder != null) {
-			return folder.getAbsolutePath();
-		}
-		
-		return null;
-	}
-	
-	
-	private String getFileName() {
-		return window.getContext().getDefaultFilename();
-	}
-	
-	
-	private String[] getFilters() {
-		return new String[] { property("SaveAction.dialog.filter.exts") };
-	}
-	
-	
-	private String[] getFilterNames() {
-		return new String[] { property("SaveAction.dialog.filter.text") };
-	}
-
-	
-	private File getFile() {
-		createSaveDialog();
-		
-		String path = dialog.open();
-		if (path != null) {
-			return new File(path);
-		}
-		
-		return null;
-	}
-	
-	
-	private void save(File file) {
-		try {
-			window.getContext().save(file);
-			window.updateWindowTitle();
-			status("Saved context %s successfully", file.getName());
-		} catch (IOException e) {
-			handleError(file, e);
-		}
-	}
-
-
-	private void handleError(File file, IOException e) {
-		
-		// Log
-		log(Level.SEVERE, "Error saving file", e);
-		
-		// Show error dialog
-		error("Error saving segmentation context %s: %s", 
-				file.getName(), e.getLocalizedMessage()
-		);
-		
-		// Set status message
-		status(Error, "Error saving segmentation context %s", file.getName());
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/SaveAsAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/SaveAsAction.java
deleted file mode 100644
index 7db1c26..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/SaveAsAction.java
+++ /dev/null
@@ -1,112 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import java.io.*;
-import java.util.logging.*;
-
-import org.eclipse.swt.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Save segmentation context as.
- * 
- * @author Kevin McGuinness
- */
-public class SaveAsAction extends AppAction {
-	
-	private FileDialog dialog;
-
-	public SaveAsAction(ActionManager m) {
-		super(m);
-	}
-	
-	@Override
-	public void run() {		
-		if (window.hasContext()) {
-			File file = getFile();
-			if (file != null) {
-				save(file);
-			}
-		}
-	}
-	
-	
-	private void createSaveDialog() {
-		if (dialog == null) {
-			dialog = new FileDialog(window.getShell(), SWT.SAVE | SWT.SHEET);
-			dialog.setText(property("SaveAction.dialog.text"));
-			dialog.setFilterExtensions(getFilters());
-			dialog.setFilterNames(getFilterNames());
-			
-			String dir = getDirectory();
-			if (dir != null) {
-				dialog.setFilterPath(dir);
-			}
-		}
-		
-		dialog.setFileName(getFileName());
-	}
-	
-	
-	private String getDirectory() {
-		File folder = window.getContext().getFolder();
-		if (folder != null) {
-			return folder.getAbsolutePath();
-		}
-		
-		return null;
-	}
-	
-	
-	
-	private String getFileName() {
-		return window.getContext().getDefaultFilename();
-	}
-	
-	
-	private String[] getFilters() {
-		return new String[] { property("SaveAction.dialog.filter.exts") };
-	}
-	
-	
-	private String[] getFilterNames() {
-		return new String[] { property("SaveAction.dialog.filter.text") };
-	}
-	
-	
-	private File getFile() {
-		createSaveDialog();
-		
-		String path = dialog.open();
-		if (path != null) {
-			return new File(path);
-		}
-		
-		return null;
-	}
-	
-	
-	private void save(File file) {
-		try {
-			window.getContext().save(file);
-			window.updateWindowTitle();
-			status("Saved context %s successfully", file.getName());
-		} catch (IOException e) {
-			handleError(file, e);
-		}
-	}
-	
-	
-	private void handleError(File file, IOException e) {
-		
-		// Log
-		log(Level.SEVERE, "Error saving file", e);
-		
-		// Show error dialog
-		error("Error saving segmentation context %s: %s", 
-				file.getName(), e.getLocalizedMessage()
-		);
-		
-		// Set status message
-		status(Error, "Error saving segmentation context %s", file.getName());
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/SelectSegmenterAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/SelectSegmenterAction.java
deleted file mode 100644
index 485ec8a..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/SelectSegmenterAction.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.SegmenterRegistry;
-import ie.dcu.apps.ist.views.SegmentationView;
-import ie.dcu.segment.Segmenter;
-
-/**
- * Segmenter radio buttons.
- * 
- * @author Kevin McGuinness
- */
-public class SelectSegmenterAction extends AppAction {
-	private final Segmenter segmenter;
-
-	public SelectSegmenterAction(ActionManager m, SegmenterRegistry r, Segmenter s) {
-		super(m, AS_RADIO_BUTTON);
-		this.segmenter = s;
-		setText(s.getName());
-		setToolTipText(s.getDescription());
-		
-		if (!s.isAvailable()) {
-			super.setEnabled(false);
-			setChecked(false);
-			
-			String naText = string("NA");
-			setToolTipText(naText);
-			setDescription(naText);
-		} else {
-			setChecked(r.isDefault(s));
-		}
-	}
-	
-	public void setEnabled(boolean enabled) {
-		// Disallow enabling unavailable segmentation algorithms
-		if (!enabled || (segmenter.isAvailable() && enabled)) {
-			super.setEnabled(enabled);
-		}
-	}
-	
-	
-	public Segmenter getSegmenter() {
-		return segmenter;
-	}
-
-	
-	@Override
-	public String id() {
-		return segmenter.getClass().getName();
-	}
-
-
-	@Override
-	public void run() {
-		if (isChecked()) {
-			SegmentationView view = window.getView();
-			view.setSegmenter(segmenter);		
-		}
-	}
-	
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/actions/UndoAction.java b/image_annotation/src/ie/dcu/apps/ist/actions/UndoAction.java
deleted file mode 100644
index d5c67f2..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/actions/UndoAction.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package ie.dcu.apps.ist.actions;
-
-import ie.dcu.apps.ist.views.SegmentationView;
-
-/**
- * Undo last annotation.
- *  
- * @author Kevin McGuinness
- */
-public class UndoAction extends AppAction {
-	public UndoAction(ActionManager m) {
-		super(m);
-	}
-
-	@Override 
-	public void run() { 
-		SegmentationView view = window.getView();
-		if (view.canUndo()) {
-			view.undo();
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/controllers/AnnotationTool.java b/image_annotation/src/ie/dcu/apps/ist/controllers/AnnotationTool.java
deleted file mode 100644
index eb89bb0..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/controllers/AnnotationTool.java
+++ /dev/null
@@ -1,314 +0,0 @@
-package ie.dcu.apps.ist.controllers;
-
-
-
-import ie.dcu.segment.annotate.*;
-import ie.dcu.swt.*;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.events.MouseEvent;
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.widgets.Canvas;
-
-public class AnnotationTool extends MouseMotionAdapter {
-	private final AnnotationManager manager;	
-	private ImageControl view;
-	private Canvas canvas;
-	
-	private Annotation current;
-	private AnnotationType type;
-	private int lineWidth;
-	private Point last;
-	private boolean invert;
-
-	
-	public AnnotationTool(AnnotationManager manager) {
-		this (manager, null);
-	}
-	
-	/**
-	 * 
-	 * @param manager
-	 * @param view
-	 */
-	public AnnotationTool(AnnotationManager manager, ImageControl view) {
-		assert (manager != null);
-		
-		this.manager = manager;
-		this.current = null;
-		this.lineWidth = 1;
-		this.type = AnnotationType.Foreground;
-		
-		attach(view);
-	}
-
-
-	/**
-	 * 
-	 * @param view
-	 */
-	public void attach(ImageControl view) {
-		detach();
-	
-		if (view != null) {
-			this.view = view;
-			canvas = view.getCanvas();
-			canvas.addMouseListener(this);
-			canvas.addMouseMoveListener(this);
-		}
-	}
-		
-
-
-	public void detach() {
-		if (view != null) {
-			canvas.removeMouseListener(this);
-			canvas.removeMouseMoveListener(this);
-			view = null;
-			canvas = null;
-			current = null;
-		}
-	}
-	
-	
-	/**
-	 * Returns the image control associated with the annotation tool.
-	 */
-	public ImageControl getView() {
-		return view;
-	}
-	
-		
-	/**
-	 * @return the line width
-	 */
-	public int getLineWidth() {
-		return lineWidth;
-	}
-
-
-	/**
-	 * @param width the line width to set
-	 */
-	public void setLineWidth(int width) {
-		assert (width > 0);
-		this.lineWidth = width;
-	}
-
-
-	/**
-	 * @return the annotation type
-	 */
-	public AnnotationType getType() {
-		return type;
-	}
-
-	
-	/**
-	 * @param type the annotation type to set
-	 */
-	public void setType(AnnotationType type) {
-		assert (type != null);
-		this.type = type;
-	}
-	
-
-
-	public void begin(Point pt) {		
-			
-		// Create a new annotation
-		current = new Annotation(getTypeForUse(), lineWidth, view.canvasToImage(pt));
-		
-		// Give immediate visual feedback
-		feedback(pt);
-		
-		// Set last
-		last = pt;
-	}
-	
-	
-	public void append(Point pt) {
-			
-		// Update the annotation
-		current.add(view.canvasToImage(pt));
-		
-		// Give immediate visual feedback
-		feedback(last, pt);
-		
-		// Set last
-		last = pt;
-	}
-	
-	
-	public void commit(Point pt) {
-		// Clip points to image bounds
-		clip(last, pt);
-		
-		// Add point to annotation
-		current.add(view.canvasToImage(pt));
-			
-		// Add annotation to annotation manager
-		manager.add(current);
-		
-		// Give immediate visual feedback
-		feedback(last, pt);
-			
-		// Mark current annotation as null
-		current = null;
-	}
-	
-	
-	public void cancel() {
-		
-		// Repaint dirty area
-		view.repaint(current.getBounds());
-		
-		// Discard annotation
-		current = null;
-	}
-	
-	
-	
-	@Override
-	public void mouseDown(MouseEvent e) {
-		if (view == null || !view.isEnabled()) {
-			current = null;
-			return;
-		}
-			
-		ObservableImage image = view.getImage();
-		if (image != null) {
-			
-			if (e.button == 1 || e.button == 3) {
-				
-				Point pt = new Point(e.x, e.y);
-				
-				if (view.imageContains(pt)) {
-				
-					// Check for right mouse button or ctrl modifier
-					
-					if (e.button == 3 || (e.stateMask & SWT.CTRL) != 0) {
-						// Invert type
-						invert = true;
-					} else {
-						invert = false;
-					}
-					
-					if (current != null) {
-						// Cancel last action
-						cancel();
-					}
-					
-					begin(pt);
-				}
-			}
-		}
-		
-		return;
-	}
-
-	
-	@Override
-	public void mouseMove(MouseEvent e) {
-		if (view == null || !view.isEnabled()) {
-			current = null;
-			return;
-		}
-		
-		if (current != null) {
-			Point pt = new Point(e.x, e.y);
-			
-			if (view.imageContains(pt)) {
-				// Normal case: append
-				append(pt);
-				
-			} else {
-				// Line drawn outside image
-				
-				if (view.getImage() != null) {
-					
-					commit(pt);
-				
-				} else {
-					// No image: cancel
-					cancel();
-				}
-			} 
-		}
-		
-	}
-
-
-	@Override
-	public void mouseUp(MouseEvent e) {
-		if (view == null || !view.isEnabled()) {
-			current = null;
-			return;
-		}
-		
-		if (current != null) {
-			Point pt = new Point(e.x, e.y);
-			
-			if (view.imageContains(pt)) {
-				
-				// Normal case: commit
-				commit(pt);
-			} else {
-				
-			  // Line drawn outside image
-				if (view.getImage() != null) {
-					
-					commit(pt);
-				} else {
-					
-					// No image
-					cancel();
-				}
-			}
-		}
-	}
-
-
-	private void clip(Point p, Point q) {
-		SwtUtils.clip(view.getCanvasImageBounds(), p, q);
-	}
-	
-
-	private GC createFeedbackGC() {
-		GC gc = new GC(canvas);
-		gc.setAntialias(SWT.ON);
-		gc.setLineCap(SWT.CAP_ROUND);
-		gc.setLineJoin(SWT.JOIN_ROUND);
-		gc.setLineWidth((int) Math.floor(lineWidth * view.getZoom()));
-		gc.setForeground(getTypeForUse().getColor());
-		return gc;
-	}
-	
-	
-	private void feedback(Point p1) {
-		feedback(p1, new Point(p1.x+1, p1.y));
-	}
-	
-	
-	private void feedback(Point p1, Point p2) {
-		GC gc = createFeedbackGC();
-		gc.setClipping(getClip(p1, p2));
-		gc.drawLine(p1.x, p1.y, p2.x, p2.y);
-		gc.dispose();
-	}
-	
-	
-	private Rectangle getClip(Point p1, Point p2) {
-		int x1 = Math.min(p1.x, p2.x) - lineWidth;
-		int x2 = Math.max(p1.x, p2.x) + lineWidth;
-		int y1 = Math.min(p1.y, p2.y) - lineWidth;
-		int y2 = Math.max(p1.y, p2.y) + lineWidth;
-		Rectangle r = new Rectangle(x1, y1, x2 - x1, y2 - y1);
-		return 	r.intersection(view.getCanvasImageBounds());
-	}
-
-	
-	private AnnotationType getTypeForUse() {
-		return (invert) ? type.invert() : type;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/controllers/MouseMotionAdapter.java b/image_annotation/src/ie/dcu/apps/ist/controllers/MouseMotionAdapter.java
deleted file mode 100644
index 70a08e4..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/controllers/MouseMotionAdapter.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package ie.dcu.apps.ist.controllers;
-
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.widgets.*;
-
-public class MouseMotionAdapter extends MouseAdapter implements MouseMoveListener {
-
-	public MouseMotionAdapter() {
-	}
-
-
-	public MouseMotionAdapter(Control control) {
-		add(control);
-	}
-
-
-	public void add(Control control) {
-		control.addMouseListener(this);
-		control.addMouseMoveListener(this);
-	}
-
-
-	public void mouseMove(MouseEvent e) {	
-	}
-
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/dialogs/ExportDialog.java b/image_annotation/src/ie/dcu/apps/ist/dialogs/ExportDialog.java
deleted file mode 100644
index 6807637..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/dialogs/ExportDialog.java
+++ /dev/null
@@ -1,368 +0,0 @@
-package ie.dcu.apps.ist.dialogs;
-
-import ie.dcu.apps.ist.export.imagemap.AreaShape;
-import ie.dcu.apps.ist.export.imagemap.RolloverEffect;
-import ie.dcu.swt.SwtUtils;
-import ie.dcu.swt.layout.LayoutFactory;
-
-import java.io.File;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.layout.FillLayout;
-import org.eclipse.swt.layout.GridData;
-import org.eclipse.swt.widgets.Button;
-import org.eclipse.swt.widgets.Combo;
-import org.eclipse.swt.widgets.Composite;
-import org.eclipse.swt.widgets.Dialog;
-import org.eclipse.swt.widgets.DirectoryDialog;
-import org.eclipse.swt.widgets.Display;
-import org.eclipse.swt.widgets.Event;
-import org.eclipse.swt.widgets.Label;
-import org.eclipse.swt.widgets.Listener;
-import org.eclipse.swt.widgets.MessageBox;
-import org.eclipse.swt.widgets.Shell;
-import org.eclipse.swt.widgets.Text;
-
-public class ExportDialog extends Dialog {
-
-	public class Result {
-		public final File folder;
-		public final String html;
-		public final String image;
-		public final String link;
-		public final String description;
-		public final AreaShape shape;
-		public final RolloverEffect effect;
-		public final boolean open;
-		
-		Result() {
-			folder = new File(folderText.getText().trim());
-			html = htmlText.getText().trim();
-			image = imageText.getText().trim();
-			link = linkText.getText().trim();
-			description = descriptionText.getText();
-			shape = getShape();
-			effect = getEffect();
-			open = openButton.getSelection();
-		}
-	};
-	
-	// Result
-	private Result result;
-	
-	// Top level components
-	private Shell shell;
-	private Composite content;
-	private Composite widgets;
-	private Composite buttons;
-	
-	// Widgets
-	private Text folderText;
-	private Button browseButton;
-	private Text htmlText;
-	private Text imageText;
-	private Text linkText;
-	private Button effectCheck;
-	private Combo effectCombo;
-	private Button[] shapeRadios;
-	private Text descriptionText;
-	private Button openButton;
-	
-	// Dialog buttons
-	private Button cancelButton;
-	private Button exportButton;
-	
-	// Effects
-	private final String[] ROLLOVER_EFFECTS = {
-		"Outline Object", "Darken Background", "Highlight Object"
-	};
-	
-	// Shapes
-	private final String[] SHAPES = {
-		"Polygon", "Rectangle", "Circle"
-	};
-	
-	// Default title
-	private static final String TITLE = "Export HTML Image Map";
-
-	public ExportDialog(Shell shell) {
-		super(shell);
-		setText(TITLE);
-	}
-
-	public ExportDialog(Shell shell, int style) {
-		super(shell, style);
-		setText(TITLE);
-	}
-	
-	public Result open() {
-		Shell parent = getParent();
-		shell = new Shell(parent, SWT.DIALOG_TRIM | 
-			SWT.APPLICATION_MODAL | SWT.SHEET);
-		shell.setText(getText());
-		shell.setLayout(new FillLayout());
-		
-		createUI();
-		
-		shell.pack();
-		
-		SwtUtils.center(parent, shell);
-		
-		shell.open();
-		Display display = parent.getDisplay();
-		while (!shell.isDisposed()) {
-			if (!display.readAndDispatch()) display.sleep();
-		}
-
-		return result;
-	}
-
-	private void createUI() {
-		// Overall layout
-		content = new Composite(shell, 0);
-		content.setLayout(LayoutFactory.createGridLayout(0, 0, 1, false));
-		widgets = new Composite(content, 0);
-		widgets.setLayout(LayoutFactory.createGridLayout(10, 5, 3, false));
-		widgets.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, true));
-		hline(content);
-		buttons = new Composite(content, 0);
-		buttons.setLayout(LayoutFactory.createGridLayout(10, 5, 3, false));
-		buttons.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, false));
-		
-		// Form content
-		label(widgets, "Export folder:");
-		folderText = text(widgets, "");
-		browseButton = button(widgets, "Browse...");
-		label(widgets, "HTML file name:");
-		htmlText = text(widgets, "imagemap.html");
-		spacer(widgets);
-		label(widgets, "Image file name:");
-		imageText = text(widgets, "image.png");
-		spacer(widgets);
-		hline(widgets);
-		label(widgets, "Export shape:");
-		shapeRadios = radios(widgets, SHAPES);
-		// TODO: Enable when available
-		shapeRadios[2].setEnabled(false);
-		spacer(widgets);
-		label(widgets, "Object link:");
-		linkText = text(widgets, "http://");
-		spacer(widgets);
-		label(widgets, "Object description:");
-		descriptionText = text(widgets, "");
-		spacer(widgets);
-		effectCheck = checkbox(widgets, "Rollover effect:", true, 1);
-		effectCombo = combo(widgets, ROLLOVER_EFFECTS);
-		spacer(widgets);
-		hline(widgets);
-		openButton = checkbox(widgets, 
-				"Open image map in browser after export completes", true, 3);
-		
-		// Button bar
-		expander(buttons);
-		cancelButton = new Button(buttons, SWT.PUSH);
-		cancelButton.setLayoutData(layout4());
-		cancelButton.setText("Cancel");
-		exportButton = new Button(buttons, SWT.PUSH);
-		exportButton.setLayoutData(layout4());
-		exportButton.setText("Export");
-		
-		// Set the default button
-		shell.setDefaultButton(exportButton);
-		
-		// Add listeners
-		addListeners();
-	}
-	
-	private void addListeners() {
-		
-		browseButton.addListener(SWT.Selection, new Listener() {
-			public void handleEvent(Event e) {
-				String dir = getDirectory();
-				if (dir != null) {
-					folderText.setText(dir);
-				}
-			}
-		});
-		
-		cancelButton.addListener(SWT.Selection, new Listener() {
-			public void handleEvent(Event e) {
-				result = null;
-				shell.dispose();
-			}
-		});
-		
-		exportButton.addListener(SWT.Selection, new Listener() {
-			public void handleEvent(Event e) {
-				if (validate()) {
-					result = new Result();
-					shell.dispose();
-				}
-			}
-		});
-		
-		effectCheck.addListener(SWT.Selection, new Listener() {
-			public void handleEvent(Event e) {
-				effectCombo.setEnabled(effectCheck.getSelection());
-			}
-		});
-	}
-	
-	private boolean validate() {
-		
-		File folder = new File(folderText.getText());
-		if (!folder.isDirectory()) {
-			validationError("The export folder must be specified");
-			folderText.setFocus();
-			return false;
-		}
-		
-		String htmlFile = htmlText.getText().trim();
-		if (htmlFile.equals("")) {
-			validationError("The HTML file name cannot be empty");
-			htmlText.setFocus();
-			return false;
-		}
-		
-		String imageFile = imageText.getText().trim();
-		if (imageFile.equals("")) {
-			validationError("The image file name cannot be empty");
-			imageText.setFocus();
-			return false;
-		}
-		
-		return true;
-	}
-	
-	private void validationError(String message) {
-		MessageBox box = new MessageBox(shell, SWT.OK | SWT.ICON_INFORMATION);
-		box.setMessage(message);
-		box.setText("Invalid Input");
-		box.open();
-	}
-
-	private AreaShape getShape() {
-		for (Button bt : shapeRadios) {
-			if (bt.getSelection()) {
-				return AreaShape.valueOf(bt.getText());
-			}
-		}
-		return null;
-	}
-	
-	private RolloverEffect getEffect() {
-		RolloverEffect effect = null;
-		if (effectCheck.getSelection()) {
-			String text = effectCombo.getText();
-			if (text.equals("Outline Object")) {
-				effect = RolloverEffect.outlineObject();
-			} else if (text.equals("Darken Background")) {
-				effect = RolloverEffect.darkenBackground();
-			} else if (text.equals("Highlight Object")) {
-				effect = RolloverEffect.brightenForeground();
-			}
-		} 
-		return effect;
-	}
-	
-	private String getDirectory() {
-		DirectoryDialog dialog = new DirectoryDialog(shell);
-		return dialog.open();
-	}
-
-	private Button[] radios(Composite parent, String ... items) {
-		Composite c = new Composite(parent, SWT.NONE);
-		c.setLayout(LayoutFactory.createGridLayout(5, 10, items.length, false));
-		c.setLayoutData(layout2());
-		
-		Button[] bts = new Button[items.length];
-		for (int i = 0; i < bts.length; i++) {
-			bts[i] = new Button(c, SWT.RADIO);
-			bts[i].setLayoutData(new GridData(SWT.LEFT, SWT.CENTER, false, false));
-			bts[i].setText(items[i]);
-			bts[i].setSelection(i == 0);
-		}
-		
-		return bts;
-	}
-	
-	private Label hline(Composite parent) {
-		Label label = new Label(parent, SWT.SEPARATOR | SWT.HORIZONTAL);
-		GridData data = new GridData(SWT.FILL, SWT.CENTER, false, false);
-		data.horizontalSpan = 3;
-		data.heightHint = 10;
-		label.setLayoutData(data);
-		return label;
-	}
-	
-	private Label spacer(Composite parent) {
-		Label label = new Label(parent, SWT.NONE);
-		label.setLayoutData(new GridData(SWT.FILL, SWT.FILL, false, false));
-		return label;
-	}
-	
-	private Label expander(Composite parent) {
-		Label label = new Label(parent, SWT.NONE);
-		label.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, false));
-		return label;
-	}
-	
-	private Combo combo(Composite parent, String ... items) {
-		Combo combo = new Combo(parent, SWT.READ_ONLY);
-		combo.setItems(items);
-		combo.setLayoutData(layout2());
-		if (items.length > 0) {
-			combo.select(0);
-		}
-		return combo;
-	}
-	
-	private Button checkbox(Composite parent, String text, 
-			boolean checked, int span) {
-		
-		Button bt = new Button(parent, SWT.CHECK);
-		bt.setText(text);
-		bt.setSelection(checked);
-		GridData data = layout1();
-		data.horizontalSpan = span;
-		bt.setLayoutData(data);
-		return bt;
-	}
-	
-	private Label label(Composite parent, String text) {
-		Label label = new Label(parent, SWT.NONE);
-		label.setText(text);
-		label.setLayoutData(layout1());
-		return label;
-	}
-	
-	private Text text(Composite parent, String value) {
-		Text text = new Text(parent, SWT.BORDER | SWT.SINGLE);
-		text.setText(value);
-		text.setLayoutData(layout2());
-		return text;
-	}
-	
-	private Button button(Composite parent, String text) {
-		Button bt = new Button(parent, SWT.PUSH);
-		bt.setText(text);
-		bt.setLayoutData(layout3());
-		return bt;
-	}
-	
-	private GridData layout1() {
-		return new GridData(SWT.LEFT, SWT.CENTER, false, false);
-	}
-	
-	private GridData layout2() {
-		return new GridData(SWT.FILL, SWT.CENTER, true, false);
-	}
-	
-	private GridData layout3() {
-		return new GridData(SWT.RIGHT, SWT.CENTER, false, false);
-	}
-	
-	private GridData layout4() {
-		return new GridData(SWT.RIGHT, SWT.BOTTOM, false, false);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/dialogs/PrefsDialog.java b/image_annotation/src/ie/dcu/apps/ist/dialogs/PrefsDialog.java
deleted file mode 100644
index 9ea4eeb..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/dialogs/PrefsDialog.java
+++ /dev/null
@@ -1,435 +0,0 @@
-package ie.dcu.apps.ist.dialogs;
-
-import static ie.dcu.segment.annotate.AnnotationType.*;
-import ie.dcu.apps.ist.*;
-import ie.dcu.apps.ist.AppPrefs.Keys;
-import ie.dcu.apps.ist.widgets.ColorSelector;
-import ie.dcu.swt.SwtUtils;
-import ie.dcu.swt.layout.LayoutFactory;
-
-import java.util.*;
-
-import org.eclipse.jface.resource.JFaceResources;
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.layout.*;
-import org.eclipse.swt.widgets.*;
-
-public class PrefsDialog {
-	private static final String APPLICATION = "application";
-	private static final String STATUS      = "status";
-	private static final String VIEW        = "view";
-	private static final String TITLE       = "title";
-	private static final String GENERAL     = "general";
-	private static final String CLOSE       = "close";
-	private static final String RESET       = "reset";
-	private static final String TEXT        = "text";
-	private static final String ICON        = "icon";
-	private static final String TTIP        = "ttip";
-	private static final String EXPERIMENT  = "experiment";
-	
-	private final AppWindow window;
-	private final AppPrefs prefs;
-	private final Shell shell;
-	private final Composite content;
-	private final TabFolder folder;
-	private final Composite buttonBar;
-	private final Composite generalTab;
-	private final Button resetButton;
-	private final Button closeButton;
-	private final HashMap<String, Object> controls;
-	
-	private transient GridData gd;
-	
-
-	public PrefsDialog(AppWindow window) {
-		this.window = window;
-		this.prefs = window.getPrefs();
-		this.shell = createShell();
-		this.content = createContent();
-		this.folder = createTabFolder();
-		this.buttonBar = createButtonBar();
-		this.generalTab = createTab(GENERAL);
-		this.resetButton = createResetButton();
-		this.closeButton = createCloseButton();
-		this.controls = new HashMap<String, Object>();
-		
-		createControls();
-		loadPreferences();
-		
-		SwtUtils.center(window.getShell(), shell);
-	}
-	
-
-	private void createControls() {
-		// Initialize general tab
-		createBanner(generalTab, APPLICATION);
-		
-		createLabel(generalTab, Keys.CONFIRM_EXIT);
-		createCheckBox(generalTab, Keys.CONFIRM_EXIT);
-		
-		createBanner(generalTab, STATUS);
-		
-		createLabel(generalTab, Keys.ENABLE_FEEDBACK);
-		createCheckBox(generalTab, Keys.ENABLE_FEEDBACK);
-		
-		createBanner(generalTab, VIEW);
-		
-		createLabel(generalTab, Keys.FOREGROUND_COLOR);
-		createColorSelector(generalTab, Keys.FOREGROUND_COLOR);
-		
-		createLabel(generalTab, Keys.BACKGROUND_COLOR);
-		createColorSelector(generalTab, Keys.BACKGROUND_COLOR);
-		
-		createBanner(generalTab, EXPERIMENT);
-		
-		createLabel(generalTab, Keys.EXPERIMENT_EMBEDDED);
-		createCheckBox(generalTab, Keys.EXPERIMENT_EMBEDDED);
-	}
-
-	
-	private void loadPreferences() {
-		
-		// Load confirm exit
-		loadBool(Keys.CONFIRM_EXIT, true);
-		
-		// Load enable feedback 
-		loadBool(Keys.ENABLE_FEEDBACK, true);
-		
-		// Load foreground color 
-		loadColor(Keys.FOREGROUND_COLOR, DEFAULT_FOREGROUND);
-		
-		// Load background color 
-		loadColor(Keys.BACKGROUND_COLOR, DEFAULT_BACKGROUND);
-		
-		// Load experiment embedded
-		loadBool(Keys.EXPERIMENT_EMBEDDED, false);
-	}
-	
-
-	private Shell createShell() {
-		Shell s = new Shell(window.getShell(), SWT.SHELL_TRIM | SWT.SHEET);
-		
-		// Add listener
-		s.addListener(SWT.Close, adapter);
-		
-		// Use a fill layout
-		s.setLayout(new FillLayout());
-		
-		// Set size and title
-		s.setSize(420, 450);
-		s.setText(property(TITLE, "Preferences"));
-		
-		return s;
-	}
-	
-	
-	private Composite createContent() {
-		
-		// Create content pane with grid layout
-		Composite c = new Composite(shell, 0);
-		c.setLayout(new GridLayout());
-		return c;
-	}
-	
-	
-	private TabFolder createTabFolder() {
-		// Create folder
-		TabFolder f = new TabFolder(content, SWT.TOP);
-		
-		// Layout folder
-		f.setLayoutData(LayoutFactory.createGridData());
-		
-		return f;
-	}
-	
-	
-	private Composite createButtonBar() {
-		// Create bar
-		Composite bar = new Composite(content, SWT.NONE);
-		
-		// Layout bar
-		bar.setLayout(LayoutFactory.createGridLayout(0, 0, 2, true));
-		bar.setLayoutData(new GridData(SWT.FILL, SWT.BOTTOM, true, false));
-		
-		return bar;
-	}
-	
-	
-	private Composite createTab(String name) {
-		// Create item
-		TabItem item = new TabItem(folder, SWT.NONE);
-		item.setText(property(name, "tab", name));
-		
-		// Create control
-		Composite control = new Composite(folder, SWT.NONE);
-		control.setLayout(LayoutFactory.createGridLayout(10, 5, 2, false));
-		
-		// Set control
-		item.setControl(control);
-		
-		// Return control (item can be ignored)
-		return control;
-	}
-	
-	
-	private Button createResetButton() {
-		// Create button
-		Button bt = createButton(buttonBar, RESET, SWT.PUSH);
-		
-		// Layout button
-		gd = new GridData(SWT.LEFT, SWT.BOTTOM, true, false);
-		gd.minimumWidth = 85;
-		bt.setLayoutData(gd);
-		
-		// Done
-		return bt;
-	}
-	
-	
-	private Button createCloseButton() {
-		// Create button
-		Button bt = createButton(buttonBar, CLOSE, SWT.PUSH);
-		
-		// Layout button
-		gd = new GridData(SWT.RIGHT, SWT.BOTTOM, true, false);
-		gd.minimumWidth = 85;
-		bt.setLayoutData(gd);
-		
-		// Done
-		return bt;
-	}
-	
-	
-	private Button createCheckBox(Composite tab, String key) {
-		Button bt = new Button(tab, SWT.CHECK);
-		
-		// Layout button
-		gd = new GridData(SWT.RIGHT, SWT.CENTER, false, false);
-		gd.horizontalIndent = 5;
-		bt.setLayoutData(gd);
-		
-		// Add listener
-		bt.addListener(SWT.Selection, adapter);
-		bt.setData(key);
-		
-		// Put into controls
-		controls.put(key, bt);
-		
-		// Done
-		return bt;
-	}
-	
-	
-	private ColorSelector createColorSelector(Composite tab, String key) {
-		ColorSelector cs = new ColorSelector(tab);
-		
-		// Layout button
-		gd = new GridData(SWT.RIGHT, SWT.CENTER, false, false);
-		gd.horizontalIndent = 10;
-		gd.minimumWidth = 80;
-		cs.setLayoutData(gd);
-		
-		// Add listener
-		cs.addListener(SWT.Selection, adapter);
-		cs.setData(key);
-		
-		// Put into controls
-		controls.put(key, cs);
-		
-		// Done
-		return cs;
-	}
-
-
-	private Label createBanner(Composite tab, String key) {
-		// Create label
-		Label lb = new Label(tab, SWT.NONE);
-		lb.setText(property(key, key));
-		lb.setFont(JFaceResources.getBannerFont());
-		
-		// Layout label
-		gd = new GridData(SWT.LEFT, SWT.CENTER, true, false, 2, 1);
-		gd.verticalIndent = 5;
-		lb.setLayoutData(gd);
-		
-		return lb;
-	}
-	
-	
-	private Label createLabel(Composite tab, String key) {
-		// Create label
-		Label lb = new Label(tab, SWT.NONE);
-		lb.setText(property(key, TEXT, key));
-		
-		// Layout label
-		gd = new GridData(SWT.LEFT, SWT.CENTER, true, false);
-		gd.horizontalIndent = 5;
-		lb.setLayoutData(gd);
-		
-		return lb;
-	}
-	
-	
-	private Button createButton(Composite parent, String key, int style) {
-		Button bt = new Button(parent, style);
-		
-		// Configure button
-		configure(bt, key);
-		
-		// Add listener
-		bt.addListener(SWT.Selection, adapter);
-		
-		// Done
-		return bt;
-	}	
-	
-	
-	protected void handleEvent(Event event) {
-		switch (event.type) {
-		case SWT.Close:
-			handleClose(event);
-			break;
-		case SWT.Selection:
-			handleSelection(event);
-			break;
-		}
-		
-	}
-	
-
-	private void handleClose(Event event) {
-		// Prevent the shell from disposing on close
-		event.doit = false;
-		close();
-	}
-	
-
-	private void handleSelection(Event event) {
-		if (event.widget == closeButton) {
-			close();
-		} else if (event.widget == resetButton) {
-			reset();
-		} else {
-			Object data = event.widget.getData();
-			if (data instanceof String) {
-				handleSelection(event, (String) data);
-			}
-		}
-		
-	}
-
-
-	private void handleSelection(Event event, String key) {
-		
-		if (key.equals(Keys.ENABLE_FEEDBACK)) {
-			storeBool(key);
-		
-		} else if (key.equals(Keys.FOREGROUND_COLOR)) {
-
-			storeColor(key);
-			
-		} else if (key.equals(Keys.BACKGROUND_COLOR)) {
-			
-			storeColor(key);
-		
-		} else if (key.equals(Keys.EXPERIMENT_EMBEDDED)) {
-		
-			storeBool(key);
-		
-		} else if (key.equals(Keys.CONFIRM_EXIT)) {
-			
-			storeBool(key);
-		}
-		
-	}
-	
-	
-	private void storeBool(String key) {
-		Boolean bool = control(Button.class, key).getSelection();
-		prefs.put(Boolean.class, key, bool);
-	}
-	
-
-	private void storeColor(String key) {
-		RGB color = control(ColorSelector.class, key).getColor();
-		if (color != null) {
-			prefs.put(RGB.class, key, color);
-		}
-	}
-	
-	
-	private void loadBool(String key, boolean def) {
-		Boolean bool = prefs.get(Boolean.class, key, def);
-		control(Button.class, key).setSelection(bool);
-	}
-	
-	
-	private void loadColor(String key, RGB def) {
-		RGB color = prefs.get(RGB.class, key, def);
-		control(ColorSelector.class, key).setColor(color);
-	}
-	
-
-	public void reset() {
-		// Set defaults
-		prefs.clear();
-		
-		// Reload
-		loadPreferences();
-	}
-
-
-	public void close() {
-		shell.setVisible(false);
-	}
-	
-	
-	public void open() {
-		shell.setVisible(true);
-	}
-	
-	
-	private void configure(Button bt, String key) {
-		// Read properties
-		String text = property(key, TEXT, "");
-		String icon = property(key, ICON, null);
-		String ttip = property(key, TTIP, null);
-		
-		// Set values
-		bt.setText(text);
-		bt.setImage(image(icon));
-		bt.setToolTipText(ttip);
-		bt.setData(key);
-	}
-	
-	
-	private <T> T control(Class<T> clazz, String key) {
-		return clazz.cast(controls.get(key));
-	}
-	
-	
-	private String property(String key, String def) {
-		Properties p = window.getProperties();
-		return p.getProperty(String.format("PrefsDialog.%s", key), def);
-	}
-	
-	
-	private String property(String key, String type, String def) {
-		Properties p = window.getProperties();
-		String prop = String.format("PrefsDialog.%s.%s", key, type);
-		return p.getProperty(prop, def);
-	}
-	
-	
-	private Image image(String url) {
-		return (url != null) ? window.getIcon(url) :  null;
-	}
-	
-	
-	private final Listener adapter = new Listener() {
-		public void handleEvent(Event event) {
-			PrefsDialog.this.handleEvent(event);
-		}		
-	};
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/event/ContextChangeListener.java b/image_annotation/src/ie/dcu/apps/ist/event/ContextChangeListener.java
deleted file mode 100644
index 8c617a0..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/event/ContextChangeListener.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package ie.dcu.apps.ist.event;
-
-import java.util.*;
-
-public interface ContextChangeListener extends EventListener {
-	public void contextChanged(ContextChangedEvent evt);
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/event/ContextChangedEvent.java b/image_annotation/src/ie/dcu/apps/ist/event/ContextChangedEvent.java
deleted file mode 100644
index 638dad9..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/event/ContextChangedEvent.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package ie.dcu.apps.ist.event;
-
-
-import ie.dcu.segment.SegmentationContext;
-
-import java.util.*;
-
-
-public class ContextChangedEvent extends EventObject {
-	private static final long serialVersionUID = 1L;
-	
-	public final SegmentationContext oldContext;
-	public final SegmentationContext newContext;
-
-	public ContextChangedEvent(
-			Object source, 
-			SegmentationContext oldContext,
-			SegmentationContext newContext
-	) {
-		super(source);
-		this.oldContext = oldContext;
-		this.newContext = newContext;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/event/StateEvent.java b/image_annotation/src/ie/dcu/apps/ist/event/StateEvent.java
deleted file mode 100644
index 38c5bbc..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/event/StateEvent.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package ie.dcu.apps.ist.event;
-
-import java.util.*;
-
-public class StateEvent extends EventObject {
-	private static final long serialVersionUID = 1L;
-
-	public StateEvent(Object source) {
-		super(source);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/event/StateListener.java b/image_annotation/src/ie/dcu/apps/ist/event/StateListener.java
deleted file mode 100644
index 525f253..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/event/StateListener.java
+++ /dev/null
@@ -1,13 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.event;
-
-import java.util.*;
-
-/**
- * @author Kevin McGuinness
- */
-public interface StateListener extends EventListener {
-	public void stateChanged(StateEvent evt);
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/event/TickerEvent.java b/image_annotation/src/ie/dcu/apps/ist/event/TickerEvent.java
deleted file mode 100644
index ae6124f..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/event/TickerEvent.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package ie.dcu.apps.ist.event;
-
-
-import ie.dcu.apps.ist.widgets.Ticker;
-
-import java.util.EventObject;
-
-public class TickerEvent extends EventObject {
-	private static final long serialVersionUID = 755693053854019177L;
-
-	private final long elapsed;
-
-	public TickerEvent(Ticker t, long elapsed) {
-		super(t);
-		this.elapsed = elapsed;
-	}
-	
-	public Ticker getTicker() {
-		return (Ticker) getSource();
-	}
-	
-	public long getElapsed() {
-		return elapsed;
-	}
-};
diff --git a/image_annotation/src/ie/dcu/apps/ist/event/TickerListener.java b/image_annotation/src/ie/dcu/apps/ist/event/TickerListener.java
deleted file mode 100644
index 26b6269..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/event/TickerListener.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package ie.dcu.apps.ist.event;
-
-import java.util.*;
-
-public interface TickerListener extends EventListener {
-	public void tick(TickerEvent evt);
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/event/TimeoutEvent.java b/image_annotation/src/ie/dcu/apps/ist/event/TimeoutEvent.java
deleted file mode 100644
index 70659c3..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/event/TimeoutEvent.java
+++ /dev/null
@@ -1,24 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.event;
-
-
-import ie.dcu.apps.ist.widgets.SwtTimer;
-
-import java.util.EventObject;
-
-/**
- * @author Kevin McGuinness
- */
-public class TimeoutEvent extends EventObject {
-	private static final long serialVersionUID = 1L;
-
-	public TimeoutEvent(SwtTimer source) {
-		super(source);
-	}
-	
-	public SwtTimer getTimer() {
-		return (SwtTimer) getSource();
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/event/TimeoutListener.java b/image_annotation/src/ie/dcu/apps/ist/event/TimeoutListener.java
deleted file mode 100644
index c682041..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/event/TimeoutListener.java
+++ /dev/null
@@ -1,13 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.event;
-
-import java.util.*;
-
-/**
- * @author Kevin McGuinness
- */
-public interface TimeoutListener extends EventListener {
-	public void timeoutOccured(TimeoutEvent evt);
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/exp/Experiment.java b/image_annotation/src/ie/dcu/apps/ist/exp/Experiment.java
deleted file mode 100644
index ef52005..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/exp/Experiment.java
+++ /dev/null
@@ -1,348 +0,0 @@
-package ie.dcu.apps.ist.exp;
-
-import ie.dcu.eval.Evaluator;
-import ie.dcu.apps.ist.*;
-import ie.dcu.segment.Segmenter;
-
-import java.io.*;
-import java.util.*;
-
-public class Experiment {
-	public static final int MAX_TASKS = 2500;
-	public static final int MAX_SEGMENTERS = 50;
-	public static final int MAX_EVALUATORS = 100;
-	
-	private String name;
-	private File dir;
-	private File outputFile;
-	private int time;
-	private List<Segmenter> segmenters;
-	private List<Evaluator> evaluators;
-	private List<Task> tasks;
-	private StorageSelection saveUserMasks;
-	private File saveUserMasksDir;
-	
-	Experiment() {
-		
-	}
-	
-	
-	public String getName() {
-		return name;
-	}
-	
-	
-	public File getDirectory() {
-		return dir;
-	}
-	
-	
-	public File getOutputFile() {
-		return outputFile;
-	}
-	
-	
-	public int getTime() {
-		return time;
-	}
-	
-	
-	public StorageSelection getStorageSelection() {
-		return saveUserMasks;
-	}
-	
-	
-	public File getStorageDirectory() {
-		return saveUserMasksDir;
-	}
-	
-	
-	public List<Segmenter> getSegmenters() {
-		return Collections.unmodifiableList(segmenters);
-	}
-	
-	
-	public List<Evaluator> getEvaluators() {
-		return Collections.unmodifiableList(evaluators);
-	}
-	
-	
-	public List<Task> getTasks() {
-		return Collections.unmodifiableList(tasks);
-	}
-	
-	
-	public boolean using(Segmenter segmenter) {
-		for (Segmenter s : segmenters) {
-			if (s.equals(segmenter)) {
-				return true;
-			}
-		}
-		return false;
-	}
-	
-	
-	public void load(File file) throws IOException, FormatException {
-		InputStream in = null;
-		try {
-			in = new FileInputStream(file);
-			load(in);
-		} finally {
-			if (in != null) {
-				in.close();
-			}
-		}
-	}
-	
-	
-	public void load(InputStream in) throws IOException, FormatException {
-		
-		// Create properties object
-		Properties props = new Properties();
-		props.load(in);
-		
-		// Load name
-		name = props.getProperty("name", "Experiment");
-		
-		// Load directory
-		dir = getDir(props, "dir");
-		
-		// Load output file
-		outputFile = getOutputFile(props);
-		
-		// Load task time
-		time = getTimeout(props, "time");
-		
-		// Get save user masks selection
-		saveUserMasks = getStorageSelection(props, "save-user-masks");
-		
-		// .. and directory
-		saveUserMasksDir = getUserMaskDir(props, "save-user-masks.dir");
-		
-		// Load segmenters
-		segmenters = new ArrayList<Segmenter>();
-		for (int i = 1; i <= MAX_SEGMENTERS; i++) {
-			String key = "segmenters." + i;
-			String val = props.getProperty(key);
-			
-			if (val == null) {
-				break;
-			}
-			
-			Segmenter segmenter = findSegmenter(val);
-			if (segmenter != null) {
-				segmenters.add(segmenter);
-			} else {
-				exception("Segmenter not found: <%s>", val);
-			}
-		}
-		
-		// Load evaluators
-		evaluators = new ArrayList<Evaluator>();
-		for (int i = 1; i <= MAX_EVALUATORS; i++) {
-			String key = "evaluators." + i;
-			String val = props.getProperty(key);
-			
-			if (val == null) {
-				break;
-			}
-			
-			Evaluator evaluator = findEvaluator(val);
-			if (evaluator != null) {
-				evaluators.add(evaluator);
-			} else {
-				exception("Evaluator not found: <%s>", val);
-			}
-		}
-		
-		// Load tasks
-		tasks = new ArrayList<Task>();
-		for (int i = 1; i <= MAX_TASKS; i++) {
-			
-			// Form keys
-			String imkey   = String.format("task.%d.im", i);
-			String gtkey   = String.format("task.%d.gt", i);
-			String desckey = String.format("task.%d.description", i);
-			
-			// Check if we're done
-			if (props.getProperty(imkey) == null) {
-				break;
-			}
-			
-			// Get image and ground truth file
-			File im = getFile(props, imkey);
-			File gt = getFile(props, gtkey);
-			
-			// Get description
-			String desc = getDescription(props, desckey);
-			
-			// Add task
-			tasks.add(new Task(im, gt, desc));
-		}
-	}
-	
-	
-	private static StorageSelection getStorageSelection(
-		Properties props, String key
-	) {
-		String prop = props.getProperty(key);
-		if (prop != null) {
-			StorageSelection selection = StorageSelection.parse(prop);
-			if (selection != null) {
-				return selection;
-			}
- 		}
-		return StorageSelection.None;
-	}
-	
-	
-	private File getUserMaskDir(Properties props, String key) 
-		throws FormatException {
-		
-		String fname = props.getProperty(key);
-		if (fname == null) {
-			fname = "user";
-		}
-		
-		File file = new File(fname);
-		if (!file.isAbsolute()) {
-			file = new File(dir, fname);
-		}
-		
-		
-		if (!file.exists()) {
-			// Try and create it
-			if (!file.mkdirs()) {
-				String path = file.getAbsolutePath();
-				exception("Couldn't create directory %s", path);
-			} 
-		
-		}	else if (!file.isDirectory()) {
-			String path = file.getAbsolutePath();
-			exception("%s is not a directory", path);
-		}
-		
-		return file;
-	}
-
-
-	private static Segmenter findSegmenter(String name) {
-		return SegmenterRegistry.getInstance().find(name);
-	}
-	
-	
-	private static Evaluator findEvaluator(String name) {
-		return EvaluatorRegistry.getInstance().find(name);
-	}
-	
-	
-	private File getOutputFile(Properties props) {
-		String fname = props.getProperty("output", "output.txt");
-		File file = new File(fname);
-		if (file.isAbsolute()) {
-			return file;
-		}
-		return new File(dir, fname);
-	}
-	
-	
-	
-	private static String getDescription(Properties props, String key) 
-		throws FormatException {
-		
-		String desc = props.getProperty(key);
-		if (desc == null) {
-			exception("Expected description property for %s", key);
-		}
-		return desc;
-	}
-	
-	
-	private File getFile(Properties props, String key) 
-		throws FormatException {
-		
-		String fname = props.getProperty(key);
-		
-		if (fname == null) {
-			exception("Expected file property for %s", key);
-		}
-		
-		File file = new File(fname);
-		if (file.isAbsolute()) {
-			if (file.isFile()) {
-				return file;
-			}
-		}
-		
-		file = new File(dir, fname);
-		if (!file.isFile()) {
-			exception("File not found %s", file.getAbsolutePath());
-		}
-		
-		return file;
-	}
-	
-	
-	private static File getDir(Properties props, String key) 
-		throws FormatException {
-		
-		String prop = props.getProperty(key);
-		if (prop == null) {
-			exception("Required directory element not found: %a",key);
-		}
-		
-		File file = new File(prop);
-		if (!file.isDirectory()) {
-			exception("%s is not a directory", prop);
-		}
-		
-		return file;
-	}
-	
-	
-	private static int getTimeout(Properties props, String key) 
-		throws FormatException {
-		
-		String prop = props.getProperty(key, "120");
-		try {
-			return Integer.parseInt(prop);
-		} catch (NumberFormatException ex) {
-			exception("%s is not an integer", key);
-		}
-		
-		return 0;
-	}
-	
-	
-	private static void exception(String format, Object ... args) 
-		throws FormatException 
-	{
-		throw new FormatException(String.format(format, args));
-	}
-	
-	
-	public String toString() {
-		StringBuilder sb = new StringBuilder();
-		
-		sb.append("name=<").append(name).append('>');
-		sb.append(" dir=<").append(dir.getAbsolutePath()).append('>');
-		sb.append(" output=<").append(outputFile.getAbsolutePath()).append('>');
-		sb.append(" time=<").append(time).append('>');
-		
-		// Evaluators
-		sb.append(" evaluators={ ");
-		for (Evaluator e : evaluators) {
-			sb.append(e.getName()).append(' ');
-		}
-		sb.append('}');
-		
-		// Tasks
-		sb.append(" tasks={ ");
-		for (Task t : tasks) {
-			sb.append(t).append(' ');
-		}
-		sb.append('}');
-		
-		return sb.toString();
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentFactory.java b/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentFactory.java
deleted file mode 100644
index 802d14a..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentFactory.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.exp;
-
-import java.io.*;
-
-/**
- * @author Kevin McGuinness
- */
-public class ExperimentFactory {
-	private static ExperimentFactory instance;
-	
-	protected ExperimentFactory() {
-		
-	}
-	
-	public static ExperimentFactory getInstance() {
-		if (instance == null) {
-			instance = new ExperimentFactory();
-		}
-		return instance;
-	}
-	
-	
-	public Experiment load(File file) 
-		throws IOException, FormatException {
-		
-		Experiment ex = new Experiment();
-		ex.load(file);
-		return ex;
-	}
-	
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentManager.java b/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentManager.java
deleted file mode 100644
index b03a6f7..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentManager.java
+++ /dev/null
@@ -1,217 +0,0 @@
-package ie.dcu.apps.ist.exp;
-
-import ie.dcu.eval.Evaluator;
-import ie.dcu.segment.SegmentationMask;
-import ie.dcu.segment.SegmentationContext;
-import ie.dcu.apps.ist.AppWindow;
-import ie.dcu.apps.ist.actions.*;
-
-import java.io.*;
-import java.util.List;
-
-public class ExperimentManager {
-	
-	private final AppWindow window;
-	
-	private Experiment experiment;
-	private SegmentationContext activeContext;
-	private SegmentationMask referenceMask;
-	private ExperimentResults results;
-	private List<Task> tasks;
-	private Task activeTask;
-	private int progress;
-	private boolean aborted;
-	
-	
-	public ExperimentManager(AppWindow window) {	
-		this.window = window;
-	}
-	
-	
-	public void beginExperiment(Experiment ex) throws IOException {
-		experiment = ex;
-		tasks = experiment.getTasks();
-		activeContext = null;
-		activeTask = null;
-		progress = 0;
-		results = new ExperimentResults(experiment.getOutputFile());
-		results.beginDocument();
-		results.beginExperiment(experiment);
-	}
-	
-	
-	public void endExperiment() throws IOException {
-		results.endExperiment();
-		results.flush();
-		results.close();
-	}
-	
-	
-	public void abortExperiment() {
-		results.endExperiment();
-		results.close();
-		aborted = true;
-	}
-	
-	
-	public void beginTask() throws IOException {
-		if (isComplete()) {
-			throw new IllegalStateException();
-		}
-		
-		// Set active task
-		activeTask = tasks.get(progress);
-		
-		// Load context into main window
-		loadContext();
-
-		// Load reference mask
-		loadReferenceMask();
-		
-		// Write task header to results
-		results.beginTask(progress, activeTask);
-	}
-	
-	
-	public void endTask() throws IOException {
-		
-		try {
-			// Save final mask
-			StorageSelection ss = experiment.getStorageSelection();
-			if (ss != StorageSelection.None) {
-				store(String.format("task-%d-final.png", progress));
-			}
-			
-		} finally {
-			
-			activeTask = null;
-			activeContext = null;
-			progress++;
-			results.endTask();
-			results.flush();
-		}
-	}
-	
-	
-	public boolean isComplete() {
-		return tasks.size() == progress || aborted;
-	}
-	
-	
-	public Experiment getExperiment() {
-		return experiment;
-	}
-	
-	
-	public String getTaskDescription() {
-		return activeTask.getDescription();
-	}
-	
-	
-	public Task getActiveTask() {
-		return activeTask;
-	}
-	
-	
-	public int getTaskCount() {
-		return tasks.size();
-	}
-	
-	
-	public int getProgress() {
-		return progress;
-	}
-	
-	
-	public SegmentationContext getActiveContext() {
-		return activeContext;
-	}
-	
-	
-	public List<Evaluator> getEvaluators() {
-		return experiment.getEvaluators();
-	}
-	
-	
-	public File getImageFile() {
-		return activeTask.getImageFile();
-	}
-	
-	
-	public SegmentationMask getCurrentMask() {
-		return activeContext.getMask();
-	}
-	
-	
-	public SegmentationMask getReferenceMask() {
-		return referenceMask;
-	}
-	
-	
-	public void evaluate(int elapsed) {
-		
-		if (!getCurrentMask().isUnknown()) {
-			SegmentationMask im = getCurrentMask();
-			SegmentationMask gt = getReferenceMask();
-			
-			results.beginEvaluation(elapsed);
-			
-			for (Evaluator evaluator : experiment.getEvaluators()) {
-				// Execute evaluator
-				evaluator.run(im, gt);
-				
-				// Add results
-				addResults(evaluator);
-			}
-			
-			results.endEvaluation();
-		}
-	}
-	
-	
-	public void store(int elapsed) throws IOException {
-		// Save current mask
-		if (!getCurrentMask().isUnknown()) {
-			// Only save non empty masks
-			StorageSelection ss = experiment.getStorageSelection();
-			if (ss == StorageSelection.All) {
-				store(String.format("task-%d-time-%d.png", progress, elapsed));
-			}
-		}
-	}
-	
-	
-	private void store(String name) throws IOException {
-		SegmentationMask im = getCurrentMask();
-		File dir = experiment.getStorageDirectory();
-		File file = new File(dir, name);
-		im.save(file);
-	}
-
-
-	private void addResults(Evaluator evaluator) {
-		String[] measures = evaluator.getMeasures();
-		for (String measure : measures) {
-			double value = evaluator.getMeasure(measure);
-			results.addMeasure(measure, value);
-		}
-	}
-
-
-	private void loadReferenceMask() throws IOException {
-		referenceMask = new SegmentationMask(activeContext.getBounds());
-		referenceMask.load(activeTask.getMaskFile());
-	}
-
-
-	private void loadContext() throws IOException {
-		ActionManager actions = window.getActions();
-		OpenAction action = actions.get(OpenAction.class);
-	
-		if (!action.open(getImageFile())) {
-			throw new IOException("Unable to load image file");
-		}
-		
-		activeContext = window.getContext();
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentResults.java b/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentResults.java
deleted file mode 100644
index 2f54026..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/exp/ExperimentResults.java
+++ /dev/null
@@ -1,109 +0,0 @@
-package ie.dcu.apps.ist.exp;
-
-import java.io.*;
-
-public class ExperimentResults {
-	private static final String XML_HEADER =
-		"<?xml version=\"1.0\" encoding=\"UTF-8\"?>%n%n";
-	
-	private static final String BEGIN_EXPERIMENT_TAG = 
-		"<experiment name=\"%s\" time=\"%d\" dir=\"%s\">%n";
-	
-	private static final String BEGIN_TASK_TAG = 
-		"  <task id=\"%d\" image=\"%s\" gt=\"%s\">%n";
-	
-	private static final String BEGIN_EVALUATION_TAG = 
-		"    <evaluation time=\"%d\">%n";
-	
-	private static final String MEASURE_TAG = 
-		"      <measure name=\"%s\" value=\"%.5f\" />%n";
-	
-	private static final String END_EVALUATION_TAG = 
-		"    </evaluation>%n";
-	
-	private static final String END_TASK_TAG = 
-		"  </task>%n";
-	
-	private static final String END_EXPERIMENT_TAG = 
-		"</experiment>%n";
-	
-	
-	private final PrintStream out;
-	
-	
-	
-	ExperimentResults(File file) throws FileNotFoundException {
-		this(new FileOutputStream(file));
-	}
-	
-	
-	ExperimentResults(OutputStream out)  {
-		this.out = new PrintStream(new BufferedOutputStream(out));
-	}
-	
-	
-	public void beginDocument() {
-		write(XML_HEADER);
-	}
-	
-	
-	public void beginExperiment(Experiment ex) {
-		String dir = ex.getDirectory().getAbsolutePath();
-		write(BEGIN_EXPERIMENT_TAG, ex.getName(), ex.getTime(), dir);
-	}
-	
-	
-	public void beginTask(int idx, Task task) {
-		String im = task.getImageFile().getName();
-		String gt = task.getMaskFile().getName();
-		write(BEGIN_TASK_TAG, idx, im, gt);
-	}
-	
-	
-	public void beginEvaluation(int time) {
-		write(BEGIN_EVALUATION_TAG, time);
-	}
-	
-	
-	public void endEvaluation() {
-		write(END_EVALUATION_TAG);
-	}
-	
-	
-	public void addMeasure(String name, double value) {
-		write(MEASURE_TAG, name, value);
-	}
-	
-	
-	public void endTask() {
-		write(END_TASK_TAG);
-	}
-	
-	
-	public void endExperiment() {
-		write(END_EXPERIMENT_TAG);
-	}
-	
-	
-	public void endDocument() throws IOException {
-		flush();
-	}
-	
-	
-	public void flush() throws IOException {
-		out.flush();
-		if (out.checkError()) {
-			throw new IOException();
-		}
-	}
-	
-	
-	public void close() {
-		out.close();
-	}
-	
-	
-	private void write(String format, Object ... args) {
-		out.printf(format, args);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/exp/FormatException.java b/image_annotation/src/ie/dcu/apps/ist/exp/FormatException.java
deleted file mode 100644
index 8553f0d..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/exp/FormatException.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.exp;
-
-/**
- * @author Kevin McGuinness
- */
-public class FormatException extends Exception {
-
-	/**
-	 * 
-	 */
-	private static final long serialVersionUID = 1L;
-
-
-	/**
-	 * 
-	 */
-	public FormatException() {
-	}
-
-
-	/**
-	 * @param message
-	 */
-	public FormatException(String message) {
-		super(message);
-	}
-
-
-	/**
-	 * @param cause
-	 */
-	public FormatException(Throwable cause) {
-		super(cause);
-	}
-
-
-	/**
-	 * @param message
-	 * @param cause
-	 */
-	public FormatException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/exp/StorageSelection.java b/image_annotation/src/ie/dcu/apps/ist/exp/StorageSelection.java
deleted file mode 100644
index aeae41f..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/exp/StorageSelection.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package ie.dcu.apps.ist.exp;
-
-/**
- * Selection of what points in time to output the masks that
- * the user has obtained so far in their interactions.
- * 
- * @author Kevin McGuinness
- */
-public enum StorageSelection {
-	All,
-	None,
-	Final;
-	
-	public static StorageSelection parse(String s) {
-		for (StorageSelection ss : values()) {
-			if (ss.toString().equalsIgnoreCase(s)) {
-				return ss;
-			}
-		}
-		return null;
-	}
-};
diff --git a/image_annotation/src/ie/dcu/apps/ist/exp/Task.java b/image_annotation/src/ie/dcu/apps/ist/exp/Task.java
deleted file mode 100644
index 754d4ed..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/exp/Task.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package ie.dcu.apps.ist.exp;
-
-import java.io.*;
-
-public class Task {
-
-	private final File imageFile;
-	private final File maskFile;
-	private final String description;
-
-
-	Task(File imFile, File gtFile, String desc) {
-		imageFile = imFile;
-		maskFile = gtFile;
-		description = desc;
-	}
-
-
-	public File getImageFile() {
-		return imageFile;
-	}
-
-
-	public File getMaskFile() {
-		return maskFile;
-	}
-
-
-	public String getDescription() {
-		return description;
-	}
-	
-	
-	public String toString() {
-		String im = imageFile.getAbsolutePath();
-		String gt = maskFile.getAbsolutePath();
-		return String.format("[ im=<%s> gt=<%s> desc=<%s> ]", im, gt, description);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/AreaShape.java b/image_annotation/src/ie/dcu/apps/ist/export/imagemap/AreaShape.java
deleted file mode 100644
index 11fc339..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/AreaShape.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.export.imagemap;
-
-/**
- * The shape of the area tag for a HTML image map. 
- * 
- * @see <a href="http://www.w3.org/TR/html401/sgml/dtd.html#Shape"/>HTML 4 DTD</a>
- * 
- * @author Kevin McGuinness
- */
-public enum AreaShape {
-	Polygon("poly"),
-	Rectangle("rect"),
-	Circle("circle");
-	
-	private String text;
-	
-	private AreaShape(String text) {
-		this.text = text;
-	}
-	
-	/**
-	 * Returns the HTML shape attribute value.
-	 */
-	public String toString() {
-		return text;
-	}
-}
\ No newline at end of file
diff --git a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/ExportException.java b/image_annotation/src/ie/dcu/apps/ist/export/imagemap/ExportException.java
deleted file mode 100644
index 51bf4c5..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/ExportException.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package ie.dcu.apps.ist.export.imagemap;
-
-/**
- * Exception thrown when there is a problem producing the export.
- * 
- * @author Kevin McGuinness
- */
-public class ExportException extends Exception {
-	private static final long serialVersionUID = 1L;
-
-	public ExportException() {
-	}
-
-	public ExportException(String message) {
-		super(message);
-	}
-
-	public ExportException(Throwable cause) {
-		super(cause);
-	}
-
-	public ExportException(String message, Throwable cause) {
-		super(message, cause);
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/Exporter.java b/image_annotation/src/ie/dcu/apps/ist/export/imagemap/Exporter.java
deleted file mode 100644
index 09fafa1..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/Exporter.java
+++ /dev/null
@@ -1,189 +0,0 @@
-package ie.dcu.apps.ist.export.imagemap;
-
-import ie.dcu.image.ContourTracer;
-import ie.dcu.segment.SegmentationMask;
-import ie.dcu.util.FileUtils;
-
-import java.awt.Polygon;
-import java.awt.image.*;
-import java.io.*;
-import java.util.*;
-
-import javax.imageio.ImageIO;
-
-/**
- * Exports HTML image maps from a segmentation mask and an image.
- * 
- * @author Kevin McGuinness
- */
-public class Exporter {
-	private final SegmentationMask mask;
-	private final BufferedImage image;
-	
-	private RolloverEffect effect;
-	private String htmlFile = "imagemap.html";
-	private String imageFile = "image.png";
-	private String imageName = "image";
-	private String objectDescription = "";
-	private String objectLink = "";
-	private String title = "";
-	private AreaShape exportShape = AreaShape.Polygon;
-	
-	public Exporter(BufferedImage image, SegmentationMask mask) {
-		this.image = image;
-		this.mask = mask;
-	}
-	
-	public RolloverEffect getEffect() {
-		return effect;
-	}
-
-	public void setEffect(RolloverEffect effect) {
-		this.effect = effect;
-	}
-
-	public String getHtmlFile() {
-		return htmlFile;
-	}
-
-	public void setHtmlFile(String htmlFile) {
-		this.htmlFile = htmlFile;
-	}
-
-	public String getImageFile() {
-		return imageFile;
-	}
-
-	public void setImageFile(String imageFile) {
-		this.imageFile = imageFile;
-	}
-
-	public String getImageName() {
-		return imageName;
-	}
-
-	public void setImageName(String imageName) {
-		this.imageName = imageName;
-	}
-
-	public String getTitle() {
-		return title;
-	}
-
-	public void setTitle(String title) {
-		this.title = title;
-	}
-	
-	public String getObjectDescription() {
-		return objectDescription;
-	}
-
-	public void setObjectDescription(String description) {
-		this.objectDescription = description;
-	}
-
-	public String getObjectLink() {
-		return objectLink;
-	}
-
-	public void setObjectLink(String link) {
-		this.objectLink = link;
-	}
-
-	public AreaShape getExportShape() {
-		return exportShape;
-	}
-
-	public void setExportShape(AreaShape shape) {
-		this.exportShape = shape;
-	}
-
-	public void export(File folder) throws IOException, ExportException {
-		ContourTracer tracer = new ContourTracer(mask, SegmentationMask.FOREGROUND);
-		List<Polygon> trace = tracer.trace();
-		
-		if (trace.size() == 0) {
-			throw new ExportException("No objects found");
-		}
-		
-		List<String> preloads = getPreloads(trace);
-		
-		// Write image
-		ImageIO.write(image, "png", new File(folder, imageFile));
-		
-		if (effect != null) {
-			int i = 1;
-			
-			// Generate effect images
-			for (Polygon object : trace) {
-				RenderedImage im = effect.createEffect(image, object);
-				File output = new File(folder, preloads.get(i++));
-				ImageIO.write(im, "png", output);
-			}
-		}
-		
-		// Create image map
-		ImageMap map = new ImageMap();
-		map.setImageHref(imageFile);
-		map.setImageName(imageName);
-		
-		// Add javascript preloads
-		for (String str : preloads) {
-			map.addPreload(str);
-		}
-		
-		// Add areas
-		int idx = 1;
-		for (Polygon polygon : trace) {
-			MapArea area = new MapArea();
-			switch (exportShape) {
-			case Polygon:
-				area.setPolygon(polygon);
-				break;
-			case Rectangle:
-				area.setRect(polygon.getBounds());
-				break;
-			case Circle:
-				// TODO: Implement circle!
-				
-			default:
-				area.setPolygon(polygon);
-				break;
-			}
-			
-			area.setAlt(objectDescription);
-			area.setHref(objectLink);
-			
-			if (effect != null) {
-				
-				
-				area.addAttr("onmouseover", 
-					String.format("rollover(document.%s, image%s)", 
-							imageName, idx++));
-				area.addAttr("onmouseout", 
-						String.format("rollover(document.%s, image0)", imageName));
-				area.addAttr("title",getTitle());
-			}
-			
-			map.addArea(area);
-		}
-		
-		map.exportToFile(new File(folder, htmlFile));
-	}
-	
-	private List<String> getPreloads(List<Polygon> trace) {
-		List<String> preloads = new ArrayList<String>();
-		preloads.add(imageFile);
-		
-		if (effect != null) {
-			
-			String basename = FileUtils.removeExtension(imageFile);
-			for (int i = 0; i < trace.size(); i++) {
-				String filename = String.format("%s-%d.png", basename, i);
-				preloads.add(filename);
-			}
-		}
-		
-		return preloads;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/HtmlTag.java b/image_annotation/src/ie/dcu/apps/ist/export/imagemap/HtmlTag.java
deleted file mode 100644
index 7b0943e..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/HtmlTag.java
+++ /dev/null
@@ -1,80 +0,0 @@
-package ie.dcu.apps.ist.export.imagemap;
-
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * Class used to generate HTML tags.
- * 
- * @author Kevin McGuinness
- */
-class HtmlTag {
-	final String name;
-	final Map<String, String> attrs;
-
-	HtmlTag(String name) {
-		this.name = name;
-		this.attrs = new HashMap<String, String>();
-	}
-	
-	HtmlTag attr(String name, String value) {
-		attrs.put(name, escape(value));
-		return this;
-	}
-	
-	private static String escape(String value) {
-		return value.replaceAll("\"", "\\\\\"");
-	}
-
-	static void indent(StringBuffer sb, int indent) {
-		for (int i = 0; i < indent; i++) {
-			sb.append(' ');
-		}
-	}
-	
-	void open(StringBuffer sb, int indent) {
-		open(sb, indent, false);
-	}
-	
-	void open(StringBuffer sb, int indent, boolean empty) {
-		
-		// Indent 
-		indent(sb, indent);
-		
-		// Write start of tag
-		sb.append('<').append(name);
-		
-		// Write attributes
-		boolean first = true;
-		for (Map.Entry<String, String> entry : attrs.entrySet()) {
-			
-			if (!first) {
-				sb.append('\n');
-				indent(sb, indent + name.length() + 1);
-			}
-			
-			sb.append(' ');
-			sb.append(entry.getKey());
-			sb.append('=');
-			sb.append('"');
-			sb.append(entry.getValue());
-			sb.append('"');
-			
-			first = false;
-		}
-		
-		if (empty) {
-			sb.append('/');
-		}
-		sb.append('>').append('\n');
-	}
-	
-	void close(StringBuffer sb, int indent) {
-		indent(sb, indent);
-		sb.append('<');
-		sb.append('/');
-		sb.append(name);
-		sb.append('>');
-		sb.append('\n');
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/ImageMap.java b/image_annotation/src/ie/dcu/apps/ist/export/imagemap/ImageMap.java
deleted file mode 100644
index 4125ccf..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/ImageMap.java
+++ /dev/null
@@ -1,184 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.export.imagemap;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-
-/**
- * Exports HTML image maps
- * 
- * @author Kevin McGuinness
- */
-public class ImageMap {
-	private static final String TEMPLATE_FILE = "template.html";
-	
-	private String pageTitle;
-	private String imageName;
-	private String imageHref;
-	private String imageAlt;
-	private String mapName;
-	private final List<MapArea> areas;
-	private final List<String> preloads;
-	
-	public ImageMap() {
-		// set defaults :
-		this.pageTitle = "Image Map";
-		this.imageName = "image";
-		this.imageHref = "";
-		this.imageAlt = "";
-		this.mapName = "imagemap";
-		this.areas = new LinkedList<MapArea>();
-		this.preloads = new LinkedList<String>();
-	}
-
-	public String getPageTitle() {
-		return pageTitle;
-	}
-
-	public void setPageTitle(String pageTitle) {
-		assert (pageTitle != null);
-		this.pageTitle = pageTitle;
-	}
-
-	public String getImageName() {
-		return imageName;
-	}
-
-	public void setImageName(String imageName) {
-		this.imageName = imageName;
-	}
-
-	public String getImageHref() {
-		return imageHref;
-	}
-
-	public void setImageHref(String imageHref) {
-		assert (imageHref != null);
-		this.imageHref = imageHref;
-	}
-
-	public String getImageAlt() {
-		return imageAlt;
-	}
-
-	public void setImageAlt(String imageAlt) {
-		assert (imageAlt != null);
-		this.imageAlt = imageAlt;
-	}
-
-	public String getMapName() {
-		return mapName;
-	}
-
-	public void setMapName(String mapName) {
-		assert (mapName != null);
-		this.mapName = mapName;
-	}
-
-	public void addArea(MapArea area) {
-		areas.add(area);
-	}
-	
-	public List<MapArea> areas() {
-		return areas;
-	}
-	
-	public void addPreload(String preload) {
-		this.preloads.add(preload);
-	}
-	
-	public List<String> preloads() {
-		return preloads;
-	}
-
-	public String export() {
-		String template = loadTemplate();
-		
-		// Create preloads buffer
-		StringBuffer preloads = new StringBuffer();
-		int idx = 0;
-		for (String s : preloads()) {
-			HtmlTag.indent(preloads, 8);
-			preloads.append("var image").append(idx);
-			preloads.append(" = new Image()\n");
-			HtmlTag.indent(preloads, 8);
-			preloads.append("image").append(idx);
-			preloads.append(".src = '").append(s).append("'\n");
-			idx++;
-		}
-		
-		StringBuffer contents = new StringBuffer();
-		for (MapArea area : areas) {
-			contents.append('\n');
-			area.export(contents, 8);
-		}
-		
-		Map<String, String> subs = new HashMap<String, String>();
-		subs.put("image-name", imageName);
-		subs.put("page-title", pageTitle);
-		subs.put("image-href", imageHref);
-		subs.put("image-alt", imageAlt);
-		subs.put("map-name", mapName);
-		subs.put("contents", contents.toString());
-		subs.put("preloads", preloads.toString());
-		
-		return substitute(template, subs);
-	}
-	
-	public void exportToFile(File file) throws IOException {
-		FileWriter writer = new FileWriter(file);
-		try {
-			writer.append(export());
-		} finally {
-			writer.close();
-		}
-	}
-	
-	private String substitute(String template, Map<String, String> subs) {
-		// This could be more efficient..
-		String result = template;
-		for (String key : subs.keySet()) {
-			String regex = String.format("\\$\\{%s\\}", key);
-			result = result.replaceAll(regex, subs.get(key));
-		}
-		
-		return result;
-	}
-	
-	private String loadTemplate() {
-		BufferedReader reader = new BufferedReader(new InputStreamReader(
-				getClass().getResourceAsStream(TEMPLATE_FILE)));
-		
-		StringBuffer buff = new StringBuffer();
-		
-		try {
-			String line;
-			while ((line = reader.readLine()) != null) {
-				buff.append(line).append('\n');
-			}
-		} catch (IOException e) {
-			throw new RuntimeException(e);
-		} finally {
-			try {
-				reader.close();
-			} catch (IOException e) {
-				// Ignore
-			}
-		}
-		
-		return buff.toString();
-	}
-	
-	public String toString() {
-		return export();
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/MapArea.java b/image_annotation/src/ie/dcu/apps/ist/export/imagemap/MapArea.java
deleted file mode 100644
index 2bc22b3..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/MapArea.java
+++ /dev/null
@@ -1,133 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.export.imagemap;
-
-import java.awt.Polygon;
-import java.awt.Rectangle;
-import java.net.*;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Map.Entry;
-
-
-public class MapArea {
-	
-	private String href;
-	private String alt;
-	private AreaShape shape;
-	private int[] coords;
-	private final Map<String, String> attrs;
-	
-	public MapArea() {
-		href = "";
-		alt = "";
-		shape = AreaShape.Polygon;
-		coords = new int[0];
-		attrs = new HashMap<String, String>();
-	}
-	
-	public void addAttr(String key, String value) {
-		attrs.put(key, value);
-	}
-
-	public String getHref() {
-		return href;
-	}
-
-	public void setHref(String href) {
-		this.href = href == null ? "" : href;
-	}
-
-	public String getAlt() {
-		return alt;
-	}
-
-	public void setAlt(String alt) {
-		this.alt = alt == null ? "" : alt;
-	}
-	
-	public AreaShape getShape() {
-		return shape;
-	}
-
-	public void setShape(AreaShape shape) {
-		this.shape = shape == null ? AreaShape.Polygon : shape;
-	}
-
-	public int[] getCoords() {
-		return coords;
-	}
-
-	public void setCoords(int[] coords) {
-		this.coords = coords == null ? new int[0] : coords;
-	}
-
-	public void setRect(Rectangle rect) {
-		setShape(AreaShape.Rectangle);
-		int[] coords = {
-				rect.x, 
-				rect.y, 
-				rect.x + rect.width, 
-				rect.y + rect.height
-		};
-		setCoords(coords);
-	}
-	
-	public void setCircle(int x, int y, int r) {
-		setShape(AreaShape.Circle);
-		int[] coords = { x, y, r };
-		setCoords(coords);
-	}
-	
-	public void setPolygon(Polygon poly) {
-		setShape(AreaShape.Polygon);
-		int[] coords = new int[2*poly.npoints];
-		for (int i = 0, j = 0; i < poly.npoints; i++) {
-			coords[j++] = poly.xpoints[i];
-			coords[j++] = poly.ypoints[i];
-		}
-		setCoords(coords);
-	}
-	
-	public void export(StringBuffer sb, int indent) {
-		String encodedHREF = href;
-		if (href.length() != 0) {
-			try {
-				URI uri = new URI(href);
-				URL url = uri.toURL();
-				encodedHREF = url.toString();
-			} catch (URISyntaxException e) {
-				// Ignore exceptions, the href string will be used instead
-			} catch (MalformedURLException e) {
-				// Ignore exceptions, the href string will be used instead
-			}
-		}
-		
-		HtmlTag tag = new HtmlTag("area");
-		tag
-		  .attr("href", encodedHREF)
-		  .attr("alt", alt)
-		  .attr("shape", shape.toString())
-		  .attr("coords", getCoordsString());
-		
-		for (Entry<String, String> entry : attrs.entrySet()) {
-			tag.attr(entry.getKey(), entry.getValue());
-		}
-		
-		tag.open(sb, indent, true);
-	}
-	
-	public String getCoordsString() {
-		StringBuffer sb = new StringBuffer();
-		boolean first = true;
-		for (int coord : coords) {
-			if (!first) {
-				sb.append(',');
-			}
-			sb.append(coord);
-			first = false;
-		}
-		return sb.toString();
-	}
-}
\ No newline at end of file
diff --git a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/RolloverEffect.java b/image_annotation/src/ie/dcu/apps/ist/export/imagemap/RolloverEffect.java
deleted file mode 100644
index 8e5ea2b..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/RolloverEffect.java
+++ /dev/null
@@ -1,191 +0,0 @@
-package ie.dcu.apps.ist.export.imagemap;
-
-import java.awt.BasicStroke;
-import java.awt.Color;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.Image;
-import java.awt.Polygon;
-import java.awt.Rectangle;
-import java.awt.RenderingHints;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.image.BufferedImage;
-import java.awt.image.RenderedImage;
-
-/**
- * The roll-over effect for the image map.
- * 
- * @author Kevin McGuinness
- */
-public abstract class RolloverEffect {
-	
-	public abstract RenderedImage createEffect(Image image, Polygon object);
-	
-	public static RolloverEffect darkenBackground(float alpha) {
-		return new DarkenBackground(alpha);
-	}
-	
-	public static RolloverEffect darkenBackground() {
-		return new DarkenBackground();
-	}
-	
-	public static RolloverEffect brightenForeground(float alpha) {
-		return new BrightenForeground(alpha);
-	}
-	
-	public static RolloverEffect brightenForeground() {
-		return new BrightenForeground();
-	}
-	
-	public static RolloverEffect outlineObject() {
-		return new OutlineObject();
-	}
-	
-	public static RolloverEffect outlineObject(Color color) {
-		return new OutlineObject(color);
-	}
-	
-	public static RolloverEffect outlineObject(Color color, Stroke stroke) {
-		return new OutlineObject(color, stroke);
-	}
-	
-	public static class DarkenBackground extends RolloverEffect {
-		
-		private float alpha = 0.5f;
-		
-		public DarkenBackground() {
-			
-		}
-
-		public DarkenBackground(float alpha) {
-			this.alpha = alpha;
-		}
-
-		public float getAlpha() {
-			return alpha;
-		}
-
-		public void setAlpha(float alpha) {
-			this.alpha = alpha;
-		}
-
-		@Override
-		public RenderedImage createEffect(Image image, Polygon object) {
-			int width = image.getWidth(null);
-			int height = image.getHeight(null);
-			BufferedImage im = new BufferedImage(width, height, 
-					BufferedImage.TYPE_INT_ARGB);
-			
-			Area area = new Area(new Rectangle(0,0,width,height));
-			area.subtract(new Area(object));
-			
-			Graphics g = im.getGraphics();
-			if (g instanceof Graphics2D) {
-				Graphics2D g2 = (Graphics2D) g;
-				g2.drawImage(image, 0, 0, null);
-				g2.setColor(new Color(0,0,0,alpha));
-				g2.fill(area);
-			}
-			
-			return im;
-		}
-	}
-	
-	public static class BrightenForeground extends RolloverEffect {
-		
-		private float alpha = 0.5f;
-		
-		public BrightenForeground() {
-			
-		}
-
-		public BrightenForeground(float alpha) {
-			this.alpha = alpha;
-		}
-
-		public float getAlpha() {
-			return alpha;
-		}
-
-		public void setAlpha(float alpha) {
-			this.alpha = alpha;
-		}
-
-		@Override
-		public RenderedImage createEffect(Image image, Polygon object) {
-			int width = image.getWidth(null);
-			int height = image.getHeight(null);
-			BufferedImage im = new BufferedImage(width, height, 
-					BufferedImage.TYPE_INT_ARGB);
-			
-			Graphics g = im.getGraphics();
-			if (g instanceof Graphics2D) {
-				Graphics2D g2 = (Graphics2D) g;
-				g2.drawImage(image, 0, 0, null);
-				g2.setColor(new Color(1,1,1,alpha));
-				g2.fill(object);
-			}
-			
-			return im;
-		}
-	}
-	
-	public static class OutlineObject extends RolloverEffect {
-		
-		private Color color = Color.white;
-		private Stroke stroke = new BasicStroke(2.0f, 
-				BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND);
-		
-		public OutlineObject() {
-			
-		}
-
-		public OutlineObject(Color color) {
-			this.color = color;
-		}
-		
-		public OutlineObject(Color color, Stroke stroke) {
-			this.color = color;
-			this.stroke = stroke;
-		}
-
-		public Color getColor() {
-			return color;
-		}
-
-		public void setColor(Color color) {
-			this.color = color;
-		}
-
-		public Stroke getStroke() {
-			return stroke;
-		}
-
-		public void setStroke(Stroke stroke) {
-			this.stroke = stroke;
-		}
-
-		@Override
-		public RenderedImage createEffect(Image image, Polygon object) {
-			int width = image.getWidth(null);
-			int height = image.getHeight(null);
-			BufferedImage im = new BufferedImage(width, height, 
-					BufferedImage.TYPE_INT_ARGB);
-			
-			Graphics g = im.getGraphics();
-			if (g instanceof Graphics2D) {
-				Graphics2D g2 = (Graphics2D) g;
-				g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, 
-						RenderingHints.VALUE_ANTIALIAS_ON);
-				g2.drawImage(image, 0, 0, null);
-				g2.setColor(color);
-				g2.setStroke(stroke);
-				g2.draw(object);
-			}
-			
-			return im;
-		}
-	}
-}
-
diff --git a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/template.html b/image_annotation/src/ie/dcu/apps/ist/export/imagemap/template.html
deleted file mode 100644
index 159d2a1..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/export/imagemap/template.html
+++ /dev/null
@@ -1,38 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-	"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html>
-<head>
-    <!-- Generated using the CDVP Interactive Segmentation Tool -->
-    <meta http-equiv="Content-type" 
-          content="text/html; charset=utf-8"/>
-    <meta name="Generator" 
-          content="Interactive Segmentation Tool"/>
-    
-    <title>${page-title}</title>
-    
-    <script type="text/javascript" language="javascript">
-  		
-${preloads}
-  		
-        function rollover(docElem, image) {
-            docElem.src = image.src
-            return true
-        }
-        
-    </script>
-  
-</head>
-<body>
-    <!-- Image -->
-    <img name="${image-name}"
-         src="${image-href}" 
-         usemap="#${map-name}" 
-         alt="${image-alt}"
-         title="${image-alt}"/>
-    
-    <!-- Image map -->
-    <map name="${map-name}" id="${map-name}">
-${contents}
-    </map>
-</body>
-</html>
\ No newline at end of file
diff --git a/image_annotation/src/ie/dcu/apps/ist/recent/RecentFiles.java b/image_annotation/src/ie/dcu/apps/ist/recent/RecentFiles.java
deleted file mode 100644
index 16ef717..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/recent/RecentFiles.java
+++ /dev/null
@@ -1,234 +0,0 @@
-package ie.dcu.apps.ist.recent;
-
-import java.io.*;
-import java.util.*;
-import java.util.logging.*;
-
-/**
- * Class for managing a recent documents list.
- * 
- * @author Kevin McGuinness
- */
-public class RecentFiles implements Iterable<File> {
-	public static final int DEFAULT_CAPACITY = 10;
-	
-	
-	private final LinkedList<File> history;
-	private final List<RecentFilesListener> listeners;
-	private final File store;
-	private int capacity;
-	
-	
-	public RecentFiles(File store) {
-		
-		// Check the store is ok
-		checkValid(store);
-		
-		// Construct
-		this.history = new LinkedList<File>();
-		this.listeners = new LinkedList<RecentFilesListener>();
-		this.store = store;
-		this.capacity = DEFAULT_CAPACITY;
-		
-		// Add a vm shutdown hook
-		addShutdownHook();
-	}
-	
-	
-	public void setCapacity(int capacity) {
-		
-		// Check positive
-		if (capacity < 0) {
-			throw new IllegalArgumentException("capacity < 0");
-		}
-		
-		if (this.capacity != capacity) {
-			this.capacity = capacity;
-		
-			// Capacity may have reduced
-			boolean reduced = history.size() > capacity;
-			while (history.size() > capacity) {
-				history.removeLast();
-			}
-			
-			// Fire change
-			if (reduced) {
-				fireHistoryChanged();
-			}
-		}
-	}
-	
-	
-	public int getCapacity() {
-		return capacity;
-	}
-	
-
-	public void add(File file) {
-		if (!history.contains(file)) {
-			history.addFirst(file);
-			
-			// Check if we have exceeded capacity
-			if (history.size() > capacity) {
-				history.removeLast();
-			}
-			
-			// Fire change
-			fireHistoryChanged();
-		}
-	}
-	
-	
-	public void clear() {
-		if (!empty()) {
-			history.clear();
-			fireHistoryChanged();
-		}
-	}
-
-
-	public List<File> files() {
-		return Collections.unmodifiableList(history);
-	}
-
-
-	public Iterator<File> iterator() {
-		return files().iterator();
-	}
-
-
-	public boolean empty() {
-		return history.isEmpty();
-	}
-
-
-	public void load() throws IOException {
-		if (!store.exists()) {
-			// Create an empty store
-			store.createNewFile();
-		}
-		
-		BufferedReader in = null;
-		try {
-			read(in = new BufferedReader(new FileReader(store)));
-		
-		} finally {
-			in.close();
-		}
-	}
-
-
-	public void store() throws IOException {
-		PrintWriter out = null;
-		try {
-			write(out = new PrintWriter(store));
-			
-		} finally {
-			out.close();
-		}
-	}
-
-
-	public void addListener(RecentFilesListener rfl) {
-		listeners.add(rfl);
-	}
-	
-	
-	public void removeListener(RecentFilesListener rfl) {
-		listeners.remove(rfl);
-	}
-	
-
-	protected static Logger getLogger() {
-		return Logger.getLogger(RecentFiles.class.getName());
-	}
-
-
-	private void shutdown() {
-		try {
-			store();
-		} catch (IOException e) {
-			getLogger().warning("Error writing recent documents to store: " + e);
-		}
-	}
-
-
-	private void fireHistoryChanged() {
-		RecentFilesEvent evt = null;
-		for (RecentFilesListener listener : listeners) {
-			if (evt == null) {
-				evt = new RecentFilesEvent(this);
-				listener.historyChanged(evt);
-			}
-		}
-	}
-
-
-	private void checkValid(File store) {
-		if (store == null) {
-			throw new IllegalArgumentException("store cannot be null");
-		}
-		
-		if (store.isDirectory()) {
-			throw new IllegalArgumentException("store cannot be a directory");
-		}
-		
-		if (store.isFile()) {
-			if (!store.canWrite()) {
-				throw new IllegalArgumentException("store not writable");
-			}
-		}
-	}
-
-
-	private void addShutdownHook() {
-		Runtime.getRuntime().addShutdownHook(new Thread() {
-			public void run() {
-				shutdown();
-			}
-		});
-	}
-
-
-	private void read(BufferedReader in) throws IOException {
-		
-		// Remember old history to check for changes
-		LinkedList<File> old = new LinkedList<File>(history);
-		
-		// Clear history if not empty
-		history.clear();
-		
-		// Read files (discarding no longer existent ones)
-		String line;
-		while ((line = in.readLine()) != null) {
-			
-			// Stop when full
-			if (history.size() == capacity) {
-				break;
-			}
-			
-			File file = new File(line);
-			if (file.exists()) {
-				history.add(file);
-			}
-		}
-		
-		// Fire change if a change occurred
-		if (!history.equals(old)) {
-			fireHistoryChanged();
-		}
-	}
-
-
-	private void write(PrintWriter out) throws IOException {
-		for (File file : history) {
-			String path = file.getAbsolutePath();
-			out.println(path);
-		}
-		
-		// Check for errors
-		if (out.checkError()) {
-			throw new IOException("Error writing to file");
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/recent/RecentFilesEvent.java b/image_annotation/src/ie/dcu/apps/ist/recent/RecentFilesEvent.java
deleted file mode 100644
index 8b0932e..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/recent/RecentFilesEvent.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package ie.dcu.apps.ist.recent;
-
-import java.util.*;
-
-public class RecentFilesEvent extends EventObject {
-	private static final long serialVersionUID = 1L;
-
-	
-	public RecentFilesEvent(RecentFiles source) {
-		super(source);
-	}
-
-	
-	public RecentFiles getList() {
-		return (RecentFiles) source;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/recent/RecentFilesListener.java b/image_annotation/src/ie/dcu/apps/ist/recent/RecentFilesListener.java
deleted file mode 100644
index 8d50258..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/recent/RecentFilesListener.java
+++ /dev/null
@@ -1,8 +0,0 @@
-package ie.dcu.apps.ist.recent;
-
-import java.util.*;
-
-public interface RecentFilesListener extends EventListener {
-
-	public void historyChanged(RecentFilesEvent evt);
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/views/ExperimentPanel.java b/image_annotation/src/ie/dcu/apps/ist/views/ExperimentPanel.java
deleted file mode 100644
index 94dc2e3..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/views/ExperimentPanel.java
+++ /dev/null
@@ -1,547 +0,0 @@
-/**
- * 
- */
-package ie.dcu.apps.ist.views;
-
-import ie.dcu.apps.ist.AppWindow;
-import ie.dcu.apps.ist.event.*;
-import ie.dcu.apps.ist.exp.*;
-import ie.dcu.apps.ist.widgets.SwtTimer;
-import ie.dcu.segment.annotate.*;
-
-import java.io.IOException;
-import java.util.Properties;
-import java.util.logging.*;
-
-import org.eclipse.jface.dialogs.MessageDialog;
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.graphics.Rectangle;
-import org.eclipse.swt.layout.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * @author Kevin McGuinness
- */
-public class ExperimentPanel extends Composite {
-	
-	// Some property keys
-	private static final String DESCRIPTION_TITLE 
-		= "description.title";
-	
-	private static final String TIMEOUT_MESSAGE 
-		= "timeout-message";
-	
-	private static final String EXPERIMENT_COMPLETE_MESSAGE 
-		= "experiment-complete-message";
-
-	// Type of button in use
-	private static enum ButtonType { Start, Finish };
-	
-	// App window and experiment
-	private final AppWindow window;
-	private final Experiment experiment;
-	private final Logger log;
-	
-	// Controls
-	private final Group group;
-	private final Button button;
-	private final SwtTimer timer;
-	private final Text text;
-	
-	// Shell if the panel is inside a shell
-	private Shell shell;
-	
-	// Experiment manager
-	private final ExperimentManager manager;
-	private final EvaluationListener evaluator;
-	
-	
-	public ExperimentPanel(AppWindow window, Composite parent, int style) {
-		super(parent, style);
-	
-		// Set app window
-		this.window = window;
-		this.experiment = window.getExperiment();
-		this.log = Logger.getLogger("Experiment");
-		
-		
-		// Create controls
-		timer  = new SwtTimer(this, SWT.NONE);
-		group = new Group(this, SWT.DEFAULT);
-		button = new Button(this, SWT.PUSH);
-		text   = new Text(group, SWT.READ_ONLY | SWT.WRAP); 
-		
-		// Create manager and evaluator
-		manager = new ExperimentManager(window);
-		evaluator = new EvaluationListener(manager, timer);
-		
-		// Setup controls
-		setupControls();
-		layoutControls();
-		addListeners();
-		
-		// Begin experiment
-		beginExperiment();
-	}
-	
-	
-	public static void open(AppWindow win) {
-		Shell app = win.getShell();
-		
-		// Style bits
-		int style = SWT.MODELESS | SWT.RESIZE | SWT.BORDER | SWT.TITLE | SWT.CLOSE;
-		
-		// Construct shell
-		Shell shell = new Shell(app, style);
-		
-		// Determine shell bounds
-		Rectangle bounds = new Rectangle(0,0,180,280);
-		
-		// Move shell to an appropriate place (right of app window)
-		Rectangle rect = app.getBounds();
-		bounds.x = rect.x + rect.width;
-		bounds.y = rect.y + rect.height / 2 - bounds.height / 2;
-		
-		// Move back if outside the screen
-		Rectangle screen = shell.getDisplay().getBounds();
-		if (bounds.x + bounds.width > screen.width) {
-			bounds.x -= bounds.x + bounds.width - screen.width;
-		}
-
-		// Set bounds
-		shell.setBounds(bounds);
-	
-		// Set layout
-		shell.setLayout(new FillLayout());
-		
-		// Create experiment panel
-		final ExperimentPanel panel 
-			= new ExperimentPanel(win, shell, SWT.NONE);
-		
-		panel.shell = shell;
-		panel.updateTitle();
-		
-		// Add shell close button listener
-		shell.addShellListener(new ShellAdapter() {
-			public void shellClosed(ShellEvent e) {
-				if (!panel.manager.isComplete()) {
-					e.doit = panel.cancelExperiment();
-				}
-			}
-		});
-		
-		// Open experiment panel
-		shell.open();
-	}
-
-	
-	private void setupControls() {
-		group.setText(property(DESCRIPTION_TITLE));
-		text.setEnabled(false);
-		enableButton(null);
-	}
-
-
-	private void layoutControls() {
-		GridLayout gl;
-		GridData   gd;
-		
-		// Setup layout manager for this
-		gl = new GridLayout();
-		gl.marginTop = 5;
-		gl.verticalSpacing = 5;
-		this.setLayout(gl);
-		
-		// Setup layout manager for group
-		gl = new GridLayout();
-		group.setLayout(gl);
-		
-		// Layout timer
-		gd = new GridData(SWT.FILL, SWT.FILL, true, false);
-		timer.setLayoutData(gd);
-		
-		// Layout group
-		gd = new GridData(SWT.FILL, SWT.FILL, true, true);
-		group.setLayoutData(gd);
-		
-		// Layout button
-		gd = new GridData(SWT.FILL, SWT.FILL, true, false);
-		button.setLayoutData(gd);
-		
-		// Layout text
-		gd = new GridData(SWT.FILL, SWT.FILL, true, true);
-		text.setLayoutData(gd);
-	}
-
-
-	private void addListeners() {
-		button.addListener(SWT.Selection, buttonListener);
-		timer.addTimeoutListener(timeListener);
-	}
-
-	
-	/**
-	 * Function to call if something goes wrong with the experiment. Shows an
-	 * error message and gracefully returns the application to normal mode.
-	 * 
-	 * @param reason
-	 *          Short description of the problem.
-	 */
-	private void abortExperiment(String reason) {
-		timer.clear();
-		evaluator.detach();
-		
-		// Show abort message
-		error("Aborting experiment!%n%s", reason);
-		
-		// Tell manager of abort
-		manager.abortExperiment();
-		
-		// Exit experiment mode
-		exitExperimentMode();
-	}
-	
-	
-	/**
-	 * Does what is necessary to exit experiment mode.
-	 */
-	private void exitExperimentMode() {
-		// Remove experiment view
-		window.setExperiment(null);
-		
-		// Re-enable interactions
-		window.getView().setEnabled(true);
-		
-		// Kill the shell
-		closeShell();
-	}
-	
-	
-	/**
-	 * Closes the encompassing (non-application) shell, if any.
-	 */
-	private void closeShell() {
-		if (shell != null) {
-			shell.close();
-			shell.dispose();
-			shell = null;
-		}
-	}
-	
-	
-	private boolean cancelExperiment() {
-		// Make sure the user knows what they're doing
-		boolean cancel = MessageDialog.openQuestion(window.getShell(), "Confirm", 
-				"Are you sure you want to cancel the experiment?");
-		
-		if (cancel) {
-			// Guess we better do what the user says, grumble grumble :-/
-			timer.clear();
-			evaluator.detach();
-			manager.abortExperiment();
-			window.setExperiment(null);
-			window.getView().setEnabled(true);
-		}
-		
-		return cancel;
-	}
-	
-	
-	/**
-	 * Start the experiment.
-	 */
-	private void beginExperiment() {
-		try {
-			manager.beginExperiment(experiment);
-			
-		} catch (IOException e) {
-			log.log(Level.SEVERE, "Error starting experiment", e);
-			abortExperiment(e.getMessage());
-		}
-		
-		// Begin first task
-		beginTask();
-	}
-	
-	
-	/**
-	 * Finish the experiment.
-	 */
-	private void endExperiment() {
-		try {
-			manager.endExperiment();
-			
-		} catch (IOException e) {
-			log.log(Level.SEVERE, "Error ending experiment", e);
-			abortExperiment(e.getMessage());
-		}
-		
-		// Tell user experiment is complete
-		notifyExperimentComplete();
-		
-		// Stop experiment mode
-		exitExperimentMode();
-	}
-	
-	
-	/**
-	 * Load the task.
-	 */
-	private void beginTask() {
-	
-		// Set timer
-		timer.set(experiment.getTime());
-		
-		// Begin task
-		try {
-			manager.beginTask();
-		} catch (IOException e) {
-			log.log(Level.SEVERE, "Error starting task", e);
-			abortExperiment(e.getMessage());
-		}
-		
-		// Disable interactions
-		window.getView().setEnabled(false);
-		
-		// Update description
-		text.setText(manager.getTaskDescription());
-		
-		// Update title text
-		updateTitle();
-		
-		// Setup start button
-		enableButton(ButtonType.Start);
-		
-		// Attach evaluator
-		evaluator.attach();
-	}
-	
-	
-	private void updateTitle() {
-		if (shell != null) {
-			int ntasks = manager.getTaskCount();
-			int progress = manager.getProgress();
-			shell.setText(String.format("Task [%d/%d]", progress+1, ntasks));
-		}
-	}
-
-
-	/**
-	 * Start the task.
-	 */
-	private void startTask() {
-		
-		// Enable interactions
-		window.getView().setEnabled(true);
-		
-		// Start clock
-		timer.start();
-		
-		// Enable finish button
-		enableButton(ButtonType.Finish);
-	}
-	
-
-	/**
-	 * End the task.
-	 */
-	private void endTask() {
-		// Detach evaluator
-		evaluator.detach();
-		
-		// Evaluate final result
-		manager.evaluate(timer.getElapsed());
-		
-		// End task
-		try {
-			manager.endTask();
-		} catch (IOException e) {
-			log.log(Level.SEVERE, "Error ending task", e);
-			abortExperiment(e.getMessage());
-		}
-		
-		// Stop and clear clock
-		timer.clear();
-	}
-	
-	
-	/**
-	 * End the current task and start the next. 
-	 * End the experiment if finished.
-	 */
-	private void nextTask() {
-		endTask();
-		if (manager.isComplete()) {
-			endExperiment();
-		} else {
-			beginTask();
-		}
-	}
-	
-
-	private void enableButton(ButtonType type) {
-		if (type != null) {
-			String name = type.toString().toLowerCase();
-			button.setText(property("button.text." + name));
-			button.setData(type);
-			button.setEnabled(true);
-			button.setFocus();
-		} else {
-			button.setText(property("button.text.start"));
-			button.setEnabled(false);
-			button.setData(null);
-		}
-	}
-	
-	
-	private ButtonType getEnabledButton() {
-		return (ButtonType) button.getData();
-	}
-
-
-	private void handleButtonClicked() {
-		ButtonType btn = getEnabledButton();
-		switch (btn) {
-		case Start:
-			startTask();
-			break;
-		case Finish:
-			// Prevent clicking finish by accident
-			if (manager.getActiveContext().getAnnotations().count() == 0) {
-				getDisplay().beep();
-			} else {
-				nextTask();
-			}
-			break;
-		}
-	}
-
-
-	private void handleTimeout() {
-		// Finish task
-		endTask();
-		
-		// Tell user
-		notifyTimeoutOccurred();
-		
-		// Next task
-		if (manager.isComplete()) {
-			endExperiment();
-		} else {
-			beginTask();
-		}
-	}
-
-
-	private void notifyExperimentComplete() {
-		message(EXPERIMENT_COMPLETE_MESSAGE);
-	}
-
-
-	private void notifyTimeoutOccurred() {
-		// BEEP BEEP!! time up :-)
-		getDisplay().beep();
-		message(TIMEOUT_MESSAGE);
-	}
-
-
-	private void message(String key) {
-		Shell main = window.getShell();
-		MessageDialog.openInformation(main, "Information", property(key));
-	}
-	
-	
-	private void error(String message, Object ... args) {
-		Shell main = window.getShell();
-		MessageDialog.openError(main, "Error", String.format(message, args));
-	}
-
-
-	private String property(String key) {
-		return property(key, key);
-	}
-
-
-	private String property(String key, String def) {
-		Properties p = window.getProperties();
-		return p.getProperty(String.format("ExperimentPanel.%s", key), def);
-	}
-
-
-	private final Listener buttonListener = new Listener() {
-		public void handleEvent(Event event) {
-			handleButtonClicked();
-		}
-	};	
-	
-	
-	private final TimeoutListener timeListener = new TimeoutListener() {
-		public void timeoutOccured(TimeoutEvent evt) {
-			handleTimeout();
-		}
-	};
-}
-
-
-class EvaluationListener implements AnnotationListener {
-	private final ExperimentManager manager;
-	private final SwtTimer timer;
-	private final Logger log;
-	
-	public EvaluationListener(ExperimentManager manager, SwtTimer timer) {	
-		this.manager = manager;
-		this.timer = timer;
-		this.log = Logger.getLogger("Experiment");
-	}
-	
-	
-	public void attach() {
-		manager.getActiveContext().addAnnotationListener(this);
-	}
-	
-	
-	public void detach() {
-		manager.getActiveContext().removeAnnotationListener(this);
-	}
-	
-	
-	private void annotationsChanged(AnnotationEvent e) {
-		// Return if there is nothing to evaluate yet
-		if (e.manager.count() == 0) {
-			return;
-		}
-				
-		// Time the change occurred
-		int time = timer.getElapsed();
-		manager.evaluate(time);
-		
-		// Store if necessary
-		try {
-			manager.store(time);
-		} catch (IOException ex) {
-			log.log(Level.SEVERE, "Error storing intermediate segmentation mask", e);
-		}
-	}
-
-	
-	public void annotationPerformed(AnnotationEvent e) {
-		annotationsChanged(e);
-	}
-
-	
-	public void annotationRedone(AnnotationEvent e) {
-		annotationsChanged(e);
-	}
-
-	
-	public void annotationUndone(AnnotationEvent e) {
-		annotationsChanged(e);
-	}
-
-	
-	public void annotationsCleared(AnnotationEvent e) {
-		annotationsChanged(e);
-	}
-}
-
diff --git a/image_annotation/src/ie/dcu/apps/ist/views/SegmentationView.java b/image_annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
deleted file mode 100644
index df08994..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
+++ /dev/null
@@ -1,1063 +0,0 @@
-package ie.dcu.apps.ist.views;
-
-
-import ie.dcu.apps.ist.PainterRegistry;
-import ie.dcu.apps.ist.event.*;
-import ie.dcu.apps.ist.widgets.*;
-import ie.dcu.segment.*;
-import ie.dcu.segment.annotate.*;
-import ie.dcu.segment.options.SegmenterOptionDialog;
-import ie.dcu.segment.painters.SegmentationPainter;
-import ie.dcu.swt.*;
-import ie.dcu.swt.event.*;
-
-import java.lang.reflect.InvocationTargetException;
-import java.net.*;
-import java.util.Properties;
-import java.util.logging.*;
-import java.io.*;
-import org.json.*;
-
-import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.jface.action.*;
-import org.eclipse.jface.operation.*;
-import org.eclipse.jface.resource.ImageDescriptor;
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.graphics.Point;
-import org.eclipse.swt.layout.*;
-import org.eclipse.swt.widgets.*;
-
-public class SegmentationView extends Composite {
-	// Logger
-	private static final Logger log = Logger.getLogger(SegmentationView.class.getName());
-	
-	
-	// Segmentation view properties
-	private final Properties props;
-	
-	
-	// Houses various painters
-	private final PainterRegistry painters;
-	
-	
-	// View handling annotations
-	private final AnnotatedImageControl view;
-	
-	
-	// Left and right tool bar
-	private final ToolBar bar1, bar2, bar3;
-	
-	private final Button assign;
-	
-	//private final StyledText text;		
-	
-	// Control to change brush size
-	private final BrushControl brushControl;
-	
-	
-	// Handles various events
-	private final EventHandler eventHandler;
-	
-	
-	// Proxy object to catch and log exceptions thrown by the segmentation
-	// algorithm, without crashing the application.
-	private RobustSegmenterProxy segmenterProxy;
-	
-	// Auto segment on update flag
-	private boolean auto = true;
-	
-	// Combo box housing the selectable views
-	private Combo combo;
-
-	public static Combo comboLabel;
-	
-	// Current segmentation tool
-	private Segmenter segmenter;
-	
-	
-	// Context to run the segmentation in, (may be null)
-	private IRunnableContext runnableContext;
-	
-	
-	// Flag to indicate that the runnable context blocks when fork is true
-	private boolean blocksOnFork;
-	
-	
-	public enum Tool {
-		Foreground,
-		Background,
-		ZoomIn,
-		ZoomOut,
-		ZoomOriginal,
-		ZoomBestFit,
-		Repaint,
-		Undo,
-		Redo,
-		Clear,
-		SetBrushSize,
-		AutoApply,
-		Apply,
-		SetPainter,
-		SetLabel,
-		SegmenterOptions;
-		
-		private ToolAction action;
-	};
-	
-	
-	public SegmentationView(Properties props, Composite parent, int style) {
-		super(parent, style);
-		this.props = props;
-		
-		painters = new PainterRegistry();
-		bar1 = new ToolBar(this, SWT.RIGHT | SWT.FLAT);
-		bar2 = new ToolBar(this, SWT.RIGHT | SWT.FLAT);
-		bar3 = new ToolBar(this, SWT.RIGHT | SWT.FLAT);
-		assign = new Button(bar3, SWT.PUSH);
-		view = new AnnotatedImageControl(this, SWT.BORDER);
-		brushControl = new BrushControl(getShell(), SWT.BORDER);
-		eventHandler = new EventHandler();
-		segmenterProxy = new RobustSegmenterProxy();
-		
-		init();
-	}
-
-
-	/**
-	 * Initialize.
-	 */
-	private void init() {
-		initTools();
-		createToolbar1();
-		createToolbar2();
-		createToolbar3();
-		layoutControls();
-		updatePainters();
-		addListeners();
-		updateToolStates();
-	}
-
-
-	private void initTools() {
-		for (Tool t : Tool.values()) {
-			if (t.action == null) {
-				new ToolAction(t);
-			}
-		}
-	}
-
-
-	private void addListeners() {
-		brushControl.addSelectionListener(eventHandler);
-		view.addContextChangeListener(eventHandler);
-		view.addZoomListener(eventHandler);
-		addDisposeListener(eventHandler);
-	}
-
-
-	private void createToolbar1() {
-		ToolBarManager m = new ToolBarManager(bar1);
-		m.add(getAction(Tool.Foreground));
-		m.add(getAction(Tool.Background));
-		m.add(new Separator());
-		m.add(getAction(Tool.ZoomIn));
-		m.add(getAction(Tool.ZoomOut));
-		m.add(getAction(Tool.ZoomOriginal));
-		m.add(getAction(Tool.ZoomBestFit));
-		m.add(new Separator());
-		m.add(getAction(Tool.Repaint));
-		m.add(getAction(Tool.Undo));
-		m.add(getAction(Tool.Redo));
-		m.add(getAction(Tool.Clear));
-		m.add(new Separator());
-		m.add(getAction(Tool.SetBrushSize));
-		m.add(new Separator());
-		m.add(getAction(Tool.AutoApply));
-		m.add(getAction(Tool.Apply));
-		m.add(getAction(Tool.SegmenterOptions));
-		m.update(true);
-	}
-	
-	
-	private void createToolbar2() {
-		SwtUtils.addLabel(bar2, getAction(Tool.SetPainter).getText());
-		combo = SwtUtils.addCombo(bar2, 115, SWT.READ_ONLY);
-		combo.setToolTipText( getAction(Tool.SetPainter).getToolTipText());
-		combo.addSelectionListener(new SelectionAdapter() {
-			public void widgetSelected(SelectionEvent e) {
-				execute(Tool.SetPainter, null);
-			}
-		});
-		bar2.pack();
-	}
-	/**
-	 * Third tool bar for holding the Annotate Combo box. 
-	 */
-	private void createToolbar3() {
-		SwtUtils.addLabel(bar3, getAction(Tool.SetLabel).getText());
-		comboLabel = SwtUtils.addCombo(bar3, 130, SWT.SIMPLE);
-		comboLabel.setToolTipText( getAction(Tool.SetLabel).getToolTipText());
-		comboLabel.addKeyListener(new KeyListener() {
-			@Override
-			public void keyReleased(KeyEvent e) {
-				comboLabel.remove(0,comboLabel.getItemCount()-1);
-				setLabel(comboLabel.getText());
-				Display.getCurrent().asyncExec(new Runnable() {
-			        public void run() {
-			        	comboLabel.setText(comboLabel.getText());
-			        	comboLabel.forceFocus();
-			        	}
-			        });
-			}
-			@Override
-			public void keyPressed(KeyEvent arg0) {
-				// TODO Auto-generated method stub
-			}
-		});
-		ToolItem item = new ToolItem(bar3, SWT.SEPARATOR);
-		assign.setText("Assign");
-		item.setWidth(50);
-		item.setControl(assign);
-		assign.addSelectionListener(new SelectionListener() {
-        public void widgetSelected(SelectionEvent arg0) {
-        	String lab = null;
-        	if(comboLabel.getText().indexOf('{') != -1)
-        	{
-        		lab = comboLabel.getText().substring(0,comboLabel.getText().indexOf('{')-1);
-        	}
-        	else
-        	{
-        		lab = comboLabel.getText();
-        	}
-        	System.out.println("selected"+lab);
-		    }
-		@Override
-		public void widgetDefaultSelected(SelectionEvent arg0) {
-			// TODO Auto-generated method stub
-		}
-		});
-		bar3.pack();
-	}
-	
-	
-	private void layoutControls() {
-		GridLayout layout = new GridLayout(3, false);
-		layout.marginHeight = 1;
-		layout.marginWidth = 2;
-		layout.horizontalSpacing = -1; // zero leaves 1 pixel gap
-		layout.verticalSpacing = 1;
-		setLayout(layout);
-		
-		Point sz1 = bar1.computeSize(SWT.DEFAULT, SWT.DEFAULT);
-		Point sz2 = bar2.computeSize(SWT.DEFAULT, SWT.DEFAULT);
-		
-		int heightHint = Math.max(sz1.y, sz2.y);
-		
-		// Layout toolbar 1
-		GridData gd = new GridData();
-		gd.grabExcessHorizontalSpace = true;
-		gd.horizontalAlignment = SWT.FILL;
-		gd.heightHint = heightHint;
-		bar1.setLayoutData(gd);
-		
-		// Layout toolbar 2
-		gd = new GridData();
-		gd.horizontalAlignment = SWT.FILL;
-		gd.heightHint = heightHint;
-		bar2.setLayoutData(gd);
-		
-		// Layout view
-		gd = new GridData();
-		gd.verticalIndent = 2;
-		gd.horizontalSpan = 3;
-		gd.grabExcessHorizontalSpace = true;
-		gd.grabExcessVerticalSpace = true;
-		gd.horizontalAlignment = SWT.FILL;
-		gd.verticalAlignment = SWT.FILL;
-		view.setLayoutData(gd);
-	}
-	
-	
-	private void updatePainters() {
-		combo.removeAll();
-		boolean first = true;
-		for (SegmentationPainter p : painters.values()) {
-			combo.add(p.getName());
-			if (first) {
-				combo.setText(p.getName());
-				first = false;
-			}
-		}
-	}
-	
-	
-	public void setSegmenter(Segmenter segmenter) {
-		if (this.segmenter != segmenter) {
-			SegmentationContext ctx = view.getContext();
-			
-			if (this.segmenter != null && ctx != null) {
-				// Finish old segmentation
-				segmenterProxy.finish(ctx);
-				
-				// Remove old segmenter
-				this.segmenter = null;
-			}
-			
-			// Set new segmenter
-			this.segmenter = segmenter;
-			
-			// Initialize a new segmentation
-			start(ctx);
-			
-			// Update enabled buttons
-			updateToolStates();
-		}
-	}
-	
-	
-	public Segmenter getSegmenter() {
-		return segmenter;
-	}
-	
-	
-	public void setContext(SegmentationContext ctx) {
-		
-		// context change handler handles initialization etc. 
-		// of segmenter and context
-		view.setContext(ctx);
-	}
-
-	
-	public SegmentationContext getContext() {
-		return view.getContext();
-	}
-	
-
-	public void setAnnotationType(AnnotationType type) {
-		view.setAnnotationType(type);
-	}
-	
-	
-	public Canvas getCanvas() {
-		return view.getCanvas();
-	}
-	
-	
-	public ImageControl getImageControl() {
-		return view.getImageControl();
-	}
-
-
-	public void zoomIn() {
-		view.zoomIn();
-	}
-
-
-	public void zoomOut() {
-		view.zoomOut();
-	}
-
-
-	public void zoomOriginal() {
-		view.zoomOriginal();
-	}
-
-
-	public void zoomBestFit() {
-		view.zoomBestFit();
-	}
-
-
-	public void repaint() {
-		view.repaint();
-	}
-
-
-	public void undo() {
-		view.undo();
-	}
-
-
-	public void redo() {
-		view.redo();
-	}
-
-
-	public void clear() {
-		view.clear();
-	}
-
-
-	public void setBrushSize(int size) {
-		view.setLineWidth(size);
-	}
-
-
-	public void setPainter(SegmentationPainter painter) {
-		view.setPainter(painter);
-		combo.setText(painter.getName());
-	}
-
-	
-	public SegmentationPainter getPainter() {
-		return view.getPainter();
-	}
-	
-
-	public void setAutoApply(boolean checked) {
-		if (!this.auto && checked) {
-			// Going from off to on, resegment now
-			apply();
-		}
-		this.auto = checked;
-	}
-	
-	
-	public boolean isAutoApply() {
-		return this.auto;
-	}
-
-
-	public boolean canZoomIn() {
-		return view.canZoomIn();
-	}
-
-
-	public boolean canZoomOut() {
-		return view.canZoomOut();
-	}
-
-
-	public boolean canZoomOriginal() {
-		return view.canZoomOriginal();
-	}
-
-
-	public boolean canZoomBestFit() {
-		return view.canZoomBestFit();
-	}
-
-
-	public boolean canUndo() {
-		return view.canUndo();
-	}
-
-
-	public boolean canRedo() {
-		return view.canRedo();
-	}
-
-
-	public boolean canClear() {
-		return view.canClear();
-	}
-	
-	
-	public boolean canShowOptions() {
-		if (hasSegmenter()) {
-			return segmenter.getOptions().size() > 0;
-		}
-		return false;
-	}
-
-
-	public Action getAction(Tool t) {
-		return t.action;
-	}
-
-
-	public void showSegmenterOptions() {
-		if (canShowOptions()) {
-			SegmenterOptionDialog dialog = 
-				new SegmenterOptionDialog(getShell(), segmenter);
-		
-			int result = dialog.open();
-			switch (result) {
-			case SegmenterOptionDialog.OK:
-				// Re-segment
-				apply();
-			}
-		}
-	}
-	
-	
-	public boolean hasSegmenter() {
-		return segmenter != null;
-	}
-	
-
-	public void performSegmentation(AnnotationEvent e, SegmentationContext ctx) {
-		
-		if (runnableContext == null) {
-			segment(e, ctx);
-		} else {
-			segmentWithRunnableContext(e, ctx);
-		}
-		
-		// Repaint everything
-		repaint();
-		
-	}
-	
-	
-	public void setRunnableContext(IRunnableContext context, boolean blocksOnFork) {
-		runnableContext = context;
-		this.blocksOnFork = blocksOnFork;
-	}
-	
-	
-	public void addContextChangeListener(ContextChangeListener listener) {
-		view.addContextChangeListener(listener);
-	}
-	
-	
-	public void removeContextChangeListener(ContextChangeListener listener) {
-		view.removeContextChangeListener(listener);
-	}
-	
-	
-	public void setEnabled(boolean enabled) {
-		super.setEnabled(enabled);
-		bar1.setEnabled(enabled);
-		bar2.setEnabled(enabled);
-		view.setEnabled(enabled);
-		updateToolStates();
-	}
-	
-
-	private void run(boolean fork, IRunnableWithProgress runnable) {
-		boolean wasEnabled = isEnabled();
-		
-		try {
-			// Disable interactions
-			setEnabled(false);
-			
-			// Run segmentation
-			runnableContext.run(fork, false, runnable);
-			
-		} catch (InvocationTargetException ex) {
-				
-			// Can't happen without a runtime exception occurring, so re-wrap
-			throw new RuntimeException(ex);
-			
-		} catch (InterruptedException ex) {
-			
-			// Can't happen because cancellable is false
-			throw new RuntimeException(ex);
-		
-		} finally {
-			setEnabled(wasEnabled);
-		}
-	}
-
-
-	private void segmentWithRunnableContext(
-			final AnnotationEvent e, 
-			final SegmentationContext ctx) 
-	{
-		// Fork if the segmenter is slow, and only if our runnable context blocks 
-		boolean fork = blocksOnFork /*&& !segmenter.isFast()*/;
-		
-		run(fork, new IRunnableWithProgress() {
-			public void run(IProgressMonitor monitor) {
-				monitor.beginTask("Segmenting", IProgressMonitor.UNKNOWN);
-				try {
-					segment(e, ctx);
-				} finally {
-					monitor.done();
-				}
-			}
-		});
-	}
-
-	
-	private void start(final SegmentationContext ctx) {
-		if (ctx != null && hasSegmenter()) {
-			if (runnableContext == null) {
-				
-				// No runnable context
-				segmenterProxy.init(ctx);
-				segmenterProxy.update(ctx);
-								
-			} else {
-				
-				// Run with progress monitor
-				run(blocksOnFork, new IRunnableWithProgress() {
-					public void run(IProgressMonitor monitor) {
-						monitor.beginTask("Initializing", IProgressMonitor.UNKNOWN);
-						try {
-							segmenterProxy.init(ctx);
-							segmenterProxy.update(ctx);
-						} finally {
-							monitor.done();
-						}
-					}
-				});
-				
-			}
-			
-			// Repaint everything
-			repaint();
-		}
-	}
-
-
-	private void segment(AnnotationEvent e, SegmentationContext ctx) {
-		if (hasSegmenter()) {
-			if (e == null) {
-				// No event triggered this, so do a full update
-				segmenterProxy.update(ctx);
-				
-			} else {
-				// Call appropriate segmenter function
-				switch (e.type) {
-				case Cleared:
-					segmenterProxy.update(ctx);
-					break;
-					
-				case Undone:
-					segmenterProxy.removed(ctx, e.annotation);
-					break;
-				
-				case Redone:
-				case Added:
-					segmenterProxy.added(ctx, e.annotation);
-					break;
-				
-				default:
-					throw new RuntimeException();
-				}
-			}
-		}
-	}
-
-
-	private boolean isAnnotatingBackground() {
-		return view.isAnnotatingBackground();
-	}
-	
-
-	private boolean isAnnotatingForeground() {
-		return view.isAnnotatingForeground();
-	}
-
-
-	private String getText(Tool a) {
-		return props.getProperty(getKey(a, "text"));
-	}
-
-
-	private String getToolTip(Tool a) {
-		return props.getProperty(getKey(a, "tooltip"));
-	}
-
-
-	private ImageDescriptor getImage(Tool a) {
-		String location = props.getProperty(getKey(a, "image"));
-		if (location != null) {
-			if (location.length() == 0) {
-				return null;
-			}
-			
-			try {
-				return ImageDescriptor.createFromURL(new URL(location));
-			} catch (MalformedURLException e) {
-				return null;
-			}
-		}
-		
-		return null;
-	}
-
-
-	private static String getKey(Tool action, String object) {
-		return String.format("SegmentationView.Action.%s.%s", action, object);
-	}
-	
-	
-	private int getType(Tool a) {
-		switch (a) {
-		case Foreground:
-		case Background:
-		case AutoApply:
-			return Action.AS_CHECK_BOX;
-		case SetBrushSize:
-			return Action.AS_DROP_DOWN_MENU;
-		case SetPainter:
-			return Action.AS_UNSPECIFIED;
-		default:
-			return Action.AS_PUSH_BUTTON;
-		}
-	}
-	
-	
-	private void execute(Tool a, Event e) {
-		switch (a) {
-		case Foreground:
-			setAnnotationType(AnnotationType.Foreground);
-			break;
-		case Background:
-			setAnnotationType(AnnotationType.Background);
-			break;
-		case ZoomIn:
-			zoomIn();
-			break;
-		case ZoomOut:
-			zoomOut();
-			break;
-		case ZoomOriginal:
-			zoomOriginal();
-			break;
-		case ZoomBestFit:
-			zoomBestFit();
-			break;
-		case Repaint:
-			repaint();
-			break;
-		case Undo:
-			undo();
-			break;
-		case Redo:
-			redo();
-			break;
-		case Clear:
-			clear();
-			break;
-		case SetBrushSize:
-			showBrushControl(e);
-			break;
-		case AutoApply:
-			setAutoApply(a.action.isChecked());
-			break;
-		case Apply:
-			apply();
-			break;
-		case SetPainter:
-			setPainter();
-			break;
-		case SegmenterOptions:
-			showSegmenterOptions();
-			break;
-		}
-		
-		updateToolStates();
-	}
-	
-	
-	private void updateToolStates() {
-		if (isEnabled()) {
-			Tool.Apply.action.setEnabled(!Tool.AutoApply.action.isChecked());
-			Tool.Undo.action.setEnabled(canUndo());
-			Tool.Redo.action.setEnabled(canRedo());
-			Tool.ZoomIn.action.setEnabled(canZoomIn());
-			Tool.ZoomOut.action.setEnabled(canZoomOut());
-			Tool.ZoomOriginal.action.setEnabled(canZoomOriginal());
-			Tool.ZoomBestFit.action.setEnabled(canZoomBestFit());
-			comboLabel.setEnabled(canZoomBestFit());
-			assign.setEnabled(canZoomBestFit() & !(comboLabel.getText().isEmpty()));
-			Tool.Foreground.action.setChecked(isAnnotatingForeground());
-			Tool.Background.action.setChecked(isAnnotatingBackground());
-			Tool.Clear.action.setEnabled(canClear());
-			Tool.AutoApply.action.setChecked(auto);
-			Tool.SegmenterOptions.action.setEnabled(canShowOptions());
-						
-			// Always enabled if view enabled
-			Tool.SetBrushSize.action.setEnabled(true);
-			Tool.SegmenterOptions.action.setEnabled(true);
-			Tool.SetPainter.action.setEnabled(true);
-			Tool.Repaint.action.setEnabled(true);
-			Tool.Foreground.action.setEnabled(true);
-			Tool.Background.action.setEnabled(true);
-			Tool.AutoApply.action.setEnabled(true);
-			
-		} else {
-			// Everything disabled
-			for (Tool t : Tool.values()) {
-				t.action.setEnabled(false);
-			}
-		}
-		
-	}
-
-	private void setPainter() {
-		SegmentationPainter painter = painters.get(combo.getText());
-		setPainter(painter);
-	}
-	
-	private void setLabel(String content) {
-		try
-	    {
-			String content1 = URLEncoder.encode(content.toString(),"UTF-8");
-			URL url = new URL("http://palea.cgrb.oregonstate.edu/services/PO_web_service.php?request_type=term_search&search_value="+content1+"&inc_synonyms&branch_filter=plant_anatomy&max=20");
-			HttpURLConnection connection = (HttpURLConnection) url.openConnection();
-			 BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()));
-	        if(connection.getResponseCode() == 200)
-	        {
-		        String inputLine;
-		        JSONObject object = null;
-		        while ((inputLine = in.readLine()) != null) 
-		        {
-		        	object = new JSONObject(inputLine);
-		      	}
-		        JSONArray array = new JSONArray(object.getString("PO_term_search_response"));
-		        String listElement;
-		        for(int i=0; i<array.length();i++)
-		        {
-		        	if(array.getJSONObject(i).getString("match_type").trim().equals("synonym"))
-		        	{
-		        		listElement = (array.getJSONObject(i).getString("match")+" {"+array.getJSONObject(i).getString("is_synonym_of")+"}");
-		        		comboLabel.add(listElement,i);
-		        	}
-		        	else if(array.getJSONObject(i).getString("match_type").equals("term"))
-		        	{
-		        		listElement = array.getJSONObject(i).getString("match");
-		        		comboLabel.add(listElement,i);
-		        	}
-		        }
-		        //comboLabel.setListVisible(true);
-	            in.close();
-	        }
-	        else
-	        {
-	        	System.out.println("Response error");
-	        }
-	    }
-	    catch(Exception ex)
-	    {
-	    }
-	    assign.setEnabled(!(comboLabel.getText().isEmpty()));
-	}
-	
-	private void apply() {
-		performSegmentation(null, view.getContext());
-	}
-
-
-	private void showBrushControl(Event e) {
-		brushControl.showBelow(bar1, (ToolItem) e.widget);
-	}
-
-
-	/**
-	 * Handles a context change in the view.
-	 * 
-	 * @param e
-	 *          The event.
-	 */
-	private void handleContextChanged(ContextChangedEvent e) {
-		if (e.oldContext != null) {
-			e.oldContext.removeAnnotationListener(eventHandler);
-	
-			// Finish old segmentation
-			segmenterProxy.finish(e.oldContext);
-		}
-		
-		if (e.newContext != null) {
-			e.newContext.addAnnotationListener(eventHandler);
-			
-			// Begin new segmentation (can cause deferred events
-			// to be processed, so we async exec to ensure that
-			// the other context change handlers are called before
-			// deferred events are processed)
-			final SegmentationContext ctx = e.newContext;
-			getDisplay().asyncExec(new Runnable() {
-				public void run() {
-					start(ctx);
-				}
-			});
-			
-		}
-		
-		updateToolStates();
-	}
-
-
-	/**
-	 * Cleans up resources when the view is disposed.
-	 */
-	private void handleDisposed() {
-		
-		SegmentationContext ctx = view.getContext();
-		if (ctx != null && !ctx.isDisposed()) {
-			
-			// Finish any segmentation		
-			segmenterProxy.finish(ctx);
-	
-			// Dispose context
-			ctx.dispose();
-		}
-		
-		// Dispose all painters
-		painters.dispose();
-	}
-
-
-	/**
-	 * Tool bar action. Delegates running to the execute method.
-	 */
-	private class ToolAction extends Action {
-		private final Tool tool;
-
-		public ToolAction(Tool tool) {
-			super(SegmentationView.this.getText(tool), getType(tool));
-			this.tool = tool;
-			setToolTipText(SegmentationView.this.getToolTip(tool));
-			setImageDescriptor(SegmentationView.this.getImage(tool));
-			tool.action = this;
-		}
-		
-		public void runWithEvent(Event e) {
-			execute(tool, e);
-		}
-	}
-	
-	
-	/**
-	 * Handles various events coming from the view and toolbar controls.
-	 * 
-	 */
-	private final class EventHandler extends SelectionAdapter implements
-		ZoomListener, 
-		SelectionListener, 
-		ContextChangeListener, 
-		AnnotationListener,
-		DisposeListener
-	{
-		
-		public void widgetDisposed(DisposeEvent e) {
-			handleDisposed();
-		}
-		
-
-		public void zoomChanged(ZoomEvent e) {
-			updateToolStates();
-		}
-		
-
-		public void widgetSelected(SelectionEvent e) {
-			setBrushSize(brushControl.getBrushSize());
-		}
-		
-
-		public void contextChanged(ContextChangedEvent e) {
-			handleContextChanged(e);
-		}
-		
-
-		public void annotationPerformed(AnnotationEvent e) {
-			if (!isEnabled()) {
-				log.warning("annotation performed while not enabled");
-			}
-			
-			if (auto && isEnabled()) {
-				performSegmentation(e, view.getContext());
-			}
-			updateToolStates();
-		}
-
-		
-		public void annotationRedone(AnnotationEvent e) {
-			if (!isEnabled()) {
-				log.warning("annotation redone while not enabled");
-			}
-			
-			if (auto && isEnabled()) {
-				performSegmentation(e, view.getContext());
-			}
-			updateToolStates();
-		}
-
-		
-		public void annotationUndone(AnnotationEvent e) {
-			if (!isEnabled()) {
-				log.warning("annotation undone while not enabled");
-			}
-			
-			if (auto && isEnabled()) {
-				performSegmentation(e, view.getContext());
-			}
-			
-			updateToolStates();
-		}
-
-		
-		public void annotationsCleared(AnnotationEvent e) {
-			if (!isEnabled()) {
-				log.warning("annotations cleared while not enabled");
-			}
-			
-			if (auto && isEnabled()) {
-				performSegmentation(e, view.getContext());
-			}
-			updateToolStates();
-		}
-	};
-	
-	/**
-	 * Class that prevents segmentation algorithms crashing the application
-	 * by catching any thrown exceptions and logging them.
-	 * 
-	 * @author Kevin McGuinness
-	 */
-	private class RobustSegmenterProxy {
-
-		public void init(SegmentationContext ctx) {
-			if (segmenter != null) {
-				try {
-					segmenter.init(ctx);
-				} catch (Throwable th) {
-					severe(th, "%s.init()", getSegmenterClassName());
-				}
-			}
-		}
-
-		public void update(SegmentationContext ctx) {
-			if (segmenter != null) {
-				try {
-					segmenter.update(ctx);
-				} catch (Throwable th) {
-					severe(th, "%s.update()", getSegmenterClassName());
-				}
-			}
-		}
-
-		public void added(SegmentationContext ctx, Annotation a) {
-			if (segmenter != null) {
-				try {
-					segmenter.added(ctx, a);
-				} catch (Throwable th) {
-					severe(th, "%s.added()", getSegmenterClassName());
-				}
-			}
-		}
-
-		public void removed(SegmentationContext ctx, Annotation a) {
-			if (segmenter != null) {
-				try {
-					segmenter.removed(ctx, a);
-				} catch (Throwable th) {
-					severe(th, "%s.removed()", getSegmenterClassName());
-				}
-			}
-		}
-
-		public void finish(SegmentationContext ctx) {
-			if (segmenter != null) {
-				try {
-					segmenter.finish(ctx);
-				} catch (Throwable th) {
-					severe(th, "%s.finish()", getSegmenterClassName());
-				}
-			}
-		}
-
-		public String getSegmenterClassName() {
-			return segmenter.getClass().getSimpleName();
-		}
-		
-		private void severe(Throwable th, String message, Object ... args) {
-			log.log(Level.SEVERE, String.format(message, args), th);
-		}
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/widgets/AnnotatedImageControl.java b/image_annotation/src/ie/dcu/apps/ist/widgets/AnnotatedImageControl.java
deleted file mode 100644
index 89eb761..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/widgets/AnnotatedImageControl.java
+++ /dev/null
@@ -1,414 +0,0 @@
-package ie.dcu.apps.ist.widgets;
-
-
-import ie.dcu.apps.ist.controllers.AnnotationTool;
-import ie.dcu.apps.ist.event.*;
-import ie.dcu.segment.SegmentationContext;
-import ie.dcu.segment.annotate.*;
-import ie.dcu.segment.painters.*;
-import ie.dcu.swt.*;
-import ie.dcu.swt.event.ZoomListener;
-
-import java.util.*;
-import java.util.List;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.layout.FillLayout;
-import org.eclipse.swt.widgets.*;
-
-public class AnnotatedImageControl extends Composite {
-	private final List<ContextChangeListener> listeners;
-	private final ImageControl view;
-	private SegmentationContext ctx;
-	private AnnotationTool tool;
-	private SegmentationPainter painter;
-	private Cursor cursor;
-	
-	public AnnotatedImageControl(Composite parent, int style) {
-		super(parent, style);
-		setLayout(new FillLayout());
-		view = new ImageControl(this, SWT.NONE);
-		listeners = new ArrayList<ContextChangeListener>(2);
-		painter = new CombinedPainter();
-		view.getCanvas().addMouseMoveListener(cursorChanger);
-		addDisposeListener(disposeListener);
-	}
-	
-	
-	public ImageControl getImageControl() {
-		return view;
-	}
-	
-	
-	public Canvas getCanvas() {
-		return view.getCanvas();
-	}
-	
-	
-	public SegmentationPainter getPainter() {
-		return painter;
-	}
-	
-	
-	public void setPainter(SegmentationPainter painter) {
-		if (this.painter != painter) {
-			this.painter = painter;
-			recreate();
-		}
-	}
-	
-	
-	public SegmentationContext getContext() {
-		return ctx;
-	}
-	
-	
-	public void setContext(SegmentationContext ctx) {
-		
-		// Remember old context for event
-		SegmentationContext old = this.ctx;
-		
-		// Detach old tool
-		int lineWidth = 1;
-		if (tool != null) {
-			lineWidth = tool.getLineWidth();
-			tool.detach();
-			tool = null;
-		}
-		
-		// Detach old annotation listener
-		if (ctx != null) {
-			ctx.getAnnotations().removeAnnotationListener(listener);
-		}
-		
-		// Assign context
-		this.ctx = ctx;
-		
-		if (ctx != null) {
-			// Attach new annotation listener
-			AnnotationManager annotations = ctx.getAnnotations();
-			annotations.addAnnotationListener(listener);
-			
-			// Attach a new annotation tool
-			tool = new AnnotationTool(annotations, view);
-			tool.setLineWidth(lineWidth);
-		}
-		
-		// Create the initial image
-		recreate();
-		
-		// Fire event
-		fireContextChanged(old);
-	}
-	
-
-	public int getLineWidth() {
-		if (tool != null) {
-			return tool.getLineWidth();
-		}
-		return 1;
-	}
-	
-	
-	public void setLineWidth(int width) {
-		if (tool != null) {
-			tool.setLineWidth(width);
-		}
-	}
-	
-	
-	public AnnotationType getAnnotationType() {
-		if (tool != null) {
-			return tool.getType();
-		}
-		return AnnotationType.Foreground;
-	}
-	
-	
-	public void setAnnotationType(AnnotationType type) {
-		if (tool != null) {
-			tool.setType(type);
-		}
-	}
-	
-	
-	public float getZoom() {
-		return view.getZoom();
-	}
-	
-	
-	public void setZoom(float zoom) {
-		view.setZoom(zoom);
-	}
-	
-	
-	public float getZoomStep() {
-		return view.getZoomStep();
-	}
-
-
-	public void setZoomStep(float zoomStep) {
-		view.setZoomStep(zoomStep);
-	}
-
-
-	public void zoomBestFit() {
-		view.zoomBestFit();
-	}
-
-
-	public void zoomIn() {
-		view.zoomIn();
-	}
-
-
-	public void zoomOriginal() {
-		view.zoomOriginal();
-	}
-
-
-	public void zoomOut() {
-		view.zoomOut();
-	}
-
-
-	public void undo() {
-		if (ctx != null) {
-			ctx.getAnnotations().undo();
-		}
-	}
-	
-	
-	public void redo() {
-		if (ctx != null) {
-			ctx.getAnnotations().redo();
-		}
-	}
-	
-	
-	public void clear() {
-		if (ctx != null) {
-			ctx.getAnnotations().clear();
-		}
-	}
-	
-	
-	public boolean canUndo() {
-		if (ctx != null) {
-			return ctx.getAnnotations().canUndo();
-		}
-		return false;
-	}
-	
-	
-	public boolean canRedo() {
-		if (ctx != null) {
-			return ctx.getAnnotations().canRedo();
-		}
-		return false;
-	}
-	
-	
-	public boolean canClear() {
-		if (ctx != null) {
-			return ctx.getAnnotations().count() > 0;
-		}
-		return false;
-	}
-	
-	
-	public boolean canZoomBestFit() {
-		return view.canZoomBestFit();
-	}
-
-
-	public boolean canZoomIn() {
-		return view.canZoomIn();
-	}
-
-
-	public boolean canZoomOriginal() {
-		return view.canZoomOriginal();
-	}
-
-
-	public boolean canZoomOut() {
-		return view.canZoomOut();
-	}
-	
-	
-	/**
-	 * Redraw the entire canvas buffer.
-	 */
-	public void repaint() {
-		if (ctx != null) {
-			painter.paint(ctx, view.getImage());
-		}
-	}
-
-
-	public boolean isAnnotatingForeground() {
-		return getAnnotationType() == AnnotationType.Foreground;
-	}
-	
-	
-	public boolean isAnnotatingBackground() {
-		return getAnnotationType() == AnnotationType.Background;
-	}
-	
-	
-	public void addAnnotationListener(AnnotationListener listener) {
-		if (ctx == null) {
-			throw new IllegalStateException();
-		}
-		ctx.getAnnotations().addAnnotationListener(listener);
-	}
-	
-
-	public void removeAnnotationListener(AnnotationListener listener) {
-		if (ctx != null) {
-			ctx.getAnnotations().removeAnnotationListener(listener);
-		}
-	}
-	
-	
-	public void addZoomListener(ZoomListener listener) {
-		view.addZoomListener(listener);
-	}
-	
-	
-	public void removeZoomListener(ZoomListener listener) {
-		view.removeZoomListener(listener);
-	}
-	
-	
-	public void addContextChangeListener(ContextChangeListener listener) {
-		listeners.add(listener);
-	}
-	
-	
-	public void removeContextChangeListener(ContextChangeListener listener) {
-		listeners.remove(listener);
-	}
-	
-	
-	private void fireContextChanged(SegmentationContext old) {
-		ContextChangedEvent e = null;
-		for (ContextChangeListener l : listeners) {
-			if (e == null) {
-				e = new ContextChangedEvent(this, old, ctx);
-			}
-			l.contextChanged(e);
-		}
-	}
-	
-	
-	/**
-	 * Re-construct the display image buffer, and dispose the old one if
-	 * necessary. If the context is <code>null</code>, then set the display
-	 * buffer to null and dispose of the old one.
-	 */
-	private void recreate() {
-		if (ctx == null) {
-			
-			// Set null image (disposing the old one)
-			view.setImage(null, true);
-			
-		} else {
-			
-			// Check if we can reuse what we have
-			boolean sameSize = false;
-			if (view.hasImage()) {
-				if (view.getImageBounds().equals(ctx.getBounds())) {
-					
-					// Okay, we can reuse the buffer we have :-)
-					sameSize = true;
-				}
-			}
-
-			if (!sameSize) {
-		
-				// Create initial image
-				ObservableImage buffer = new ObservableImage(
-						SwtUtils.createImage(ctx.getBounds())
-				);
-				
-				// Set the image (disposing the old one)
-				view.setImage(buffer, true);
-			}
-			
-			// Draw the image
-			repaint();
-		}
-	}
-	
-	
-	private final DisposeListener disposeListener = new DisposeListener() {
-		public void widgetDisposed(DisposeEvent e) {
-			if (cursor != null) {
-				cursor.dispose();
-			}
-		}
-	};
-
-	
-	/**
-	 * Changes the cursor to a cross-hair when mouse is over the image.
-	 * 
-	 */
-	private final MouseMoveListener cursorChanger = new MouseMoveListener() {
-
-		public void mouseMove(MouseEvent e) {
-			Canvas canvas = view.getCanvas();
-			if (view.imageContains(new Point(e.x, e.y))) {
-				if (cursor == null) {
-					cursor = CursorFactory.createCrosshairCursor();
-				}
-				canvas.setCursor(cursor);
-			} else {
-				canvas.setCursor(getDisplay().getSystemCursor(SWT.CURSOR_ARROW));
-			}
-		}
-	};
-
-
-	/**
-	 * Listens for annotations and updates the buffer and view accordingly.
-	 */
-	private final AnnotationListener listener = new AnnotationListener() {
-		
-		public void annotationUndone(AnnotationEvent e) {
-			// Suspend notifications to prevent repainting the whole thing
-			view.getImage().setSuspendNotifications(true);
-			
-			// Redraw all to buffer
-			repaint();
-			
-			// Re-enable notifications
-			view.getImage().setSuspendNotifications(false);
-			
-			// Repaint just the changed area
-			view.getImage().fireImageChanged(e.annotation.getBounds());
-		}
-			
-		
-		public void annotationsCleared(AnnotationEvent e) {
-			// Repaint everything
-			repaint();
-		}
-		
-		
-		public void annotationRedone(AnnotationEvent e) {	
-			// Paint the new annotation
-			e.annotation.paint(view.getImage());
-		}
-	
-		
-		public void annotationPerformed(AnnotationEvent e) {
-			// Paint the new annotation
-			e.annotation.paint(view.getImage());
-		}
-	};
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/widgets/BrushControl.java b/image_annotation/src/ie/dcu/apps/ist/widgets/BrushControl.java
deleted file mode 100644
index 9459f79..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/widgets/BrushControl.java
+++ /dev/null
@@ -1,101 +0,0 @@
-package ie.dcu.apps.ist.widgets;
-
-import ie.dcu.swt.PopupComposite;
-
-import org.eclipse.swt.*;
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.layout.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Pop up control for changing brush sizes.
- * 
- * @author Kevin McGuinness
- */
-public class BrushControl extends PopupComposite {
-	private static final int MAX_BRUSH_SIZE = 20;
-
-	private final Label label;
-	private final Scale scale;
-	
-	
-	public BrushControl(Shell parent, int style) {
-		super(parent, style);
-		
-		// Create controls
-		label = new Label(this, SWT.NONE);
-		scale = new Scale(this, SWT.NONE);
-		
-		configureControls();
-		configureListeners();
-		layoutControls();
-	}
-
-
-	public void setBrushSize(int size) {
-		scale.setSelection(size);
-		updateLabel();
-	}
-	
-	
-	public int getBrushSize() {
-		return scale.getSelection();
-	}
-	
-	
-	public void addSelectionListener(SelectionListener listener) {
-		scale.addSelectionListener(listener);
-	}
-	
-	
-	public void removeSelectionListener(SelectionListener listener) {
-		scale.removeSelectionListener(listener);
-	}
-	
-	
-	private void configureControls() {
-		scale.setMinimum(1);
-		scale.setMaximum(MAX_BRUSH_SIZE);
-		scale.setIncrement(1);
-		scale.setPageIncrement(2);
-		setBrushSize(1);
-	}
-
-
-	private void configureListeners() {
-		scale.addSelectionListener(new ScaleChangeListener());
-	}
-
-
-	private void layoutControls() {
-		setLayout(new GridLayout());
-		
-		// Layout label
-		GridData gd = new GridData();
-		gd.grabExcessHorizontalSpace = true;
-		gd.horizontalAlignment = SWT.FILL;
-		label.setLayoutData(gd);
-		
-		// Layout scale control
-		gd = new GridData();
-		gd.grabExcessHorizontalSpace = true;
-		gd.horizontalAlignment = SWT.FILL;
-		gd.minimumWidth = 150;
-		scale.setLayoutData(gd);
-	}
-
-
-	private void updateLabel() {
-		int size = scale.getSelection();
-		label.setText(String.format("Brush Size:  %dpx ", size));
-	}
-
-
-	private final class ScaleChangeListener 
-		extends SelectionAdapter {
-		
-		public void widgetSelected(SelectionEvent e) {
-			updateLabel();
-		}
-	};
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/widgets/ColorSelector.java b/image_annotation/src/ie/dcu/apps/ist/widgets/ColorSelector.java
deleted file mode 100644
index 7efcf9d..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/widgets/ColorSelector.java
+++ /dev/null
@@ -1,175 +0,0 @@
-package ie.dcu.apps.ist.widgets;
-
-import java.beans.*;
-
-import org.eclipse.jface.resource.*;
-import org.eclipse.swt.*;
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * Button for selecting colors.
- * 
- * @author Kevin McGuinness
- */
-public class ColorSelector  {
-	public static final String DATA_KEY = "ColorEditor";
-	public static final String COLOR_PROPERTY = "color";
-
-	private final PropertyChangeSupport pcs;
-	private final Point extent;
-	private final Button button;
-	private final ControlListener listener;
-	
-	private Image image;
-	private RGB rgb;
-
-
-	public ColorSelector(Composite parent) {
-		
-		pcs = new PropertyChangeSupport(this);
-		button = new Button(parent, SWT.PUSH);
-		extent = computeImageSize(parent);
-		image = new Image(parent.getDisplay(), extent.x, extent.y);
-		listener = new ControlListener();
-
-		GC gc = new GC(image);
-		gc.setBackground(button.getBackground());
-		gc.fillRectangle(0, 0, extent.x, extent.y);
-		gc.dispose();
-
-		
-		button.setData(DATA_KEY, this);
-		button.setImage(image);
-		button.addListener(SWT.Selection, listener);
-		button.addListener(SWT.Dispose, listener);
-	}
-
-
-	public void addPropertyChangeListener(PropertyChangeListener listener) {
-		pcs.addPropertyChangeListener(listener);
-	}
-
-	
-	public void addPropertyChangeListener(String name, PropertyChangeListener listener) {
-		pcs.addPropertyChangeListener(name, listener);
-	}
-
-
-	public PropertyChangeListener[] getPropertyChangeListeners() {
-		return pcs.getPropertyChangeListeners();
-	}
-
-	
-	public PropertyChangeListener[] getPropertyChangeListeners(String name) {
-		return pcs.getPropertyChangeListeners(name);
-	}
-
-	
-	public void removePropertyChangeListener(PropertyChangeListener listener) {
-		pcs.removePropertyChangeListener(listener);
-	}
-
-
-	public void removePropertyChangeListener(String name, PropertyChangeListener listener) {
-		pcs.removePropertyChangeListener(name, listener);
-	}
-
-
-	public RGB getColor() {
-		return rgb;
-	}
-
-
-	public void setColor(RGB rgb) {
-		if (rgb != null && this.rgb != rgb) {
-			RGB old = rgb;
-			this.rgb = rgb;
-			updateImage();
-			pcs.firePropertyChange(COLOR_PROPERTY, old, rgb);
-		}
-	}
-	
-
-	public Button getButton() {
-		return button;
-	}
-
-
-	public void addListener(int eventType, Listener listener) {
-		button.addListener(eventType, listener);
-	}
-
-
-	public void setLayoutData(Object layoutData) {
-		button.setLayoutData(layoutData);
-	}
-	
-	
-	public void setData(Object data) {
-		button.setData(data);
-	}
-	
-	
-	public Object getData() {
-		return button.getData();
-	}
-
-
-	protected void updateImage() {
-		Display display = button.getDisplay();
-
-		GC gc = new GC(image);
-		gc.setForeground(display.getSystemColor(SWT.COLOR_BLACK));
-		gc.drawRectangle(0, 2, extent.x - 1, extent.y - 4);
-
-		Color color = new Color(display, rgb);
-		gc.setBackground(color);
-		gc.fillRectangle(1, 3, extent.x - 2, extent.y - 5);
-		gc.dispose();
-
-		button.setImage(image);
-		color.dispose();
-	}
-
-
-	protected Point computeImageSize(Composite parent) {
-		GC gc = new GC(parent);
-		Font f = JFaceResources.getFontRegistry().get(JFaceResources.DEFAULT_FONT);
-		gc.setFont(f);
-		int height = gc.getFontMetrics().getHeight();
-		gc.dispose();
-		Point p = new Point(height * 3 - 6, height);
-		return p;
-	}
-	
-	
-	private void handleDispose(Event e) {
-		if (image != null) {
-			image.dispose();
-			image = null;
-		}
-	}
-	
-	
-	private void handleSelection(Event e) {
-		ColorDialog dialog = new ColorDialog(button.getShell());
-		dialog.setRGB(rgb);
-		RGB rgb = dialog.open();
-		setColor(rgb);
-	}
-	
-	
-	private final class ControlListener implements Listener {
-		public void handleEvent(Event e) {
-			switch (e.type) {
-			case SWT.Selection:
-				handleSelection(e);
-				break;
-			case SWT.Dispose:
-				handleDispose(e);
-				break;
-			}
-		}
-	}
-}
\ No newline at end of file
diff --git a/image_annotation/src/ie/dcu/apps/ist/widgets/ImageMenuManager.java b/image_annotation/src/ie/dcu/apps/ist/widgets/ImageMenuManager.java
deleted file mode 100644
index cfe0050..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/widgets/ImageMenuManager.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package ie.dcu.apps.ist.widgets;
-
-import java.net.URL;
-
-import org.eclipse.jface.action.MenuManager;
-import org.eclipse.jface.resource.ImageDescriptor;
-import org.eclipse.swt.graphics.Image;
-import org.eclipse.swt.widgets.Menu;
-import org.eclipse.swt.widgets.MenuItem;
-
-public class ImageMenuManager extends MenuManager {
-	private Image image;
-	
-	public ImageMenuManager() {
-		super();
-	}
-
-	public ImageMenuManager(String text) {
-		super(text);
-	}
-	
-	public ImageMenuManager(String text, URL imageURL) {
-		super(text);
-		setImageURL(imageURL);
-	}
-	
-	public void setImageURL(URL url) {
-		ImageDescriptor descriptor = ImageDescriptor.createFromURL(url);
-		this.image = descriptor.createImage();
-	}
-	
-	@Override
-	public void dispose() {
-		super.dispose();
-		
-		if (image != null) {
-			image.dispose();
-		}
-	}	
-	
-	@Override
-	public void fill(Menu parent, int index) {
-		super.fill(parent, index);
-		MenuItem item = getMenuItem();
-		if (item != null) {
-			item.setImage(image);
-		}
-	}
-
-	protected MenuItem getMenuItem() {
-		Menu menu = getMenu();
-		return (menu != null) ? menu.getParentItem() : null;
-	}
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/widgets/SwtTimer.java b/image_annotation/src/ie/dcu/apps/ist/widgets/SwtTimer.java
deleted file mode 100644
index 6d1f97c..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/widgets/SwtTimer.java
+++ /dev/null
@@ -1,642 +0,0 @@
-package ie.dcu.apps.ist.widgets;
-
-
-import ie.dcu.apps.ist.event.*;
-
-import java.util.ArrayList;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.events.*;
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.layout.FillLayout;
-import org.eclipse.swt.widgets.*;
-
-/**
- * A timer user interface element. Displays a component used
- * to implement a count-down.
- * 
- * @author Kevin McGuinness
- */
-public class SwtTimer implements TickerListener {
-	
-	/**
-	 * Timer is modeled as a state machine. These are the states.
-	 */
-	public static enum State {	Initial, Ready, Running, Paused };
-	
-	
-	/**
-	 * List of listeners interested in changes to the object state.
-	 */
-	private final ArrayList<StateListener> stateListeners;
-	
-	
-	/**
-	 * List of listeners interested in timeouts.
-	 */
-	private final ArrayList<TimeoutListener> timeoutListeners;
-	
-	
-	/**
-	 * The drawing canvas where the numbers are drawn.
-	 */
-	private final Canvas canvas;
-	
-	
-	/**
-	 * The ticker posts tick events every second or so.
-	 */
-	private Ticker ticker;
-	
-	
-	/**
-	 * The current state of the timer.
-	 */
-	private State state;
-	
-	
-	/**
-	 * The font used to render the numbers.
-	 */
-	private Font font;
-	
-	
-	/**
-	 * Total time for the timer, in seconds.
-	 */
-	private int time;
-	
-	
-	/**
-	 * Remaining (displayed) time, in seconds. 
-	 */
-	private int remaining;
-	
-	
-	/**
-	 * Create the timer. Style bits are passed to the underlying canvas.
-	 * 
-	 * @param parent
-	 *          Parent container.
-	 * @param style
-	 *          Style bits.
-	 */
-	public SwtTimer(Composite parent, int style) {
-		stateListeners = new ArrayList<StateListener>(1);
-		timeoutListeners = new ArrayList<TimeoutListener>(1);
-		canvas = new Canvas(parent, style);
-		addListeners();
-		enter(State.Initial);
-	}
-	
-	
-	/**
-	 * Add listeners to various components.
-	 */
-	private void addListeners() {
-		// Listen for paint events
-		canvas.addPaintListener(new PaintListener() {
-			public void paintControl(PaintEvent e) {
-				paint(e.gc);
-			}
-		});
-		
-		// Listen for dispose event
-		canvas.addDisposeListener(new DisposeListener() {
-			public void widgetDisposed(DisposeEvent e) {
-				dispose();		
-			}
-		});
-	}
-	
-	
-	/**
-	 * Set the layout data for the component.
-	 * 
-	 * @param data
-	 *          The layout data.
-	 */
-	public void setLayoutData(Object data) {
-		canvas.setLayoutData(data);
-	}
-	
-	
-	/**
-	 * Returns the layout data for the component.
-	 * 
-	 * @return The layout data.
-	 */
-	public Object getLayoutData() {
-		return canvas.getLayoutData();
-	}
-	
-	
-	/**
-	 * Get the contained canvas.
-	 * 
-	 * @return The contained canvas.
-	 */
-	public Canvas getCanvas() {
-		return canvas;
-	}
-	
-	
-	/**
-	 * Returns the shell associated with the canvas.
-	 * 
-	 * @return The shell.
-	 */
-	public Shell getShell() {
-		return canvas.getShell();
-	}
-	
-	
-	/**
-	 * Get the state of the timer.
-	 * 
-	 * @return The timer state.
-	 */
-	public State getState() {
-		return state;
-	}
-	
-	
-	/**
-	 * Add a state change listener.
-	 * 
-	 * @param listener
-	 *          The listener.
-	 */
-	public void addStateListener(StateListener listener) {
-		stateListeners.add(listener);
-	}
-	
-	
-	/**
-	 * Remove a state change listener.
-	 * 
-	 * @param listener
-	 *          The listener.
-	 */
-	public void removeStateListener(StateListener listener) {
-		stateListeners.remove(listener);
-	}
-	
-	
-	/**
-	 * Add a time-out listener.
-	 * 
-	 * @param listener
-	 *          The listener.
-	 */
-	public void addTimeoutListener(TimeoutListener listener) {
-		timeoutListeners.add(listener);
-	}
-	
-	
-	/**
-	 * Remove a time-out listener.
-	 * 
-	 * @param listener
-	 *          The listener.
-	 */
-	public void removeTimeoutListener(TimeoutListener listener) {
-		timeoutListeners.remove(listener);
-	}
-	
-	
-	/**
-	 * Returns an estimate of the elapsed time, in seconds.
-	 * 
-	 * @return The elapsed time.
-	 */
-	public int getElapsed() {
-		return time - remaining;
-	}
-	
-	
-	/**
-	 * Set the timeout for the timer, in seconds.
-	 * 
-	 * @param seconds
-	 *          The number of seconds on the timer.
-	 * @throws IllegalStateException
-	 *          If {@link #canSet()} is <code>false</code>.
-	 */
-	public void set(int seconds) throws IllegalStateException {
-		switch (state) {
-		case Initial:
-		case Ready:
-			time = seconds;
-			remaining = time;
-			break;		
-		default:
-			throw new IllegalStateException();
-		}
-		enter(State.Ready);
-		
-		repaint();
-	}
-	
-	
-	/**
-	 * Returns <code>true</code> if set can be called. Set cannot be called when
-	 * the timer is running or paused.
-	 * 
-	 * @return <code>true</code> if set can be called.
-	 */
-	public boolean canSet() {
-		switch (state) {
-		case Initial:
-		case Ready:
-			return true;
-		}
-		return false;
-	}
-	
-	
-	/**
-	 * Start the timer. A new thread will control the timer count-down, so this
-	 * method returns once it has started.
-	 * 
-	 * @throws IllegalStateException
-	 *           If {@link #canStart()} is <code>false</code>.
-	 */
-	public void start() throws IllegalStateException {
-		switch (state) {
-		case Ready:
-			ticker = new Ticker(this, 1000);
-			ticker.start();
-			break;
-		case Paused:
-			ticker.resume();
-			break;
-		default:
-			throw new IllegalStateException();
-		}
-		
-		enter(State.Running);
-		
-		repaint();
-	}
-	
-	
-	/**
-	 * Returns <code>true</code> if start can be called. Start cannot be called
-	 * when the timer is in it's initial or running state.
-	 * 
-	 * @return <code>true</code> if start can be called.
-	 */
-	public boolean canStart() {
-		switch (state) {
-		case Ready:
-		case Paused:
-			return true;
-		}
-		return false;
-	}
-	
-	
-	/**
-	 * Pause the count-down. Temporarily suspends the count-down thread.
-	 * 
-	 * @throws IllegalStateException
-	 *           If {@link #canPause()} is <code>false</code>.
-	 */
-	public void pause() throws IllegalStateException {
-		switch (state) {
-		case Running:
-			ticker.pause();
-			break;
-		case Paused:
-			break;
-		default:
-			throw new IllegalStateException();
-		}
-		
-		enter(State.Paused);
-		
-		repaint();
-	}
-	
-	
-	/**
-	 * Returns <code>true</code> if pause can be called. Pause cannot be called
-	 * when the timer is in it's initial or ready state.
-	 * 
-	 * @return <code>true</code> if pause can be called.
-	 */
-	public boolean canPause() {
-		switch (state) {
-		case Running:
-		case Paused:
-			return true;
-		}
-		return false;
-	}
-	
-	
-	/**
-	 * Reset the timer. Causes the timer to stop and return to the ready
-	 * state, reseting the time-out to the last one set.
-	 * 
-	 * @throws IllegalStateException
-	 *           If {@link #canReset()} is <code>false</code>.
-	 */
-	public void reset() throws IllegalStateException {
-		switch (state) {
-		case Ready:
-			break;
-		case Running:
-		case Paused:
-			ticker.stop();
-			ticker = null;
-			remaining = time;
-			break;
-		default:
-			throw new IllegalStateException();
-		}
-		
-		enter(State.Ready);
-		
-		repaint();
-	}
-	
-	
-	/**
-	 * Returns <code>true</code> if reset can be called. Reset cannot be called
-	 * when the timer is in it's initial state.
-	 * 
-	 * @return <code>true</code> if reset can be called.
-	 */
-	public boolean canReset() {
-		switch (state) {
-		case Ready:
-		case Running:
-		case Paused:
-			return true;
-		}
-		return false;
-	}
-	
-	
-	/**
-	 * Clear the timer. Returns the timer to its initial state, stopping
-	 * it if necessary.
-	 */
-	public void clear() {
-		switch (state) {
-		case Initial:
-			break;
-		case Ready:
-			time = 0;
-			remaining = 0;
-			break;
-		case Running:
-		case Paused:
-			ticker.stop();
-			ticker = null;
-			remaining = 0;
-			time = 0;
-			break;
-		}
-		
-		enter(State.Initial);
-		
-		repaint();
-	}
-	
-	
-	/**
-	 * Returns <code>true</code> if clear can be called.
-	 * 
-	 * @return Always returns <code>true</code>.
-	 */
-	public boolean canClear() {
-		return true;
-	}
-	
-	
-	/**
-	 * Tell the timer to repaint itself.
-	 */
-	public void repaint() {
-		if (!canvas.isDisposed()) {
-			canvas.redraw();
-		}
-	}
-	
-	
-	/**
-	 * Called at each ticker tick interval. Should not be invoked by clients.
-	 */
-	public void tick(final TickerEvent evt) {
-		if (canvas.isDisposed()) {
-			// Widget is disposed, ignore timer events
-			return;
-		}
-		
-		long elapsed = evt.getElapsed();
-		int remaining = time - (int) (elapsed / 1000); 
-		
-		if (remaining <= 0) {
-			// We're done
-			this.remaining = 0;
-			
-			// Stop and nullify ticker
-			if (ticker != null) {
-				ticker.stopLater();
-				ticker = null;
-			}
-			
-			// Enqueue the ui update the event dispatch thread
-			canvas.getDisplay().asyncExec(new Runnable() {
-				public void run() {
-					enter(State.Initial);
-					
-					// repaint
-					repaint();
-					
-					// fire timeout event
-					fireTimeoutEvent();
-				}
-			});
-		
-		} else if (this.remaining != remaining) {
-		
-			// Update remaining 
-			this.remaining = remaining;
-			
-			// Enqueue a repaint
-			canvas.getDisplay().asyncExec(new Runnable() {
-				public void run() {
-					// repaint
-					repaint();
-				}
-			});
-		}
-	}
-	
-	
-	/**
-	 * Enter the given state.
-	 * 
-	 * @param state The state.
-	 */
-	private void enter(State state) {
-		if (this.state != state) {
-			this.state = state;
-			fireStateChanged();
-		}
-	}
-	
-	
-	/**
-	 * Fires a state changed event.
-	 */
-	private void fireStateChanged() {
-		if (!stateListeners.isEmpty()) {
-			StateEvent evt = new StateEvent(this);
-			for (StateListener s : stateListeners) {
-				s.stateChanged(evt);
-			}
-		}
-	}
-
-
-	/**
-	 * Sends a timeout event to listeners.
-	 */
-	private void fireTimeoutEvent() {
-		if (!timeoutListeners.isEmpty()) {
-			TimeoutEvent evt = new TimeoutEvent(this);
-			for (TimeoutListener t : timeoutListeners) {
-				t.timeoutOccured(evt);
-			}
-		}
-	}
-	
-	
-	/**
-	 * Paints the timer.
-	 * 
-	 * @param gc
-	 *          The graphics context.
-	 */
-	private void paint(GC gc) {
-		gc.setFont(getTimerFont());
-		
-		int ss = remaining % 60;
-		int mm = (remaining % 3600) / 60;
-		int hh = remaining / 3600;
-		
-		String timestr = formatTime(ss, mm, hh);
-		
-		Point t = getStringDimensions(gc, timestr);
-		Point c = getCanvasDimension();
-		
-		int x = c.x / 2 - t.x / 2;
-		int y = c.y / 2 - t.y / 2;
-		
-		if (remaining < 20 && state != State.Initial) {
-			gc.setForeground(getWarningColor());
-		} else {
-			gc.setForeground(getTimerColor());
-		}
-		
-		gc.drawString(timestr, x, y);
-	}
-	
-
-	/**
-	 * Tidies native resources. Called automatically.
-	 */
-	private void dispose() {
-		if (font != null) {
-			font.dispose();
-			font = null;
-		}
-	}
-	
-	
-	/**
-	 * Formats a time string.
-	 */
-	private String formatTime(int ss, int mm, int hh) {
-		String timestr;
-		if (hh == 0) {
-			timestr = String.format("%02d:%02d", mm, ss);
-		} else {
-			timestr = String.format("%02d:%02d:%02d", hh, mm, ss);
-		}
-		return timestr;
-	}
-	
-	
-	/**
-	 * Returns the dimensions of a given string as drawn with the current font on
-	 * the given graphics context.
-	 */
-	private static Point getStringDimensions(GC gc, String str) {
-		int x = 0;
-		for (int i = 0; i < str.length(); i++) {
-			x += gc.getAdvanceWidth(str.charAt(i));
-		}
-		int y = gc.getFontMetrics().getHeight();
-		return new Point(x,y);
-	}
-	
-	
-	/**
-	 * Returns the dimensions of the canvas as a point.
-	 * 
-	 * @return A point where x is the width and y is the height.
-	 */
-	private Point getCanvasDimension() {
-		Rectangle bounds = canvas.getBounds();
-		return new Point(bounds.width, bounds.height);
-	}
-	
-
-	private Color getWarningColor() {
-		return getSystemColor(SWT.COLOR_RED);
-	}
-	
-	
-	private Color getTimerColor() {
-		return getSystemColor(SWT.COLOR_DARK_BLUE);
-	}
-	
-	
-	private Font getTimerFont() {
-		if (font == null) {
-			font = new Font(canvas.getDisplay(), "Sans", 30, SWT.NONE);
-		}
-		return font;
-	}
-	
-	
-	private Color getSystemColor(int id) {
-		return canvas.getDisplay().getSystemColor(id);
-	}
-
-	public static void main(String[] args) {
-		Display display = new Display();
-		Shell shell = new Shell(display, SWT.SHELL_TRIM);
-		shell.setBounds(800, 100, 220, 200);
-		shell.setLayout(new FillLayout());
-		
-		SwtTimer timer = new SwtTimer(shell, SWT.NONE);
-		timer.set(120);
-		timer.start();
-		
-		shell.open();
-		while (!shell.isDisposed()) {
-			if (!display.readAndDispatch()) {
-				display.sleep();
-			}
-		}
-		display.dispose();
-	}
-	
-}
diff --git a/image_annotation/src/ie/dcu/apps/ist/widgets/Ticker.java b/image_annotation/src/ie/dcu/apps/ist/widgets/Ticker.java
deleted file mode 100644
index c2d48ab..0000000
--- a/image_annotation/src/ie/dcu/apps/ist/widgets/Ticker.java
+++ /dev/null
@@ -1,246 +0,0 @@
-package ie.dcu.apps.ist.widgets;
-
-import ie.dcu.apps.ist.event.*;
-
-
-public class Ticker implements Runnable {
-	private final TickerListener listener;
-	
-	private Thread thread   = null;
-	private boolean pause   = false;
-	private boolean stop    = false; 
-	private long napTime    = 100;
-	private long interval   = 1000;
-	private long elapsed    = 0;
-	private long startTime  = 0;
-	private long pausedTime = 0;
-	
-	// State variables
-	private boolean paused  = false;
-	private boolean stopped = true;
-	
-	public Ticker(TickerListener listener) {
-		
-		// Check listener
-		if (listener == null) {
-			throw new IllegalArgumentException();
-		}
-		
-		this.listener = listener;
-	}
-	
-	
-	public Ticker(TickerListener listener, long interval) {
-		
-		// Check listener
-		if (listener == null) {
-			throw new IllegalArgumentException();
-		}
-		
-		// Check interval
-		if (interval < 0) {
-			throw new IllegalArgumentException();
-		}
-		
-		// Assign
-		this.listener = listener;
-		this.interval = interval;
-		this.napTime  = interval / 10;
-	}
-	
-	
-	public synchronized long elapsed() {
-		return elapsed;
-	}
-	
-	
-	public void start() {
-		if (thread != null) {
-			throw new IllegalStateException("Cannot restart threads");
-		}
-		thread = new Thread(this, "TimerThread");
-		thread.start();
-	}
-	
-	
-	public void run() {
-		
-		synchronized (this) {
-			stopped = false;
-		}
-		
-		// Set start time
-		startTime = System.currentTimeMillis();
-		
-		// Loop
-		while (true) {
-			
-			// Yawn! Z Z z z z Z Z Z z z z Z Z Z ...
-			sleep(napTime);
-			
-			// Wait while thread is paused
-			synchronized (this) {
-				if (pause) {
-					
-					// Remember when pausing started
-					long now = System.currentTimeMillis();
-					
-					// Set paused flag to true and notify
-					paused = true;
-					notifyAll();
-					
-					// Wait until woken up
-					while (paused) doWait();
-					
-					// Add duration we've been paused for
-					pausedTime += System.currentTimeMillis() - now;
-					
-					// Clear pause flag && notify
-					pause = false;
-					notifyAll();
-				}
-			}
-			
-			// Check for stop flag
-			synchronized (this) {
-				if (stop) {
-					stopped = true;
-					notifyAll();
-					break;
-				}
-			}
-			
-			// HI-HO-HI-HO ...
-			
-			work();
-		}
-	}
-	
-	
-	private void work() { 
-		boolean event = false;
-		
-		synchronized (this) {
-			// Calculate total elapsed time in milliseconds
-			long now = System.currentTimeMillis();
-			long elapsed = now - (startTime + pausedTime); 
-			
-			// Calculate time elapsed since last event
-			long sinceLast = elapsed - this.elapsed;
-			if (interval <= sinceLast) {
-				
-				// Compensate for any difference
-				long diff = sinceLast - interval;
-				
-				// Its time for another event
-				this.elapsed = elapsed - diff;
-				
-				// Fire event flag
-				event = true;
-			}
-		}
-		
-		// Do event
-		if (event) {
-			synchronized (listener) {
-				listener.tick(new TickerEvent(this, elapsed));
-			}
-		}
-	}
-
-
-	public void pause() {
-		// Pause running thread
-		synchronized (this) {
-			pause = true;
-			
-			// Wait for pause to occur
-			while (!paused) doWait();
-		}
-	}
-	
-	
-	public void resume() {
-		// Wake up paused threads
-		synchronized (this) {
-			if (paused) {
-				paused = false;
-				notifyAll();
-			}
-			
-			while (pause) doWait();
-		}
-	}
-	
-	
-	public boolean isPaused() {
-		synchronized (this) {
-			return paused;
-		}
-	}
-	
-	
-	public void stop() {
-		
-		synchronized (this) {
-			
-			// Resume paused threads
-			if (paused) {
-				paused = false;
-				notifyAll();
-			}
-			
-			while (pause) doWait();
-			
-			// Stop
-			stop = true;
-			
-			// Wait until stop block reached
-			while (!stopped) doWait();
-		}
-	}
-	
-	
-	public void stopLater() {
-		synchronized (this) {
-			
-			// Resume paused threads
-			if (paused) {
-				paused = false;
-				notifyAll();
-			}
-			
-			while (pause) doWait();
-			
-			// Stop
-			stop = true;
-		}
-	}
-	
-	
-	public boolean isStopped() {
-		synchronized (this) {
-			return stopped;
-		}
-	}
-	
-	
-	private void sleep(long millis) {
-		try {
-			Thread.sleep(millis);
-		} catch (InterruptedException e) {
-			// Ignore
-		}
-	}
-	
-	
-	private void doWait() {
-		try {
-			wait();
-		} catch (InterruptedException e) {
-			// ignore
-		}
-	}
-}
-
-