moved files to top level

src/main/assembly/assembly.xml

@@ -0,0 +1,54 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" 
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+  
+  
+    <id>bin</id>
+    <!-- Generates a zip package containing the needed files -->
+    <formats>
+        <format>zip</format>
+    </formats>
+
+    <!-- Adds dependencies to zip package under lib directory -->
+    <dependencySets>
+        <dependencySet>
+            <outputDirectory>lib</outputDirectory>
+            <unpack>false</unpack>
+        </dependencySet>
+    </dependencySets>
+
+    <fileSets>
+        <!--  Adds startup scripts to the root directory of zip package -->
+        <fileSet>
+        	<fileMode>0755</fileMode>
+            <directory>src/main/assembly/bin</directory>
+            <outputDirectory>bin</outputDirectory>
+            <includes>
+                <include>*</include>
+            </includes>
+        </fileSet>
+        <!-- <fileSet>
+        	<directory>src/main/assembly/www</directory>
+            <outputDirectory>www</outputDirectory>
+            <includes>
+                <include>**/*</include>
+            </includes>
+        </fileSet> -->
+        <!-- <fileSet>
+        	<fileMode>0755</fileMode>
+        	<directory>src/main/assembly/var</directory>
+            <outputDirectory>var</outputDirectory>
+            <includes>
+                <include>**/*</include>
+            </includes>
+        </fileSet> -->
+        <!-- adds jar package to the root directory of zip package -->
+        <!-- <fileSet>
+            <directory>target</directory>
+            <outputDirectory></outputDirectory>
+            <includes>
+                <include>*.jar</include>
+            </includes>
+        </fileSet> -->
+    </fileSets>
+</assembly>

src/main/assembly/bin/convert

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ui.ConversionMain $ARGUMENTS

src/main/assembly/bin/scan

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS -cp $CLASSPATH ch.psi.fda.ui.RemoteAcquisitionMain $ARGUMENTS

src/main/assembly/bin/scan_local

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS -cp $CLASSPATH ch.psi.fda.ui.AcquisitionMain $ARGUMENTS

src/main/assembly/bin/server

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+
+#HUB_BASE=$BASEDIR/../
+#export HUB_BASE
+java $VM_ARGUMENTS -cp $CLASSPATH -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties ch.psi.fda.rest.FdaServer $ARGUMENTS

src/main/assembly/bin/viewer

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ui.VisualizationZMQMain $ARGUMENTS

src/main/assembly/bin/visualize

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ui.VisualizationMain $ARGUMENTS

src/main/assembly/www/css/main.css

@@ -0,0 +1,22 @@
+
+
+/* ==========================================================================
+   Author's custom styles
+   ========================================================================== */
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

src/main/assembly/www/index.html

@@ -0,0 +1,222 @@
+<!DOCTYPE html>
+<!--[if lt IE 7]>      <html class="no-js lt-ie9 lt-ie8 lt-ie7"> <![endif]-->
+<!--[if IE 7]>         <html class="no-js lt-ie9 lt-ie8"> <![endif]-->
+<!--[if IE 8]>         <html class="no-js lt-ie9"> <![endif]-->
+<!--[if gt IE 8]><!-->
+<html class="no-js">
+<!--<![endif]-->
+<head>
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
+<title></title>
+<meta name="description" content="">
+<meta name="viewport" content="width=device-width">
+
+<link rel="stylesheet" href="css/bootstrap.min.css">
+<style>
+body {
+	padding-top: 60px;
+	padding-bottom: 40px;
+}
+</style>
+<link rel="stylesheet" href="css/bootstrap-responsive.min.css">
+<link rel="stylesheet" href="css/main.css">
+
+<script src="js/vendor/modernizr-2.6.2-respond-1.1.0.min.js"></script>
+<script src="js/jquery-2.0.0.min.js"></script>
+<script type='text/javascript'>
+	var base = '../hub';
+	var stream;
+
+	function getVersion() {
+		$.get(base+'/version', function(data) {
+			$('#version').empty();
+			$('#version').append(data)
+		});
+	}
+	
+	function getBeamlines() {
+		$.get(base, function(data) {
+			/* update beamlines selection */
+			
+			$('#selectionBeamline').empty();
+			for (var i in data){
+				beamline = data[i];
+				$('#selectionBeamline').append('<option value="'+beamline+'">'+beamline+'</option>')
+			}
+			/* $('#selectionBeamline')[0].selectedIndex=0; */
+			connectStream(data[0]);
+		});
+	}
+	
+	function updateKeys(beamline, keys){
+		keytag = $('#beamlineKeys');
+		keytag.empty();
+		table='<table class="table table-hover"><thead><tr><td>Key</td><td>Value</td></tr></thead><tbody>';
+		
+		for(k in keys){
+			table=table+'<tr><td>'+k+'</td><td>'+
+			'<div class="input-append">'+
+			'<input type="text" value="'+keys[k]+'" onchange="setKey(\''+beamline+'\',\''+k+'\',$(this).val())">'+
+			//'<button class="btn" type="button" onclick="setKey(\''+beamline+'\',\''+k+'\',$(this).prev().val())">Update</button>'+
+			'<button class="btn" type="button" onclick="deleteKey(\''+beamline+'\',\''+k+'\')">Delete</button>'+
+			'</div>'+
+			'</td></tr>';
+		}
+		
+		table = table+'<tr>'+
+			'<td><input id="keyToAdd" type="text" placeholder="Key"></td>'+
+			'<td><div class="input-append">'+
+			'<input id="valueToAdd"type="text" placeholder="Value">'+
+			'<button class="btn" type="button" onclick="setKey(\''+beamline+'\',$(\'#keyToAdd\').val(),$(\'#valueToAdd\').val())">Add</button>'+
+			'</div></td>'+
+			'</tr>';
+		
+		table = table+'</table></tbody>';
+		keytag.append(table);
+	}
+
+	function connectStream(beamline) {
+		closeStream();
+		stream = new EventSource(base + '/' + beamline + '/stream');
+		stream.onmessage = function(event) {
+			keys=JSON.parse(event.data)
+			updateKeys(beamline, keys);
+			
+		};
+		getKeys(beamline);
+	}
+
+	function closeStream() {
+		try {
+			stream.close();
+		} catch (e) {
+		}
+	}
+	
+	function getKeys(beamline){
+		$.get(base+'/'+beamline+'/keys', function(data) {
+			updateKeys(beamline, data );
+		});
+	}
+	
+	function setKey(beamline, key, value){
+		$.ajax({
+		    url: base+'/'+beamline+'/keys/'+key,
+		    type: 'PUT',
+		    data: value,
+		    success: function(result) {
+		    }
+		});
+	}
+	
+	function deleteKey(beamline, key){
+		$.ajax({
+		    url: base+'/'+beamline+'/keys/'+key,
+		    type: 'DELETE',
+		    success: function(result) {
+		    }
+		});
+	}
+	
+	function addBeamline(beamline){
+		getKeys(beamline); /*create beamline*/
+		getBeamlines();
+	}
+	
+	function deleteBeamline(beamline){
+		$.ajax({
+		    url: base+'/'+beamline,
+		    type: 'DELETE',
+		    success: function(result) {
+		    	getBeamlines(); /* Update beamline list */
+		    }
+		});
+		
+	}
+	
+</script>
+</head>
+<body>
+	<!-- <script>
+        var source = new EventSource('../server-sent-events/');
+        source.onmessage = function(e) {
+        	$('#messagefield') = e.data;
+        };
+        </script> -->
+
+	<!--[if lt IE 7]>
+            <p class="chromeframe">You are using an <strong>outdated</strong> browser. Please <a href="http://browsehappy.com/">upgrade your browser</a> or <a href="http://www.google.com/chromeframe/?redirect=true">activate Google Chrome Frame</a> to improve your experience.</p>
+        <![endif]-->
+
+	<!-- This code is taken from http://twitter.github.com/bootstrap/examples/hero.html -->
+
+	<div class="navbar navbar-inverse navbar-fixed-top">
+		<div class="navbar-inner">
+			<div class="container">
+				<a class="btn btn-navbar" data-toggle="collapse"
+					data-target=".nav-collapse"> <span class="icon-bar"></span> <span
+					class="icon-bar"></span> <span class="icon-bar"></span>
+				</a> <a class="brand" href="#">hub</a>
+			</div>
+		</div>
+	</div>
+
+	<div class="container">
+
+		<!-- Main hero unit for a primary marketing message or call to action -->
+		<!-- <div class="hero-unit">
+			<p>This is the central Hub administration page ...</p>
+		</div> -->
+
+		<!-- Example row of columns -->
+		<div class="row">
+			<div class="span5">
+				<h2>Key Group</h2>
+				<div>
+					<select id="selectionBeamline">
+						<!-- <option value="sydney">Sydney</option> -->
+					</select>
+				</div>
+				<div id="beamlineKeys"></div>
+			</div>
+		</div>
+		<div class="row">
+			<div class="span5">
+				<h2>Key Group Management</h2>
+				<div class="input-append">
+					  <input class="span2" id="appendedInputButton" placeholder="Key Group" type="text">
+					  <button id="addBeamlineBtn" class="btn" type="button" onclick="addBeamline($(this).prev().val());$(this).prev().val('')">Add</button>
+					  <button id="addBeamlineBtn" class="btn" type="button" onclick="deleteBeamline($(this).prev().prev().val());$(this).prev().prev().val('')">Delete</button>
+				</div>
+			</div>
+		</div>
+
+		<hr>
+
+		<footer>
+			<p>Hub - Version <span id='version'></span> - &copy; Paul Scherrer Institute 2013</p>
+		</footer>
+
+	</div>
+	<!-- /container -->
+
+	<script>
+		/* update beamlines */
+		getVersion();
+		getBeamlines();
+		$('#selectionBeamline').change(function(){connectStream($('#selectionBeamline').val())});
+	</script>
+
+	
+	<script>
+		window.jQuery
+				|| document
+						.write('<script src="js/vendor/jquery-1.9.1.min.js"><\/script>')
+	</script>
+
+	<script src="js/vendor/bootstrap.min.js"></script>
+
+	<script src="js/main.js"></script>
+</body>
+</html>

src/main/assembly/www/js/main.js

@@ -0,0 +1 @@
+

src/main/java/ch/psi/fda/deserializer/DataDeserializer.java

@@ -0,0 +1,24 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.deserializer;
+
+public interface DataDeserializer {
+	public void read();
+}

src/main/java/ch/psi/fda/deserializer/DataDeserializerMDA.java

@@ -0,0 +1,589 @@
+package ch.psi.fda.deserializer;
+
+import hep.io.xdr.XDRInputStream;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+
+/**
+ * Deserializer MDA file
+ * TODO Need to be optimized as currently the while file is read into memory when creating this object.
+ */
+public class DataDeserializerMDA implements DataDeserializer {
+
+	private static Logger logger = Logger.getLogger(DataDeserializerMDA.class.getName());
+	
+	private EventBus bus;
+	private RecursiveReturnContainer c;
+	
+	public DataDeserializerMDA(EventBus b, File file){
+		this.bus = b;
+		
+		try{
+		c = read(new FileInputStream(file));
+		} catch (FileNotFoundException e) {
+			throw new RuntimeException(e);
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
+	}
+	
+	private RecursiveReturnContainer read(InputStream in) throws IOException {
+		logger.fine("Read MDA input stream");
+		
+		XDRInputStream x = new XDRInputStream(in);
+		
+		
+		/**
+		 * Read file header
+		 */
+		float version = x.readFloat();
+		logger.fine("MDA - version:: "+version);
+		int scanNumber = x.readInt();
+		logger.fine("MDA - scan number:: "+scanNumber);
+		int rank = x.readInt();
+		logger.fine("MDA - rank:: "+rank);
+		
+		for(int i=rank;i>0; i--){
+			// Read dimension size
+			int dimension = x.readInt();
+			logger.fine("MDA - dimension["+i+"] :: "+dimension);
+		}
+		
+		int isRegular = x.readInt(); //(true=1, false=0)
+		logger.fine("MDA - isRegular:: "+isRegular);
+		int pExtra = x.readInt(); // Number of extra pvs
+		logger.fine("MDA - pExtra:: "+pExtra);
+		
+		
+		/**
+		 * Read data
+		 */
+		RecursiveReturnContainer container = readData(x);
+		
+		/**
+		 * Read extra PVs
+		 */
+		if(pExtra > 0){
+			int length;
+			logger.fine("Extra PVs");
+
+			int numExtra = x.readInt();
+			logger.fine("MDA - number of extra pvs:: "+numExtra);
+
+			for(int i = 0;i<numExtra; i++){
+
+				length = x.readInt();
+				if(length > 0){
+					String pvName = x.readString();
+					logger.fine("MDA - pv name:: "+pvName);
+				}
+
+				length = x.readInt();
+				if(length > 0){
+					String pvDescription = x.readString(); // description
+					logger.fine("MDA - pv desciption:: "+pvDescription);
+				}
+				
+				int pvType = x.readInt();
+				logger.fine("MDA - pv type:: "+pvType);
+
+				
+				int pvCount = 0;
+				String pvUnit;
+				if(pvType != 0){ // if pv type != DBR_STRING
+					pvCount = x.readInt();
+					logger.fine("MDA - pv count:: "+pvCount);
+					length = x.readInt();
+					if(length > 0){
+						pvUnit = x.readString();
+						logger.fine("MDA - pv unit:: "+ pvUnit);
+					}
+				}
+				
+				
+				if(pvType == 0){ // pvType == DBR_STRING
+					length = x.readInt();
+					if(length > 0){
+						String pvValue = x.readString();
+						logger.fine("MDA - pv value:: "+pvValue);
+					}
+				}
+				else if(pvType == 32){ // pvType == DBR_CTRL_CHAR
+					for(int u=0;u<pvCount; u++){
+						char pvValue = x.readChar();
+						logger.fine("MDA - pv value:: "+pvValue);
+					}
+				}
+				else if(pvType == 29){ // pvType == DBR_CTRL_SHORT
+					for(int u=0;u<pvCount; u++){
+						int pvValue = x.readInt();
+						logger.fine("MDA - pv value:: "+pvValue);
+					}
+				}
+				else if(pvType == 33){ // pvType == DBR_CTRL_LONG
+					for(int u=0;u<pvCount; u++){
+						int pvValue = x.readInt();
+						logger.fine("MDA - pv value:: "+pvValue);
+					}
+				}
+				else if(pvType == 30){ // pvType == DBR_CTRL_FLOAT
+					for(int u=0;u<pvCount; u++){
+						float pvValue = x.readFloat();
+						logger.fine("MDA - pv value:: "+pvValue);
+					}
+				}
+				else if(pvType == 34){ // pvType == DBR_CTRL_DOUBLE
+					for(int u=0;u<pvCount; u++){
+						double pvValue = x.readDouble();
+						logger.fine("MDA - pv value:: "+pvValue);
+					}
+				}
+				
+			}
+		}
+		
+		logger.fine("Reading and conversion done ...");
+		
+		return container;
+	}
+
+	
+	private RecursiveReturnContainer readData(XDRInputStream x) throws IOException {
+		
+		int length;
+		
+		logger.fine("Read scan");
+		
+		/**
+		 * Read scan header
+		 */
+		int scanRank = x.readInt();
+		logger.fine("MDA - scan rank (this):: " + scanRank);
+		int npts = x.readInt();
+		logger.fine("MDA - number of requested points (npts):: " + npts);
+		int currentPoint = x.readInt();
+		logger.fine("MDA - current point:: " + currentPoint);
+
+		// Read pointers to lower scans
+		if(scanRank > 1){
+ 			// For 1D scans this block is never reached
+			for(int i=0;i<npts;i++){
+				int pointerLowerScans = x.readInt(); // pointer to lower scans
+				logger.fine("MDA - pointer lower scans:: "+pointerLowerScans);
+			}
+		}
+		
+		
+		/**
+		 * Read scan info
+		 */
+		length = x.readInt();
+		if(length > 0){
+			String scanName = x.readString();
+			logger.fine("MDA - scanName:: "+scanName);
+		}
+
+		length = x.readInt();
+		if(length > 0){
+			String scanTime = x.readString(); // timestamp
+			logger.fine("MDA - scanTime:: "+ scanTime);
+		}
+
+		
+		int numberOfPositioners = x.readInt();
+		logger.fine("MDA - number of positioners:: "+numberOfPositioners);
+		int numberOfDetectors = x.readInt();
+		logger.fine("MDA - number of detectors:: "+ numberOfDetectors);
+		int numberOfTriggers = x.readInt();
+		logger.fine("MDA - number of triggers:: "+ numberOfTriggers);
+		
+
+		List<Metadata> componentMetadataList = new ArrayList<>();
+		/**
+		 * Read positioners metadata
+		 */
+		for(int i = 0; i<numberOfPositioners; i++){
+			
+			logger.fine("Read positioner metadata");
+			
+			int positionerNumber = x.readInt();
+			logger.fine("MDA - positioner number:: "+positionerNumber);
+
+			length = x.readInt();
+			if(length>0){
+				String positionerName = x.readString();
+				logger.fine("MDA - positioner name:: "+positionerName);
+				// MDA starts at dimension number 1 we start at 0
+				componentMetadataList.add(new Metadata(positionerName,scanRank-1));
+			}
+
+			length = x.readInt();
+			if(length > 0){
+				String positionerDescription = x.readString();
+				logger.fine("MDA - positioner description:: "+positionerDescription);
+			}
+
+			length = x.readInt();
+			if(length > 0){
+				String positionerStepMode = x.readString();
+				logger.fine("MDA - positioner step mode:: "+positionerStepMode);
+			}
+
+			length = x.readInt();
+			if(length > 0){
+				String positionerUnit = x.readString();
+				logger.fine("MDA - positioner unit:: "+positionerUnit);
+			}
+
+			length = x.readInt();
+			if(length > 0){
+				String readbackName = x.readString();
+				logger.fine("MDA - readback name:: "+readbackName);
+			}
+
+			length = x.readInt();
+			if(length > 0){
+				String readbackDescription = x.readString();
+				logger.fine("MDA - readback description:: "+readbackDescription);
+			}
+
+			length = x.readInt();
+			if(length > 0){
+				String readbackUnit = x.readString();
+				logger.fine("MDA - readback unit:: "+readbackUnit);
+			}
+		}
+
+		/**
+		 * Read detector metadata
+		 */
+		for(int i=0; i<numberOfDetectors; i++){
+			logger.fine("Read detector metadata");
+			
+			int detectorNumber = x.readInt();
+			logger.fine("MDA - detector number:: "+ detectorNumber);
+			
+			length = x.readInt();
+			if(length > 0){
+				String detectorName = x.readString();
+				logger.fine("MDA - detector name:: "+detectorName);
+				// MDA starts at dimension number 1 we start at 0
+				componentMetadataList.add(new Metadata(detectorName, scanRank-1));
+			}
+
+			length = x.readInt();
+			if(length > 0){
+				String detectorDescription = x.readString();
+				logger.fine("MDA - detector description:: "+detectorDescription);
+			}
+
+			length = x.readInt();
+			if(length > 0){
+				String detectorUnit = x.readString();
+				logger.fine("MDA - detector unit:: "+detectorUnit);
+			}
+		}
+
+		/**
+		 * Read trigger metadata
+		 */
+		for(int i=0; i<numberOfTriggers; i++){
+			logger.fine("Read trigger metadata");
+			
+			int triggerNumber = x.readInt();
+			logger.fine("MDA - trigger number:: "+triggerNumber);
+
+			length = x.readInt();
+			if(length > 0){
+				String triggerName = x.readString();
+				logger.fine("MDA - trigger name:: "+triggerName);
+			}
+
+			float triggerCommand = x.readFloat();
+			logger.fine("MDA - trigger command:: "+triggerCommand);
+		}
+		
+		
+		ArrayList<Double[]> data = new ArrayList<Double[]>();
+		
+		/**
+		 * Read positioner data (readback)
+		 */
+		for(int i = 0; i<numberOfPositioners; i++){
+			
+			logger.fine("Read positioner data");
+			
+			Double[] pdata = new Double[npts]; 
+
+			StringBuffer b = new StringBuffer();
+			b.append("[ ");
+			for(int t=0; t<npts; t++){
+				pdata[t]=x.readDouble();
+				b.append(pdata[t]+" ");
+			}
+			b.append("]");
+			logger.fine("MDA - positioner "+b.toString());
+			
+			data.add(pdata);
+		}
+
+		
+		/**
+		 * Read detector data
+		 */
+		for(int i=0; i<numberOfDetectors; i++){
+			logger.fine("Read detector data");
+			Double[] pdata = new Double[npts];
+			
+			StringBuffer b = new StringBuffer();
+			b.append("[ ");
+			for(int t=0; t<npts; t++){
+				pdata[t] = new Double(x.readFloat());
+				b.append(pdata[t]+" ");
+			}
+			b.append("]");
+			logger.fine("MDA - detector "+b.toString());
+			
+			data.add(pdata);
+		}
+		
+		logger.fine("Read scan done ...");
+		
+		
+		RecursiveReturnContainer cont = new RecursiveReturnContainer();
+		// Update component metadata
+		cont.getMetadata().addAll(componentMetadataList);
+		
+		if(scanRank > 1){
+			/**
+			 * Conversion logic if scan rank is > 1
+			 */
+			
+			/**
+			 * Read all scans recursively
+			 */
+			for(int i=0;i<npts;i++){
+				
+				// Recursive call
+				RecursiveReturnContainer container = readData(x);
+				
+				if(i==0){
+					// For the first scan of each dimension component data is read and stored
+					cont.getMetadata().addAll(container.getMetadata());
+				}
+				
+				logger.fine("Convert data structure [rank="+scanRank+"] ...");
+				for(Message m: container.getMessage()){
+					if(m instanceof DataMessage){
+						// Add own data to message and pass it to container
+						DataMessage mm = new DataMessage(new ArrayList<Metadata>()); // Workaround
+						for(Double[] d: data){
+							mm.getData().add(d[i]);
+						}
+						mm.getData().addAll(((DataMessage) m).getData());
+						cont.getMessage().add(mm);
+					}
+					else if(m instanceof StreamDelimiterMessage){
+						// Just pass message to own container
+						cont.getMessage().add(m);
+					}
+				}
+				
+				logger.fine("Conversion done [rank="+scanRank+"]");
+			}
+			
+			// Add dimension delimiter message
+			StreamDelimiterMessage m = new StreamDelimiterMessage(scanRank);
+			cont.getMessage().add(m);
+		}
+		else{
+			/**
+			 * Conversion logic if scan rank is 1
+			 */
+			
+			logger.fine("Convert data structure [rank="+scanRank+"]...");
+			
+			for(int t = 0; t<npts ; t++){
+				DataMessage m = new DataMessage(new ArrayList<Metadata>()); // workaround
+				for(Double[] d: data){
+					m.getData().add(d[t]);
+				}
+				cont.getMessage().add(m);
+			}
+			
+			// Add dimension delimiter message
+			StreamDelimiterMessage m = new StreamDelimiterMessage(scanRank);
+			cont.getMessage().add(m);
+			
+			
+			logger.fine("Conversion done [rank="+scanRank+"]");
+		}
+				
+		return(cont);
+		
+	}
+	
+	@Override
+	public void read() {
+		// Add data to queue
+		for(Message m: c.getMessage()){
+			if(m instanceof DataMessage){
+				DataMessage dm = (DataMessage)m;
+				dm.getMetadata().addAll(c.getMetadata()); // WORKAROUND !!!! ideally the reference to metadata is set while creating the
+				// data message. Then there would be only one list with one reference. In this case we now have multiple lists!
+			}
+			bus.post(m);
+		}
+		bus.post(new EndOfStreamMessage());
+	}
+}
+
+class RecursiveReturnContainer{
+	private List<Message> message = new ArrayList<Message>();
+	private List<Metadata> metadata = new ArrayList<>();
+	
+	public List<Message> getMessage() {
+		return message;
+	}
+	public List<Metadata> getMetadata() {
+		return metadata;
+	}
+}
+
+/**
+*
+* http://www.aps.anl.gov/bcda/synApps/sscan/saveData_fileFormat.txt
+* 
+* scan file format
+
+* FILE HEADER
+* 	xdr_float:	VERSION  (1.3)
+* 	xdr_long:	scan number
+* 	xdr_short	data's rank
+* 	xdr_vector(rank, xdr_int) dims;
+* 	xdr_int		isRegular (true=1, false=0)			
+* 	xdr_long:	pointer to the extra pvs
+* 
+* 
+* SCAN
+* 	HEADER:
+* 	xdr_short:		this scan's rank
+* 	xdr_long:		number of requested points (NPTS)
+* 	xdr_long:		current point (CPT)
+* 	if the scan rank is > 1
+* 	  xdr_vector(NPTS, xdr_long)	pointer to the lower scans
+* 
+* 	INFO:
+* 	xdr_counted_string:	scan name
+* 	xdr_counted_string:	time stamp
+* 
+* 
+* 	xdr_int:		number of positioners
+* 	xdr_int:		number of detectors
+* 	xdr_int:		number of triggers
+* 
+* 	for each positioner
+* 	  xdr_int:		positioner number
+* 	  xdr_counted_string:	positioner name
+* 	  xdr_counted_string:	positioner desc
+* 	  xdr_counted_string:	positioner step mode
+* 	  xdr_counted_string:	positioner unit
+* 	  xdr_counted_string:	readback name
+* 	  xdr_counted_string:	readback description
+* 	  xdr_counted_string:	readback unit
+* 
+* 	for each detector
+* 	  xdr_int:		detector number
+* 	  xdr_counted_string:	detector name
+* 	  xdr_counted_string:	detector desc
+* 	  xdr_counted_string:	detector unit
+* 
+* 	for each trigger
+* 	  xdr_int:		trigger number
+* 	  xdr_counted_string:	trigger name
+* 	  xdr_float:		trigger command
+* 
+* 	DATA:
+* 	for each positioner
+* 	  xdr_vector(NPTS, xdr_double):	readback array
+* 
+* 	for each detector
+* 	  xdr_vector(NPTS, xdr_float):	detector array
+* 
+* [SCAN]
+* ...
+* ...
+* ...
+* [SCAN]
+* 
+* EXTRA PVs
+* 	xdr_int:	number of extra pvs
+* 
+* 	for each pv
+* 	  xdr_counted_string:	name
+* 	  xdr_counted_string:	desc
+* 	  xdr_int:		type
+* 	  if type != DBR_STRING
+* 	    xdr_long:		count
+* 	    xdr_counted_string:	unit
+* 
+* 	  depending on the type:
+* 	    DBR_STRING:
+* 		xdr_counted_string:		value
+* 	    DBR_CTRL_CHAR:
+* 		xdr_vector(count, xdr_char):	value
+* 	    DBR_CTRL_SHORT:
+* 		xdr_vector(count, xdr_short):	value
+* 	    DBR_CTRL_LONG:
+* 		xdr_vector(count, xdr_long):	value
+* 	    DBR_CTRL_FLOAT:
+* 		xdr_vector(count, xdr_float):	value
+* 	    DBR_CTRL_DOUBLE:
+* 		xdr_vector(count, xdr_double):	value
+* -----------------------------------------------------------------------
+* 
+* A 1D scan looks like this:
+* 
+* header
+* extra PV's
+* 
+* A 2D scan looks like this
+* 
+* header
+* scan2
+* 	scan1
+* 	scan1
+* 	...
+* extra PV's
+* 
+* A 3D scan looks like this
+* 
+* header
+* scan3
+* 	scan2
+* 		scan1
+* 		scan1
+* 		...
+* 	scan2
+* 		scan1
+* 		scan1
+* 		...
+* 	...
+* extra PV's
+* 
+*/

src/main/java/ch/psi/fda/deserializer/DataDeserializerTXT.java

@@ -0,0 +1,205 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.deserializer;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+
+/**
+ * Deserializer for text files
+ */
+public class DataDeserializerTXT implements DataDeserializer {
+	
+	private static Logger logger = Logger.getLogger(DataDeserializerTXT.class.getName());
+
+	private EventBus bus;
+	private List<Metadata> metadata;
+	private File file;
+	
+	private List<Integer> dindex;
+	private List<Integer> iindex;
+	
+	public DataDeserializerTXT(EventBus b, File file){
+		this.bus = b;
+		this.file = file;
+		this.dindex = new ArrayList<Integer>();
+		this.iindex = new ArrayList<Integer>();
+		
+		
+		this.metadata = new ArrayList<>();
+		try{
+			// Read metadata
+			// Open file
+			BufferedReader reader = new BufferedReader(new FileReader(file));
+			
+			// Read file
+			String line;
+			
+			// First line is id
+			line = reader.readLine();
+			line = line.replaceAll("^ *# *", "");
+			String[] ids = line.split("\t");
+			
+			// Second line dimension
+			line = reader.readLine();
+			line = line.replaceAll("^ *# *", "");
+			String[] dimensions = line.split("\t");
+			
+			// Create data message metadata
+			Integer d = -1;
+			for(int i=0;i<ids.length;i++){
+				Integer dimension = Integer.parseInt(dimensions[i]);
+				metadata.add(new Metadata(ids[i], dimension));
+				
+				// Store the first index of the first component
+				// in each dimension ...
+				if(!d.equals(dimension)){
+					logger.finest("Add component index: "+i);
+					dindex.add(dimension);
+					iindex.add(i);
+					d=dimension;
+				}
+			}
+			
+			// Close file
+			reader.close();
+		}
+		catch(Exception e){
+			throw new RuntimeException("Unable to read file metadata and initialize data queue",e);
+		}
+	}
+	
+	@Override
+	public void read() {
+		try{
+			
+			List<Double> checklist = new ArrayList<Double>(dindex.size());
+			for(int i=0;i<dindex.size();i++){
+				checklist.add(null);
+			}
+			
+			// Open file
+			BufferedReader reader = new BufferedReader(new FileReader(file));
+			
+			// Read file
+			String line;
+			while((line=reader.readLine())!=null){
+			
+				// Ignore empty lines
+				if(line.matches("^ *$")){
+					continue;
+				}
+				
+				// Ignore comment lines
+				if(line.matches("^ *# *.*")){
+					continue;
+				}
+
+				// Create and populate new data message
+				String[] data = line.split("\t");
+				DataMessage message = new DataMessage(metadata);
+				for (String d : data) {
+					// Remove spaces at the end and beginning of the value
+					d = d.trim();
+					
+					// If the String does not contains spaces we assume that it is a double
+					if (! d.contains(" ")) {
+						// Scalar value
+
+						Object value;
+						try {
+							value = new Double(d);
+						} catch (NumberFormatException e) {
+							// We treat it as a String
+							// TODO Need to find a way to treat other data formats
+							value = d;
+						}
+
+						// Add data to message
+						message.getData().add(value);
+					} else {
+						try {
+							// If the string contains spaces we treat it as an array
+							String[] values = d.split(" ");
+							double[] dv = new double[values.length];
+							for (int i = 0; i < values.length; i++) {
+								dv[i] = new Double(values[i]);
+							}
+							// Add data to message
+							message.getData().add(dv);
+						} catch (NumberFormatException e) {
+							// Workaround
+							// TODO Need to find a way to treat the array if it is not a double array
+							message.getData().add(new Object());
+						}
+					}
+
+				}
+				
+				// Check whether to issue a end of dimension control message
+				for(int t=0;t<iindex.size();t++){
+					Integer i = iindex.get(t);
+					if(dindex.get(t)>0){
+						Double d = (Double) message.getData().get(i);
+						if(checklist.get(i)!=null &&!checklist.get(i).equals(d)){
+							// If value changes issue a dimension delimiter message
+							bus.post(new StreamDelimiterMessage(dindex.get(t)-1));
+						}
+						checklist.set(i, d);
+					}
+				}
+				
+				// Put message to queue
+				bus.post(message);
+				
+				// TODO Need to detect dimension boundaries
+			
+			}
+			
+			// Add delimiter for all the dimensions
+			for(int i=dindex.size()-1;i>=0;i--){
+				bus.post(new StreamDelimiterMessage(dindex.get(i)));
+			}
+
+			// Place end of stream message
+			bus.post(new EndOfStreamMessage());
+			
+			// Close file
+			reader.close();
+			
+		} catch (IOException e) {
+			throw new RuntimeException("Data deserializer had a problem reading the specified datafile",e);
+		}
+		
+	}
+	
+}

src/main/java/ch/psi/fda/gui/ProgressPanel.java

@@ -0,0 +1,75 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+/*
+ * ScanProgressPanel.java
+ *
+ * Created on Dec 1, 2009, 2:20:26 PM
+ */
+
+package ch.psi.fda.gui;
+
+import java.awt.event.ActionListener;
+
+public class ProgressPanel extends javax.swing.JPanel {
+
+	private static final long serialVersionUID = 1L;
+	
+	private javax.swing.JButton abortButton;
+    private javax.swing.JProgressBar progressBar;
+	
+    /** Creates new form ScanProgressPanel */
+    public ProgressPanel() {
+        initComponents();
+    }
+
+    /** 
+     * This method is called from within the constructor to
+     * initialize the form.
+     */
+    private void initComponents() {
+
+        progressBar = new javax.swing.JProgressBar();
+        abortButton = new javax.swing.JButton();
+
+        progressBar.setIndeterminate(true);
+        progressBar.setPreferredSize(new java.awt.Dimension(100, 24));
+
+        abortButton.setText("Abort");
+        abortButton.setFocusable(false);
+        abortButton.setPreferredSize(new java.awt.Dimension(70, 25));
+
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
+        this.setLayout(layout);
+        layout.setHorizontalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(progressBar, javax.swing.GroupLayout.DEFAULT_SIZE, 152, Short.MAX_VALUE)
+                    .addComponent(abortButton, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addContainerGap())
+        );
+        layout.setVerticalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(layout.createSequentialGroup()
+                .addContainerGap()
+                .addComponent(progressBar, javax.swing.GroupLayout.PREFERRED_SIZE, 18, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addComponent(abortButton, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+        );
+    }
+
+    public void addActionListener(ActionListener l){
+    	abortButton.addActionListener(l);
+    }
+    
+    public void done(){
+    	progressBar.setIndeterminate(false);
+        progressBar.setValue(100);
+        abortButton.setEnabled(false);
+    }
+}

src/main/java/ch/psi/fda/gui/ScrollableFlowPanel.java

@@ -0,0 +1,64 @@
+package ch.psi.fda.gui;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Rectangle;
+
+import javax.swing.JPanel;
+import javax.swing.Scrollable;
+import javax.swing.SwingConstants;
+
+public class ScrollableFlowPanel extends JPanel implements Scrollable {
+
+	private static final long serialVersionUID = 1L;
+
+	@Override
+	public void setBounds(int x, int y, int width, int height) {
+		super.setBounds(x, y, getParent().getWidth(), height);
+	}
+
+	@Override
+	public Dimension getPreferredSize() {
+		return new Dimension(getWidth(), getPreferredHeight());
+	}
+
+	@Override
+	public Dimension getPreferredScrollableViewportSize() {
+		return super.getPreferredSize();
+	}
+
+	@Override
+	public int getScrollableUnitIncrement(Rectangle visibleRect, int orientation, int direction) {
+		int hundredth = (orientation == SwingConstants.VERTICAL ? getParent().getHeight() : getParent().getWidth()) / 100;
+		return (hundredth == 0 ? 1 : hundredth);
+	}
+
+	@Override
+	public int getScrollableBlockIncrement(Rectangle visibleRect, int orientation, int direction) {
+		return orientation == SwingConstants.VERTICAL ? getParent().getHeight() : getParent().getWidth();
+	}
+
+	@Override
+	public boolean getScrollableTracksViewportWidth() {
+		return true;
+	}
+
+	@Override
+	public boolean getScrollableTracksViewportHeight() {
+		return false;
+	}
+
+	private int getPreferredHeight() {
+		int rv = 0;
+		for (int k = 0, count = getComponentCount(); k < count; k++) {
+			Component comp = getComponent(k);
+			Rectangle r = comp.getBounds();
+			int height = r.y + r.height;
+			if (height > rv)
+				rv = height;
+		}
+		rv += ((FlowLayout) getLayout()).getVgap();
+		return rv;
+	}
+}

src/main/java/ch/psi/fda/rest/ExecutionEngine.java

@@ -0,0 +1,152 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.CancellationException;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.inject.Inject;
+import javax.ws.rs.WebApplicationException;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.jcae.ChannelService;
+
+/**
+ * Main engine for data acquisition.
+ */
+public class ExecutionEngine {
+	
+	private static final Logger logger = Logger.getLogger(ExecutionEngine.class.getName());
+	
+	private final ChannelService cService;
+	private final ZMQDataService zmqService;
+	
+	private final ExecutorService eservice = Executors.newSingleThreadExecutor();
+	private final Map<String, JobEntry> erequests = new HashMap<>();
+	
+	@Inject
+	public ExecutionEngine(ChannelService cService, ZMQDataService zmqService) {
+		this.zmqService = zmqService;
+		this.cService = cService;
+	}
+	
+	/**
+	 * Submit a scan to be executed. This will generate an execution request which is
+	 * enqueued in the execution queue.
+	 * 
+	 * @param trackingId Tracking id
+	 * @param edescriptor	Edescriptor
+	 */
+	public void submit(String trackingId, EDescriptor edescriptor){
+
+		logger.info("Submitting job with trackingId ----" + trackingId);
+		if(erequests.keySet().contains(trackingId) && !erequests.get(trackingId).getFuture().isDone()){ // Allow finished tracking ids to be reused for new tasks
+			throw new IllegalArgumentException("A request with tracking ID "+trackingId+" is already submitted");
+		}
+		
+		ExecutionJob job = new ExecutionJob(cService, zmqService, trackingId, edescriptor);
+		Future<?> future = eservice.submit(job);
+		erequests.put(trackingId, new JobEntry(future, job));
+	}
+	
+	
+	public void terminateAll() {
+		logger.info("Terminate all jobs");
+		Set<String> keys = new HashSet<String>();
+		keys.addAll(erequests.keySet());
+		for(String trackingId: keys){
+			try{
+				terminate(trackingId);
+			}
+			catch(Exception e){
+				logger.log(Level.WARNING, "", e);
+			}
+		}
+	}
+	
+	/**
+	 * Terminate the request which is identified by its tracking id. If the request
+	 * is still in the execution queue it gets removed there.
+	 * 
+	 * @param trackingId	Tracking ID
+	 */
+	public void terminate(String trackingId){
+		logger.info("Terminate TrackingId: "+trackingId);
+		
+		if(!erequests.containsKey(trackingId)){
+			throw new WebApplicationException("There is no request for tracking id "+trackingId, 404);
+		}
+		
+		final JobEntry f = erequests.get(trackingId);
+		f.getFuture().cancel(true);
+		f.getJob().stop();
+		
+		
+		try{
+			f.getFuture().get(10, TimeUnit.SECONDS);
+		}
+		catch(CancellationException | InterruptedException | ExecutionException | TimeoutException e){
+			// Nothing to be done here
+			throw new WebApplicationException("Unable to terminate job");
+		}
+		
+		erequests.remove(trackingId);
+	}
+
+	public boolean isActive(String trackingId) {
+		logger.info("Checking whether trackingId "+trackingId+" is active.");
+		if(!erequests.containsKey(trackingId)){
+			throw new IllegalArgumentException("There is no request for tracking id "+trackingId);
+		}
+		
+		Future<?> f = erequests.get(trackingId).getFuture();
+		return !f.isDone();
+	}
+	
+	/**
+	 * Wait for the termination of the scan request
+	 * @param trackingId Tracking ID
+	 * @throws ExecutionException -
+	 * @throws InterruptedException -
+	 */
+	public void wait(String trackingId) throws InterruptedException, ExecutionException{
+		logger.info("Waiting for termination for trackingId "+trackingId);
+		if(!erequests.containsKey(trackingId)){
+			throw new IllegalArgumentException("There is no request for tracking id "+trackingId);
+		}
+		
+		Future<?> f = erequests.get(trackingId).getFuture();
+		if(f==null){
+			throw new IllegalArgumentException("There is no request for tracking id "+trackingId);
+		}
+		f.get();
+		logger.info("TrackingId "+trackingId+" terminated");
+	}
+}

src/main/java/ch/psi/fda/rest/ExecutionJob.java

@@ -0,0 +1,106 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest;
+
+import java.util.ServiceLoader;
+import java.util.logging.Logger;
+
+import ch.psi.fda.EContainer;
+import ch.psi.fda.EContainerFactory;
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.jcae.ChannelService;
+
+import com.google.common.eventbus.EventBus;
+import com.google.inject.Guice;
+import com.google.inject.Injector;
+
+/**
+ * "Wrapper" around the execution container. Depending on the edescriptor this class takes care of loading the
+ * correct execution container. It also takes care of all common stuff described in the edescriptor like 
+ * streaming for plotting, etc.
+ */
+public class ExecutionJob implements Runnable {
+
+	private static final Logger logger = Logger.getLogger(ExecutionJob.class.getName());
+
+	private final ChannelService cService;
+	private final ZMQDataService zmqService;
+
+	private final String trackingId;
+	private final EDescriptor edescriptor;
+
+	private EventBus ebus;
+	
+	private EContainer econtainer = null;
+	
+	public ExecutionJob(ChannelService cService, ZMQDataService zmqService, String trackingId, EDescriptor edescriptor) {
+		this.zmqService = zmqService;
+		this.cService = cService;
+		this.trackingId = trackingId;
+		this.edescriptor = edescriptor;
+	}
+
+	@Override
+	public void run() {
+
+		 
+		try {
+
+			logger.info("Execute ----" + trackingId);
+
+			ebus = new EventBus();
+			
+			// Configure ZMQ streaming service and attach it to event bus
+			zmqService.setTrackingId(trackingId);
+			// TODO e.g. set some filters on what is streamed
+			// TODO stream a metadata message on what is streamed via the zmq service
+			ebus.register(zmqService);
+
+
+			Injector injector = Guice.createInjector(new InjectionModule(cService));
+
+			ServiceLoader<EContainerFactory> factories = ServiceLoader.load(EContainerFactory.class);
+	        for (EContainerFactory factory : factories) {
+	        	if(factory.supportsEDescriptor(edescriptor)){
+	        		injector.injectMembers(factory);
+	        		econtainer = factory.getEContainer(edescriptor, ebus);
+	        		break;
+	        	}
+	        }
+			
+        	econtainer.initialize();
+        	econtainer.execute();
+	        
+			logger.info("Done ----" + trackingId);
+
+		} finally {
+			ebus.unregister(zmqService);
+			if(econtainer!=null){
+				econtainer.destroy();
+			}
+			econtainer=null;
+		}
+	}
+	
+	public void stop(){
+		if(econtainer!=null){
+			econtainer.abort();
+		}
+	}
+}

src/main/java/ch/psi/fda/rest/FdaServer.java

@@ -0,0 +1,112 @@
+package ch.psi.fda.rest;
+
+import java.io.IOException;
+import java.net.InetAddress;
+import java.net.URI;
+import java.util.concurrent.CountDownLatch;
+import java.util.logging.Logger;
+
+import javax.ws.rs.core.UriBuilder;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpServerFactory;
+import org.glassfish.jersey.jackson.JacksonFeature;
+import org.glassfish.jersey.server.ResourceConfig;
+import org.glassfish.grizzly.http.server.HttpServer;
+import org.glassfish.grizzly.http.server.StaticHttpHandler;
+
+import ch.psi.fda.ui.ApplicationConfigurator;
+import sun.misc.Signal;
+import sun.misc.SignalHandler;
+
+@SuppressWarnings("restriction")
+public class FdaServer {
+	
+	private static final Logger logger = Logger.getLogger(FdaServer.class.getName());
+
+	public static void main(String[] args) throws IOException, ParseException {
+
+		int port = 8080;
+		String hostname = InetAddress.getLocalHost().getHostName();
+
+		Options options = new Options();
+		options.addOption("h", false, "Help");
+		options.addOption("p", true, "Server port (default: "+port+")");
+		options.addOption("s", true, "Server address (default: "+hostname+")");
+
+		GnuParser parser = new GnuParser();
+		CommandLine line = parser.parse(options, args);
+
+		if (line.hasOption("p")) {
+			port = Integer.parseInt(line.getOptionValue("p"));
+		}
+		if (line.hasOption("s")) {
+			hostname = line.getOptionValue("s");
+		}
+		if (line.hasOption("h")) {
+			HelpFormatter f = new HelpFormatter();
+			f.printHelp("fda", options);
+			return;
+		}
+
+		// set the correct environment variable based on ch.psi.fda.home variable
+		ApplicationConfigurator ac = new ApplicationConfigurator();
+		ac.initializeApplication();
+		
+		URI baseUri = UriBuilder.fromUri("http://" + hostname + "/").port(port).build();
+
+		ResourceBinder binder = new ResourceBinder();
+		
+		ResourceConfig resourceConfig = new ResourceConfig();
+		resourceConfig.packages(FdaServer.class.getPackage().getName()+".services"); // Services are located in services package
+		resourceConfig.register(binder);
+		
+		resourceConfig.register(JacksonFeature.class);
+		
+		HttpServer server = GrizzlyHttpServerFactory.createHttpServer(baseUri, resourceConfig);
+
+		// Static content
+		String home = System.getenv("FDA_BASE");
+		if (home == null) {
+			home = "src/main/assembly";
+		}
+		home = home + "/www";
+		server.getServerConfiguration().addHttpHandler(new StaticHttpHandler(home), "/static");
+		logger.info(String.format("Management interface available at %sstatic/", baseUri));
+
+		
+		logger.info("Server started");
+		logger.info("Use ctrl+c to stop ...");
+
+		// Signal handling
+		final CountDownLatch latch = new CountDownLatch(1);
+		Signal.handle(new Signal("INT"), new SignalHandler() {
+			public void handle(Signal sig) {
+				if(latch.getCount()==0){
+					logger.info("Terminate broker by System.exit()");
+					System.exit(1); // Terminate program after 2 ctrl+c 
+				}
+				latch.countDown();
+			}
+		});
+
+		// Wait for termination, i.e. wait for ctrl+c
+		try {
+			latch.await();
+		} catch (InterruptedException e) {
+		}
+		
+		server.shutdownNow();
+		logger.info("Server terminated");
+		
+		// Destroy global resources
+		binder.destroy();
+		
+		// Using System.exit() to ensure that JVM is going down
+		System.exit(0);
+	}
+}

src/main/java/ch/psi/fda/rest/InjectionModule.java

@@ -0,0 +1,21 @@
+package ch.psi.fda.rest;
+
+import ch.psi.jcae.ChannelService;
+
+import com.google.inject.AbstractModule;
+
+public class InjectionModule extends AbstractModule{
+
+	private ChannelService cservice;
+	public InjectionModule(ChannelService cservice){
+		this.cservice = cservice;
+	}
+	
+	@Override
+	protected void configure() {
+		bind(ChannelService.class).toInstance(cservice);
+	}
+	
+	
+
+}

src/main/java/ch/psi/fda/rest/JobEntry.java

@@ -0,0 +1,21 @@
+package ch.psi.fda.rest;
+
+import java.util.concurrent.Future;
+
+public class JobEntry {
+
+	private final Future<?> future;
+	private final ExecutionJob job;
+	
+	public JobEntry(Future<?> future, ExecutionJob job){
+		this.future=future;
+		this.job=job;
+	}
+
+	public Future<?> getFuture() {
+		return future;
+	}
+	public ExecutionJob getJob() {
+		return job;
+	}
+}

src/main/java/ch/psi/fda/rest/ResourceBinder.java

@@ -0,0 +1,34 @@
+package ch.psi.fda.rest;
+
+
+
+import javax.inject.Singleton;
+
+import org.glassfish.hk2.utilities.binding.AbstractBinder;
+
+import ch.psi.jcae.ChannelService;
+import ch.psi.jcae.impl.DefaultChannelService;
+
+public class ResourceBinder extends AbstractBinder {
+
+	private ChannelService channelService = new DefaultChannelService();
+	private ZMQDataService zmqService = new ZMQDataService(10000);
+	
+    @Override
+    protected void configure() {
+    	bind(channelService).to(ChannelService.class);
+    	bind(ExecutionEngine.class).to(ExecutionEngine.class).in(Singleton.class);
+    	bind(zmqService).to(ZMQDataService.class);
+    }
+    
+    /**
+     * Destroy the allocated global resource.
+     * Resources destroyed are:
+     * - ChannelService
+     * - ZMQDataService
+     */
+    public void destroy(){
+    	channelService.destroy();
+    	zmqService.terminate();
+    }
+}

src/main/java/ch/psi/fda/rest/ZMQDataService.java

@@ -0,0 +1,101 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.ObjectOutputStream;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.zeromq.ZMQ;
+
+import ch.psi.fda.messages.Message;
+
+import com.google.common.eventbus.Subscribe;
+
+/**
+ * Service to stream out messages via ZMQ
+ */
+public class ZMQDataService {
+	
+	private static final Logger logger = Logger.getLogger(ZMQDataService.class.getName());
+	
+	private final int bufferSize = 5;
+	private final int port;
+	
+	private ZMQ.Context context;
+	private ZMQ.Socket socket;
+	
+	private String trackingId;
+	
+	public ZMQDataService(int port){
+		this.port = port;
+		initialize();
+	}
+
+	public void initialize(){
+		context = ZMQ.context(1);
+//		zmq.ZError.clear(); // Clear error code
+		socket = context.socket(ZMQ.PUB);
+		socket.setHWM(bufferSize);
+		socket.bind("tcp://*:"+port);
+	}
+	
+	public void terminate(){
+		socket.close();
+		context.term();
+//		zmq.ZError.clear(); // Clear error code
+	}
+	
+	@Subscribe
+	public void onMessage(Message m) {
+//		logger.fine(m.toString());
+		socket.sendMore("{\"htype\": [\"fda-2.1\"], \"trackingId\":\"" + trackingId + "\"}");
+		try (
+				ByteArrayOutputStream b = new ByteArrayOutputStream(); 
+				ObjectOutputStream o = new ObjectOutputStream(b);
+			) {
+			o.writeObject(m);
+			socket.send(b.toByteArray());
+		} catch (IOException e) {
+			logger.log(Level.WARNING, "Unable to serialize message", e);
+		}
+	}
+	
+	// TODO Need to revive this
+//	@Subscribe
+//	public void onMessage(List<Visualization> vis){
+//		logger.fine("Sending plotting filters");
+//		socket.sendMore("{\"htype\": [\"fda-plot-2.1\"], \"trackingId\":\"" + trackingId + "\"}");
+//		try (
+//				ByteArrayOutputStream b = new ByteArrayOutputStream(); 
+//				ObjectOutputStream o = new ObjectOutputStream(b);
+//			) {
+//			o.writeObject(vis);
+//			socket.send(b.toByteArray());
+//		} catch (IOException e) {
+//			logger.log(Level.WARNING, "Unable to serialize message", e);
+//		}
+//	}
+	
+	public void setTrackingId(String id){
+		trackingId = id;
+	}
+}

src/main/java/ch/psi/fda/rest/services/EDescriptorJAXBContextProvider.java

@@ -0,0 +1,52 @@
+package ch.psi.fda.rest.services;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.ServiceLoader;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.ws.rs.ext.ContextResolver;
+import javax.ws.rs.ext.Provider;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+
+import ch.psi.fda.DescriptorProvider;
+import ch.psi.fda.edescriptor.EDescriptor;
+
+/**
+ * JAXB Context Provider for the EDescriptor class
+ * This class registers all implementations of the EDescriptor interfaces to the context
+ */
+@Provider
+ public class EDescriptorJAXBContextProvider implements ContextResolver<JAXBContext> {
+	private static final Logger logger = Logger.getLogger(EDescriptorJAXBContextProvider.class.getName());
+	
+	List<Class<?>> classes = new ArrayList<>();
+	
+	public EDescriptorJAXBContextProvider(){
+		classes.add(EDescriptor.class);
+		ServiceLoader<DescriptorProvider> providers = ServiceLoader.load(DescriptorProvider.class);
+        for (DescriptorProvider provider : providers) {
+        	classes.add(provider.getEDescriptorClass());
+        }
+	}
+	
+     private JAXBContext context = null;
+ 
+     public JAXBContext getContext(Class<?> type) {
+         if(type != EDescriptor.class){
+             return null; // No support for other classes than EDescriptor
+         }
+ 
+         if(context == null) {
+             try {
+                 context = JAXBContext.newInstance(classes.toArray(new Class[]{}));
+             } catch (JAXBException e) {
+            	 
+				logger.log(Level.WARNING, "Unable to create JAXB Context", e);
+             }
+         }
+         return context;
+     }
+}

src/main/java/ch/psi/fda/rest/services/ExecutionService.java

@@ -0,0 +1,80 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.rest.services;
+
+import java.util.concurrent.ExecutionException;
+import java.util.logging.Logger;
+
+import javax.inject.Inject;
+import javax.ws.rs.Consumes;
+import javax.ws.rs.DELETE;
+import javax.ws.rs.GET;
+import javax.ws.rs.PUT;
+import javax.ws.rs.Path;
+import javax.ws.rs.PathParam;
+import javax.ws.rs.core.MediaType;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.fda.rest.ExecutionEngine;
+
+@Path("fda")
+public class ExecutionService {
+	
+	private static final Logger logger = Logger.getLogger(ExecutionService.class.getName());
+	
+	@Inject
+	private ExecutionEngine aengine;
+	
+	@PUT
+	@Path("{trackingId}")
+	@Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
+	public void execute(@PathParam("trackingId") String trackingId, EDescriptor edescriptor) throws InterruptedException{
+		logger.info("Submitting job with tracking id "+trackingId);
+		aengine.submit(trackingId, edescriptor);
+	}
+	
+	@DELETE
+	@Path("{trackingId}")
+	public void stop(@PathParam("trackingId") String trackingId){
+		logger.info("Stopping job with tracking id "+trackingId);
+		aengine.terminate(trackingId);
+	}
+	
+	@DELETE
+	public void terminateAll(){
+		logger.info("Terminate all jobs");
+		aengine.terminateAll();
+	}
+	
+	@GET
+	@Path("{trackingId}/running")
+	public boolean isActive(@PathParam("trackingId") String trackingId){
+		logger.info("Check whether job with tracking id "+trackingId+" is running");
+		return aengine.isActive(trackingId);
+	}
+	
+	@GET
+	@Path("{trackingId}/done")
+	public void wait(@PathParam("trackingId") String trackingId) throws InterruptedException, ExecutionException{
+		logger.info("Wait for job with tracking id "+trackingId+" to be finished");
+		aengine.wait(trackingId);
+	}
+	
+}

src/main/java/ch/psi/fda/serializer/SerializerMAT.java

@@ -0,0 +1,163 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.serializer;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.google.common.eventbus.Subscribe;
+import com.jmatio.io.MatFileWriter;
+import com.jmatio.types.MLArray;
+import com.jmatio.types.MLDouble;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+
+/**
+ * Serialize data received by a DataQueue into a Matlab file
+ */
+public class SerializerMAT {
+	
+	private File file;
+	
+	private boolean appendSuffix = false;
+	private boolean first = true;
+	
+	/**
+	 * Construtor
+	 * @param file	Name of the Matlab file to serialize the data to
+	 */
+	public SerializerMAT(File file){
+		this.file = file;
+	}
+
+	File outfile;
+	List<List<Object>> dlist;
+	List<Class<?>> clist;
+	
+	private List<Metadata> metadata;	
+	@Subscribe
+	public void onMessage(Message message) {
+		try {
+
+			
+
+			if (message instanceof DataMessage) {
+				DataMessage m = (DataMessage) message;
+
+				// Initialize list
+				if (first) {
+					first = false;
+					
+					this.metadata = m.getMetadata();
+					
+					// WORKAROUND BEGIN
+					if (appendSuffix) {
+						// Append a count suffix to the file. If there is already a
+						// file with
+						// this suffix increase the counter for the suffix
+						int cnt = 0;
+						String fname = this.file.getAbsolutePath(); // Determine
+																	// file name
+						String extension = fname.replaceAll("^.*\\.", ""); // Determine
+																			// extension
+						fname = fname.replaceAll("\\." + extension + "$", "");
+
+						outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+
+						while (outfile.exists()) {
+							cnt++;
+							outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+						}
+					} else {
+						outfile = this.file;
+					}
+					// WORKAROUND END
+
+					// Transposed data list
+					dlist = new ArrayList<List<Object>>();
+					clist = new ArrayList<Class<?>>();
+
+					for (Object o : m.getData()) {
+						dlist.add(new ArrayList<Object>());
+						clist.add(o.getClass());
+					}
+				}
+
+				// Put data into data list
+				for (int i = 0; i < m.getData().size(); i++) {
+					Object object = m.getData().get(i);
+					dlist.get(i).add(object);
+				}
+			} else if (message instanceof EndOfStreamMessage) {
+
+				// Create Matlab vectors
+				ArrayList<MLArray> matlablist = new ArrayList<MLArray>();
+				for (int t = 0; t < dlist.size(); t++) {
+					// Get component metadata
+					Metadata c = metadata.get(t);
+					c.getId();
+
+					List<Object> list = dlist.get(t);
+
+					if (clist.get(t).isArray()) {
+						// Array Handling
+					} else if (clist.get(t).equals(Double.class)) {
+						// Data is of type Double
+						MLDouble darray = new MLDouble(escapeString(c.getId()), (Double[]) list.toArray(new Double[list.size()]), 1);
+						matlablist.add(darray);
+					}
+
+				}
+
+				// Write Matlab file
+				MatFileWriter writerr = new MatFileWriter();
+				writerr.write(outfile, matlablist);
+			}
+
+		} catch (IOException e) {
+			throw new RuntimeException("Data serializer had a problem writing to the specified file", e);
+		}
+	}
+	
+	/**
+	 * Escape string to be Matlab key conform
+	 * @param value
+	 * @return	Escaped string value
+	 */
+	private String escapeString(String value){
+		
+		String evalue = value.replaceAll("-", "_");
+		evalue = evalue.replaceAll(":", "_");
+		evalue = evalue.replaceAll("\\.", "_");
+		evalue = evalue.replaceAll(" ", "_");
+		evalue = evalue.replaceAll("\\(", "_");
+		evalue = evalue.replaceAll("\\)", "_");
+		evalue = evalue.replaceAll("\\[", "_");
+		evalue = evalue.replaceAll("\\]", "_");
+		
+		return(evalue);
+	}
+	
+}

src/main/java/ch/psi/fda/serializer/SerializerMAT2D.java

@@ -0,0 +1,246 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.serializer;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import com.google.common.eventbus.Subscribe;
+import com.jmatio.io.MatFileWriter;
+import com.jmatio.types.MLArray;
+import com.jmatio.types.MLDouble;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+
+/**
+ * Serialize data received by a DataQueue into a Matlab file
+ */
+public class SerializerMAT2D {
+
+	private static final Logger logger = Logger.getLogger(SerializerMAT2D.class.getName());
+	
+	private File file;
+	private boolean appendSuffix = false;
+	
+	private boolean first = true;
+	
+	private List<List<List<Object>>> dlist;
+	private List<Class<?>> clist;
+	private int dsize;
+	private int dcount;
+	private Integer mindsize;
+	private File outfile;
+	
+	private List<Metadata> metadata;
+	
+	/**
+	 * @param file	Name of the Matlab file to serialize the data to
+	 */
+	public SerializerMAT2D(File file){
+		this.file = file;
+		
+		
+	}
+
+	@Subscribe
+	public void onMessage(Message message) {
+		try{
+				if(message instanceof DataMessage){
+					DataMessage m = (DataMessage) message;
+					
+					// Initialize list
+					if(first){
+						first=false;
+						
+						this.metadata = m.getMetadata();
+						
+						// Check if input queue does only hold 2D data
+						int maxdim=0;
+						for(Metadata me: metadata){
+							if(me.getDimension()>maxdim){
+								maxdim=me.getDimension();
+							}
+							
+							if(me.getDimension()>1){
+								throw new RuntimeException("Serializer does only support 2D data (XD data found)");
+							}
+						}
+						
+						if(maxdim<1){
+							throw new RuntimeException("Serializer does only support 2D data ("+maxdim+"D data found)");
+						}
+						
+						
+						// WORKAROUND BEGIN
+						if(appendSuffix){
+							// Append a count suffix to the file. If there is already a file with 
+							// this suffix increase the counter for the suffix
+							int cnt = 0;
+							String fname = this.file.getAbsolutePath(); // Determine file name
+							String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
+							fname = fname.replaceAll("\\."+extension+"$", "");
+							
+							outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+							
+							while(outfile.exists()){
+								cnt++;
+								outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+							}
+						}
+						else{
+							outfile = this.file;
+						}
+						// WORKAROUND END
+			
+						
+						// Transposed data list
+						dlist = new ArrayList<List<List<Object>>>();
+						clist = new ArrayList<Class<?>>();
+						dsize = 0; // Size of the dimension
+						dcount = 0;
+						mindsize = null;
+
+						for(Object o: m.getData()){
+							// TODO Create list of lists (for each line one list - to
+							// be able to fill up empty data points if there are some)
+							List<List<Object>> l = new ArrayList<List<Object>>();
+							l.add(new ArrayList<Object>());
+							dlist.add(l);
+							
+							clist.add(o.getClass());
+						}
+					}
+					
+					// Put data into data list
+					for(int i=0;i< m.getData().size();i++){
+						Object object = m.getData().get(i);
+						List<List<Object>> lo = dlist.get(i);
+						lo.get(lo.size()-1).add(object); // add data to latest list
+					}
+					
+					dcount++;
+				}
+				else if(message instanceof StreamDelimiterMessage){
+					StreamDelimiterMessage m = (StreamDelimiterMessage) message;
+					if(m.getNumber()==0){
+						// Determine minimum dimension size
+						if(dsize<dcount){
+							dsize=dcount;
+						}
+						
+						// Determine maximum dimension size
+						if(mindsize == null){
+							mindsize=dcount;
+						}
+						if(mindsize>dcount){
+							mindsize=dcount;
+						}
+						
+						// Add a new list for all component to the dlist
+						for(List<List<Object>> lo:dlist){
+							lo.add(new ArrayList<Object>());
+						}
+						
+						dcount=0;
+					}
+				}
+				
+				else if(message instanceof EndOfStreamMessage){
+				logger.info("dsize: "+dsize + " mindsize:"+mindsize);
+				
+				// Create Matlab vectors
+				ArrayList<MLArray> matlablist = new ArrayList<MLArray>();
+				logger.info("dlist size: "+dlist.size());
+				for(int t=0; t<dlist.size(); t++ ){
+					
+					// Get component metadata
+					Metadata c = metadata.get(t);
+					
+					// Combine all lists to one big list (pad if there are data points missing)
+					List<Object> list = new ArrayList<Object>();
+					List<List<Object>> ol = dlist.get(t);
+					
+					// Remove last array list as it is empty
+					ol.remove(ol.size()-1);
+					
+					for(List<Object> li: ol){
+						list.addAll(li);
+						// Pad list if there are missing data points for some lines
+						for(int i=li.size();i<dsize;i++){
+							logger.info("Pad data point: "+i);
+							list.add(Double.NaN);
+						}
+					}
+					
+					
+	//				List<Object> list = dlist.get(t);
+					logger.info("List: "+list.size());
+					
+					
+					if(clist.get(t).isArray()){
+						// Array Handling
+					}
+					else if(clist.get(t).equals(Double.class)){
+						// Data is of type Double
+						MLDouble darray = new MLDouble(escapeString(c.getId()),(Double[])list.toArray(new Double[list.size()]), dsize);
+						matlablist.add(darray);
+					}
+					
+					
+				}
+				
+				// Write Matlab file
+				MatFileWriter writerr = new MatFileWriter();
+				writerr.write(outfile, matlablist);
+			}
+			
+		} catch (IOException e) {
+			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
+		}
+		
+	}
+	
+	/**
+	 * Escape string to be Matlab key conform
+	 * @param value
+	 * @return	Escaped string value
+	 */
+	private String escapeString(String value){
+		
+		String evalue = value.replaceAll("-", "_");
+		evalue = evalue.replaceAll(":", "_");
+		evalue = evalue.replaceAll("\\.", "_");
+		evalue = evalue.replaceAll(" ", "_");
+		evalue = evalue.replaceAll("\\(", "_");
+		evalue = evalue.replaceAll("\\)", "_");
+		evalue = evalue.replaceAll("\\[", "_");
+		evalue = evalue.replaceAll("\\]", "_");
+		
+		return(evalue);
+	}
+	
+}

src/main/java/ch/psi/fda/serializer/SerializerMAT2DZigZag.java

@@ -0,0 +1,241 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.serializer;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.logging.Logger;
+
+import com.google.common.eventbus.Subscribe;
+import com.jmatio.io.MatFileWriter;
+import com.jmatio.types.MLArray;
+import com.jmatio.types.MLDouble;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+
+/**
+ * Serialize data received by a DataQueue into a Matlab file
+ */
+public class SerializerMAT2DZigZag {
+	
+	private static final Logger logger = Logger.getLogger(SerializerMAT2DZigZag.class.getName());
+	
+	private List<Metadata> metadata;
+	private File file;
+	private boolean appendSuffix = false;
+	private boolean first = true;
+	
+	private File outfile;
+	private List<List<Object>> dlist;
+	private List<List<Object>> dlistTmp;
+	private List<Class<?>> clist;
+	private int dsize; // Size of the dimension
+	private int dcount;
+	
+	private int delimiterCount;
+	
+	private boolean firstF;
+	private boolean firstC;
+	
+	/**
+	 * Construtor
+	 * @param file	Name of the Matlab file to serialize the data to
+	 */
+	public SerializerMAT2DZigZag(File file){
+		this.file = file;
+		
+		
+	}
+
+	@Subscribe
+	public void onMessage(Message message) {
+		try{
+			
+			
+			
+			
+				if(message instanceof DataMessage){
+					DataMessage m = (DataMessage) message;
+					
+					if(first){
+						first=false;
+						
+						this.metadata = m.getMetadata();
+						
+						// Check if input queue does only hold 2D data
+						int maxdim=0;
+						for(Metadata me: metadata){
+							if(me.getDimension()>maxdim){
+								maxdim=me.getDimension();
+							}
+							
+							if(me.getDimension()>1){
+								throw new RuntimeException("Serializer does only support 2D data (XD data found)");
+							}
+						}
+						
+						if(maxdim<1){
+							throw new RuntimeException("Serializer does only support 2D data ("+maxdim+"D data found)");
+						}
+						
+						// WORKAROUND BEGIN
+						if(appendSuffix){
+							// Append a count suffix to the file. If there is already a file with 
+							// this suffix increase the counter for the suffix
+							int cnt = 0;
+							String fname = this.file.getAbsolutePath(); // Determine file name
+							String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
+							fname = fname.replaceAll("\\."+extension+"$", "");
+							
+							outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+							
+							while(outfile.exists()){
+								cnt++;
+								outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+							}
+						}
+						else{
+							outfile = this.file;
+						}
+						// WORKAROUND END
+			
+						
+						// Transposed data list
+						dlist = new ArrayList<List<Object>>();
+						dlistTmp = new ArrayList<List<Object>>();
+						clist = new ArrayList<Class<?>>();
+						dsize = 0; // Size of the dimension
+						dcount = 0;
+						
+						delimiterCount = 0;
+						
+						firstF = true;
+						firstC = true;
+					}
+					
+					
+					if(firstC){
+						for(Object o: m.getData()){
+							dlist.add(new ArrayList<Object>());
+							clist.add(o.getClass());
+							firstC=false;
+						}
+					}
+					
+					// Initialize list
+					if(firstF){
+						for(int i=0;i<m.getData().size();i++){
+							dlistTmp.add(new ArrayList<Object>());
+						}
+						firstF=false;
+					}
+					
+					// Put data into data list
+					for(int i=0;i< m.getData().size();i++){
+						Object object = m.getData().get(i);
+						dlistTmp.get(i).add(object);
+					}
+					
+					dcount++;
+				}
+				else if(message instanceof StreamDelimiterMessage){
+					StreamDelimiterMessage m = (StreamDelimiterMessage) message;
+					if(m.getNumber()==0){
+						if(dsize<dcount){
+							dsize=dcount;
+						}
+						dcount=0;
+						
+						// Add temporary list to final list
+						for(int i=0;i<dlist.size();i++){
+							if(delimiterCount%2==1){
+								Collections.reverse(dlistTmp.get(i));
+							}
+							dlist.get(i).addAll(dlistTmp.get(i));
+						}
+						
+						dlistTmp.clear();
+						
+						firstF=true;
+						delimiterCount++;
+					}
+				}
+			
+			else if(message instanceof EndOfStreamMessage){
+				// Create Matlab vectors
+				ArrayList<MLArray> matlablist = new ArrayList<MLArray>();
+				logger.info("dlist size: "+dlist.size());
+				for(int t=0; t<dlist.size(); t++ ){
+					// Get component metadata
+					Metadata c = metadata.get(t);
+					
+					List<Object> list = dlist.get(t);
+					
+					if(clist.get(t).isArray()){
+						// Array Handling
+					}
+					else if(clist.get(t).equals(Double.class)){
+						// Data is of type Double
+						MLDouble darray = new MLDouble(escapeString(c.getId()),(Double[])list.toArray(new Double[list.size()]), dsize);
+						matlablist.add(darray);
+					}
+					
+					
+				}
+				
+				// Write Matlab file
+				MatFileWriter writerr = new MatFileWriter();
+				writerr.write(outfile, matlablist);
+			}
+			
+			
+		} catch (IOException e) {
+			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
+		}
+		
+	}
+	
+	/**
+	 * Escape string to be Matlab key conform
+	 * @param value
+	 * @return	Escaped string value
+	 */
+	private String escapeString(String value){
+		
+		String evalue = value.replaceAll("-", "_");
+		evalue = evalue.replaceAll(":", "_");
+		evalue = evalue.replaceAll("\\.", "_");
+		evalue = evalue.replaceAll(" ", "_");
+		evalue = evalue.replaceAll("\\(", "_");
+		evalue = evalue.replaceAll("\\)", "_");
+		evalue = evalue.replaceAll("\\[", "_");
+		evalue = evalue.replaceAll("\\]", "_");
+		
+		return(evalue);
+	}
+	
+}

src/main/java/ch/psi/fda/serializer/SerializerMDA.java

@@ -0,0 +1,375 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.serializer;
+
+import hep.io.xdr.XDRRandomAccessFile;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.logging.Logger;
+
+import com.google.common.eventbus.Subscribe;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+
+/**
+ * Serialize data received by a DataQueue
+ * 
+ * http://www.aps.anl.gov/bcda/synApps/sscan/saveData_fileFormat.txt
+ */
+public class SerializerMDA {
+	
+	private static final Logger logger = Logger.getLogger(SerializerMDA.class.getName());
+	
+	private File file;
+	
+	private boolean first = true;
+	
+	private List<Boolean> firstL;
+	private List<Boolean> takeData;
+	private List<Integer> dcountL;
+	private List<List<List<List<Double>>>> dimensionList;
+	private HashMap<Integer,List<Integer>> dMap;
+	private HashMap<Integer,List<String>> idMap;
+	private int numberOfDimensions;
+	
+	public SerializerMDA(File file){
+		this.file = file;
+	}
+
+	@Subscribe
+	public void onMessage(Message message) {
+			
+						
+			// Write data
+			// Read Message
+				if(message instanceof DataMessage){
+					DataMessage m = (DataMessage) message;
+					
+					
+					if(first){
+						first = false;
+						// Analyze header
+						
+						// Map holding all indexes for a given dimension
+						dMap = new HashMap<Integer, List<Integer>>();
+						// Map holding all ids for a given dimension
+						idMap = new HashMap<Integer, List<String>>();
+						
+						int index=0;
+						for(Metadata me: m.getMetadata()){
+							if(!dMap.containsKey(me.getDimension())){
+								dMap.put(me.getDimension(), new ArrayList<Integer>());
+							}
+							if(!idMap.containsKey(me.getDimension())){
+								idMap.put(me.getDimension(), new ArrayList<String>());
+							}
+							dMap.get(me.getDimension()).add(index);
+							idMap.get(me.getDimension()).add(me.getId());
+							index++;
+						}
+						
+						//dimensions/dimension/dimensioncomponents/component/componentvalue
+						dimensionList = new ArrayList<List<List<List<Double>>>>();
+						
+						numberOfDimensions = dMap.size();
+						logger.info("Number of dimensions: "+numberOfDimensions);
+						for(int i=0;i<numberOfDimensions; i++){
+							// For each dimension add an list
+							dimensionList.add(new ArrayList<List<List<Double>>>());
+						}
+						
+						firstL = new ArrayList<Boolean>();
+						takeData = new ArrayList<Boolean>(); // Flag whether to take data for this dimension
+						dcountL = new ArrayList<Integer>(); // How many times this dimension is there
+						
+						for(int i=0;i<numberOfDimensions;i++){
+							firstL.add(true);
+							takeData.add(true);
+							dcountL.add(0);
+						}
+					}
+					
+					
+					
+					for(Integer dimensionNumberKey : dMap.keySet()){
+						if(firstL.get(dimensionNumberKey)){
+							List<List<Double>> l = new ArrayList<List<Double>>();
+							dimensionList.get(dimensionNumberKey).add(l);
+							
+							for(int y=0;y<dMap.get(dimensionNumberKey).size(); y++){
+								l.add(new ArrayList<Double>());
+							}
+							
+							// Set first flag to false
+							firstL.set(dimensionNumberKey, false);
+						
+						}
+						
+						// Read data from data message
+						if(takeData.get(dimensionNumberKey) || dimensionNumberKey == 0){
+							for(int y=0;y<dMap.get(dimensionNumberKey).size(); y++){
+								int ind = dMap.get(dimensionNumberKey).get(y);
+							
+								// Get data of component at index
+								Object value = m.getData().get(ind);
+								if(value instanceof Double){
+									dimensionList.get(dimensionNumberKey).get(dcountL.get(dimensionNumberKey)).get(y).add((Double)value);
+								}
+							}
+							
+							takeData.set(dimensionNumberKey,false);
+						}
+					}
+				}
+				else if(message instanceof StreamDelimiterMessage){
+					StreamDelimiterMessage m = (StreamDelimiterMessage) message;
+					logger.fine("----Delimiter "+m.getNumber()+"----");
+					
+					// Increase dimension count
+					dcountL.set(m.getNumber(), (dcountL.get(m.getNumber())+1));
+					
+					// Set flag that next message in the stream will be the first again of the dimension
+					firstL.set(m.getNumber(), true);
+
+					// Every time a delimiter comes set take data of the dimension above to true
+					int c = m.getNumber()+1;
+					if(c<takeData.size()){
+						takeData.set(c, true);
+					}
+				}
+				
+			else if(message instanceof EndOfStreamMessage){
+				// Write MDA file
+				logger.info("Write MDA data file");
+				
+				try {
+					if(file.exists()){
+						file.delete();
+					}
+	//				XDROutputStream x = new XDROutputStream(new FileOutputStream(file));
+					XDRRandomAccessFile x = new XDRRandomAccessFile(file, "rw");
+					
+					
+					/**
+					 * Read file header
+					 */
+					x.writeFloat(0f); // Version
+					x.writeInt(0); // Scan number
+					x.writeInt(numberOfDimensions); // Rank/Number of dimensions
+					
+					for(int i=numberOfDimensions-1;i>=0; i--){
+						int s = dimensionList.get(i).get(0).get(0).size();
+						x.writeInt(s); // Dimension size
+						logger.info("Size: "+i+" - "+s+" ");
+					}
+					
+					x.writeInt(1); // Is Regular (true=1, false=0)
+					x.writeInt(0); // Number of extra pvs
+		
+					// Write data
+					HashMap<Integer,Integer> indexCount = new HashMap<Integer,Integer>();
+					for(int i=0;i<dimensionList.size();i++){
+						indexCount.put(i, 0);
+					}
+	
+					// The highest dimension only consist of one data list
+					int dnum = dimensionList.size()-1;
+					writeDimension(x, dimensionList, indexCount, idMap, dnum);
+				
+			
+				} catch (FileNotFoundException e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				} catch (IOException e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+	}
+	
+	private long writeDimension(XDRRandomAccessFile x, List<List<List<List<Double>>>> dimensionList, HashMap<Integer,Integer> icount, HashMap<Integer,List<String>> idMap, int dnum) throws IOException{
+		
+		int ic = icount.get(dnum);
+		List<List<Double>> l = dimensionList.get(dnum).get(ic);
+		// Increment count for dimension
+		icount.put(dnum,(ic+1));
+		
+		logger.info("Write data: "+dnum+"["+ic+"]");
+		
+		// Write data to file
+		// Address of this dimension (block)
+		long daddress = x.getFilePointer();
+		List<Long> dpaddressL = writeData(x, l, idMap.get(dnum), dnum);
+		
+
+		if(dnum>0){
+			for(int i=0;i<l.get(0).size();i++){
+//				long caddress = x.getFilePointer();
+				
+				// Write lower level dimensions to file
+				long p = writeDimension(x, dimensionList, icount, idMap, dnum-1);
+				
+				// Write pointer to pdaddress+i*long
+				x.seek(dpaddressL.get(i));
+				x.writeInt((int)p);
+				
+				// Got to caddress again
+//				x.seek(caddress);
+				x.seek(x.length());
+			}
+		}
+		
+		return daddress;
+	}
+	
+	/**
+	 * Write data of a dimension
+	 * @param x
+	 * @param list
+	 * @param dimension
+	 * @throws IOException
+	 * 
+	 * @return Address where the pointers lower level dimensions are stored
+	 */
+	private List<Long> writeData(XDRRandomAccessFile x, List<List<Double>> list, List<String> ids, int dimension) throws IOException{
+		int npoints = list.get(0).size();
+		
+		logger.info("Dimension rank: "+(dimension+1));
+		x.writeInt(dimension+1); // Scan rank
+		x.writeInt(npoints); // Number of points
+		x.writeInt(npoints); // Current Point
+
+		// Address of the place where the pointers to the lower level dimensions
+		// are stored.
+		List<Long> dpaddressList = new ArrayList<Long>();
+//		long dpaddress = x.getFilePointer();
+		// Read pointers to lower scans
+		if(dimension > 0){
+ 			// For 1D scans this block is never reached
+			for(int i=0;i<npoints;i++){
+				dpaddressList.add(x.getFilePointer());
+				x.writeInt(0); // pointer to lower scans (data is not correct)
+			}
+		}
+		
+		
+		/**
+		 * Read scan info
+		 */
+		String sname = "dimension: "+dimension;
+		x.writeInt(sname.length()); // Length
+		x.writeString(sname); // Scan name
+
+		
+		Date d = new Date();
+//		String tstamp = "Oct 04, 2008 19:17:43.633180";
+		String tstamp = d.toString(); // Take current time as timestamp
+		x.writeInt(tstamp.length()); // Length
+		x.writeString(tstamp); // timestamp
+
+
+		int nPosDet = list.size();
+		
+		int nPositioner = 1; // Assume that first in list is always the positioner
+		int nDetector = nPosDet-1; // Assume that the rest are detectors
+		x.writeInt(nPositioner); // Number of positioners
+		x.writeInt(nDetector); // Number of detectors
+		x.writeInt(0); // Number of triggers
+		
+		int cnt = 0;
+
+		// Positioners metadata
+		for(int i = 0; i<nPositioner; i++){
+			String pos = ids.get(cnt);
+			cnt++;
+			
+			x.writeInt(i); // Positioner number
+
+			x.writeInt(pos.length());
+			x.writeString(pos); // Positioner name
+			
+			x.writeInt(0);
+//			x.writeString(); // Description
+
+			x.writeInt(0);
+//			x.writeString(); // Step mode
+
+			x.writeInt(0);
+//			x.writeString("mm"); // Unit
+
+			x.writeInt(pos.length());
+			x.writeString(pos); // Readback name
+
+			x.writeInt(0);
+//			x.writeString(); // Readback description
+
+			x.writeInt(0);
+//			x.writeString(); // Readback unit
+		}
+
+		// Detector metadata
+		for(int i=0; i<nDetector; i++){
+			String det = ids.get(cnt);
+			cnt++;
+			
+			x.writeInt(i); // Detector number
+			
+			x.writeInt(det.length());
+			x.writeString(det); // Detector name
+
+			x.writeInt(0);
+//			x.writeString(); // Description
+
+			x.writeInt(0);
+//			x.writeString(); // Unit
+		}
+
+		// No trigger metadata (as there are no triggers)
+		
+		
+		// Positioner data
+		for(int i = 0; i<nPositioner; i++){
+			for(int t=0; t<npoints; t++){
+				x.writeDouble(list.get(i).get(t));
+			}
+		}
+
+		
+		// Detector data 
+		for(int i=0; i<nDetector; i++){
+			for(int t=0; t<npoints; t++){
+				x.writeFloat(list.get(i+nPositioner).get(t).floatValue());
+			}
+		}
+		
+		return dpaddressList;
+	}
+	
+}

src/main/java/ch/psi/fda/serializer/SerializerTXT2D.java

@@ -0,0 +1,200 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.serializer;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.google.common.eventbus.Subscribe;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+
+/**
+ * Serialize data received by a DataQueue into a Matlab file
+ */
+public class SerializerTXT2D {
+	
+	private File file;
+	private boolean appendSuffix = false;
+	
+	private boolean first = true;
+	
+	File outfile;
+	List<List<Object>> dlist;
+	List<Class<?>> clist;
+	int dsize;
+	int dcount;
+	
+	private List<Metadata> metadata;
+	
+	/**
+	 * @param file	Name of the Matlab file to serialize the data to
+	 */
+	public SerializerTXT2D(File file){
+		this.file = file;
+	}
+
+	@Subscribe
+	public void onMessage(Message message) {
+		try{
+			
+			
+			
+			
+				if(message instanceof DataMessage){
+					DataMessage m = (DataMessage) message;
+					
+					
+					if(first){
+						first = false;
+						
+						// Check if input queue does only hold 2D data
+						int maxdim=0;
+						metadata = m.getMetadata();
+						for(Metadata me: m.getMetadata()){
+							if(me.getDimension()>maxdim){
+								maxdim=me.getDimension();
+							}
+							
+							if(me.getDimension()>1){
+								throw new RuntimeException("Serializer does only support 2D data (XD data found)");
+							}
+						}
+						
+						if(maxdim<1){
+							throw new RuntimeException("Serializer does only support 2D data ("+maxdim+"D data found)");
+						}
+						
+						
+						// WORKAROUND BEGIN
+						
+						if(appendSuffix){
+							// Append a count suffix to the file. If there is already a file with 
+							// this suffix increase the counter for the suffix
+							int cnt = 0;
+							String fname = this.file.getAbsolutePath(); // Determine file name
+							String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
+				//			fname = fname.replaceAll("(_[0-9]+)?\\."+extension+"$", "");
+							fname = fname.replaceAll("\\."+extension+"$", "");
+							
+							outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+							
+							while(outfile.exists()){
+								cnt++;
+								outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+							}
+						}
+						else{
+							outfile = this.file;
+						}
+						// WORKAROUND END
+			
+						
+						// Transposed data list
+						dlist = new ArrayList<List<Object>>();
+						clist = new ArrayList<Class<?>>();
+						dsize = 0; // Size of the dimension
+						dcount = 0;
+						
+						
+						for(Object o: m.getData()){
+							dlist.add(new ArrayList<Object>());
+							clist.add(o.getClass());
+						}
+					}
+					
+					// Put data into data list
+					for(int i=0;i< m.getData().size();i++){
+						Object object = m.getData().get(i);
+						dlist.get(i).add(object);
+					}
+					
+					dcount++;
+				}
+				else if(message instanceof StreamDelimiterMessage){
+					StreamDelimiterMessage m = (StreamDelimiterMessage) message;
+					if(m.getNumber()==0){
+						if(dsize<dcount){
+							dsize=dcount;
+						}
+						dcount=0;
+					}
+				}
+				
+			
+			else if(message instanceof EndOfStreamMessage){
+				// Open file
+				BufferedWriter writer = new BufferedWriter(new FileWriter(outfile));
+				
+				// Create text images
+				for(int t=0; t<dlist.size(); t++ ){
+					// Get component metadata
+					Metadata c = metadata.get(t);
+					
+					writer.write(c.getId()+"\n");
+					
+					List<Object> list = dlist.get(t);
+					
+					
+					
+					if(clist.get(t).isArray()){
+						// Array Handling
+					}
+					else if(clist.get(t).equals(Double.class)){
+						// Data is of type Double
+						
+						StringBuffer b = new StringBuffer();
+						int counter = 0;
+						for(Object o: list){
+							b.append(o);
+							counter++;
+							if(counter==dsize){
+								b.append("\n");
+								counter=0;
+							}
+							else{
+								b.append(" ");
+							}
+						}
+						
+						writer.write(b.toString());
+					}
+					
+					writer.write("\n");
+					
+				}
+				
+				// Close file
+				writer.close();
+			}
+			
+		} catch (IOException e) {
+			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
+		}
+	}
+}

src/main/java/ch/psi/fda/serializer/SerializerTXTSplit.java

@@ -0,0 +1,195 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.serializer;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.google.common.eventbus.Subscribe;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+
+/**
+ * Serialize data received by a DataQueue
+ */
+public class SerializerTXTSplit {
+
+	private File file;
+
+	private int maxdim = 0;
+
+	private boolean first = true;
+
+	private List<String> header;
+	private List<String> data;
+
+	public SerializerTXTSplit(File file) {
+		this.file = file;
+	}
+
+	@Subscribe
+	public void onMessage(Message message) {
+		try {
+			// Write data
+			// Read Message
+
+			if (message instanceof DataMessage) {
+
+				if (first) {
+					first = false;
+
+					header = new ArrayList<String>();
+					data = new ArrayList<String>();
+
+					// Write header
+					StringBuffer b = new StringBuffer();
+					StringBuffer b1 = new StringBuffer();
+					b.append("#");
+					b1.append("#");
+					for (Metadata c : ((DataMessage) message).getMetadata()) {
+
+						b.append(c.getId());
+						b.append("\t");
+
+						b1.append(c.getDimension());
+						b1.append("\t");
+
+						if (c.getDimension() > maxdim) {
+							maxdim = c.getDimension();
+						}
+					}
+					b.setCharAt(b.length() - 1, '\n');
+					b1.setCharAt(b1.length() - 1, '\n');
+					header.add(b.toString());
+					header.add(b1.toString());
+
+					if (maxdim < 1) {
+						throw new RuntimeException("Split serializer only supports data > 1 dimension");
+					}
+				}
+
+				// Write message to file - each message will result in one line
+				DataMessage m = (DataMessage) message;
+				StringBuffer buffer = new StringBuffer();
+				for (Object o : m.getData()) {
+					if (o.getClass().isArray()) {
+						// If the array object is of type double[] display its
+						// content
+						if (o instanceof double[]) {
+							double[] oa = (double[]) o;
+							for (double o1 : oa) {
+								buffer.append(o1);
+								buffer.append(" "); // Use space instead of tab
+							}
+							buffer.replace(buffer.length() - 1, buffer.length() - 1, "\t"); // Replace
+																							// last
+																							// space
+																							// with
+																							// tab
+						} else if (o instanceof Object[]) {
+							// TODO need to be recursive ...
+							Object[] oa = (Object[]) o;
+							for (Object o1 : oa) {
+								buffer.append(o1);
+								buffer.append(" "); // Use space instead of tab
+							}
+							buffer.replace(buffer.length() - 1, buffer.length() - 1, "\t"); // Replace
+																							// last
+																							// space
+																							// with
+																							// tab
+						} else {
+							buffer.append("-"); // Not supported
+						}
+					} else {
+						buffer.append(o);
+						buffer.append("\t");
+					}
+				}
+
+				buffer.deleteCharAt(buffer.length() - 1); // Remove last
+															// character (i.e.
+															// \t)
+				buffer.append("\n"); // Append newline
+				data.add(buffer.toString());
+			} else if (message instanceof StreamDelimiterMessage) {
+				StreamDelimiterMessage m = (StreamDelimiterMessage) message;
+				if (m.getNumber() == maxdim - 1) {
+					writeData(header, data);
+					// Clear data
+					data.clear();
+				}
+			}
+
+		} catch (IOException e) {
+			throw new RuntimeException("Data serializer had a problem writing to the specified file", e);
+		}
+
+	}
+
+	private void writeData(List<String> header, List<String> data) throws IOException {
+
+		// WORKAROUND BEGIN
+		File outfile;
+		// if(appendSuffix){
+		// Append a count suffix to the file. If there is already a file with
+		// this suffix increase the counter for the suffix
+		int cnt = 0;
+		String fname = this.file.getAbsolutePath(); // Determine file name
+		String extension = fname.replaceAll("^.*\\.", ""); // Determine
+															// extension
+		fname = fname.replaceAll("\\." + extension + "$", "");
+
+		outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+
+		while (outfile.exists()) {
+			cnt++;
+			outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
+		}
+		// }
+		// else{
+		// outfile = this.file;
+		// }
+		// WORKAROUND END
+
+		// Open file
+		BufferedWriter writer = new BufferedWriter(new FileWriter(outfile));
+
+		// Write header
+		for (String s : header) {
+			writer.write(s);
+		}
+
+		// Write data
+		for (String s : data) {
+			writer.write(s);
+		}
+
+		// Close file
+		writer.close();
+	}
+}

src/main/java/ch/psi/fda/ui/AcquisitionMain.java

@@ -0,0 +1,376 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui;
+
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.ServiceLoader;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.ScrollPaneLayout;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+import com.google.common.eventbus.AsyncEventBus;
+import com.google.common.eventbus.EventBus;
+import com.google.inject.Guice;
+import com.google.inject.Injector;
+
+import sun.misc.Signal;
+import sun.misc.SignalHandler;
+import ch.psi.fda.DescriptorProvider;
+import ch.psi.fda.EContainer;
+import ch.psi.fda.EContainerFactory;
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.fda.gui.ProgressPanel;
+import ch.psi.fda.gui.ScrollableFlowPanel;
+import ch.psi.fda.rest.InjectionModule;
+import ch.psi.fda.ui.visualizer.Visualizer;
+import ch.psi.fda.vdescriptor.VDescriptor;
+import ch.psi.jcae.ChannelService;
+import ch.psi.jcae.impl.DefaultChannelService;
+
+/**
+ * Entry class for command line based data acquisition
+ */
+@SuppressWarnings("restriction")
+public class AcquisitionMain {
+
+	private static Logger logger = Logger.getLogger(AcquisitionMain.class.getName());
+	
+	/**
+	 * Main Program
+	 * Process exit code: -1 if wrong number of arguments are passed
+	 * 
+	 * @param args	Arguments of the program
+	 */
+	public static void main(String[] args) {
+
+		String scriptname = "fda_scan";
+		
+		Integer iterations = null;
+		boolean autoclose = false;
+		boolean nogui = false;
+		String files[] = null;
+		
+		// Iterations option
+		OptionBuilder.hasArg();
+        OptionBuilder.withArgName("iterations");
+        OptionBuilder.withDescription("Number of iterations");
+        OptionBuilder.withType(new Integer(1));
+        Option o_iterations = OptionBuilder.create( "iterations");
+        
+        Option o_autoclose = new Option( "autoclose", "Close down application after scan" );
+        Option o_init = new Option( "initialize", "Initialize application directories and configuration files" );
+        Option o_nogui = new Option( "nogui", "Do not show scan GUI" );
+        
+        Options options = new Options();
+        options.addOption(o_iterations);
+        options.addOption(o_autoclose);
+        options.addOption(o_init);
+        options.addOption(o_nogui);
+        
+        CommandLineParser parser = new GnuParser();
+        // Parse the command line arguments
+        try {
+			CommandLine line = parser.parse( options, args );
+			
+			// Initialize application
+			if( line.hasOption(o_init.getOpt()) ){
+				// Initialize application
+				ApplicationConfigurator ac = new ApplicationConfigurator();
+				ac.initializeApplication();
+				System.exit(0);
+			}
+			
+			if(line.getArgs().length<1){
+				throw new ParseException("One argument is required");
+			}
+			
+			files=line.getArgs();
+			
+			// Iterations option
+			if( line.hasOption(o_iterations.getOpt()) ){
+            	iterations = Integer.parseInt(line.getOptionValue(o_iterations.getOpt()));
+            }
+		
+			// Autoclose option
+            if( line.hasOption( o_autoclose.getOpt() ) ) {
+                autoclose = true;
+            }
+            
+            // No GUI option
+            if( line.hasOption( o_nogui.getOpt() ) ) {
+                nogui = true;
+            }
+		
+        } catch (ParseException e) {
+			System.err.println(e.getMessage());
+			HelpFormatter formatter = new HelpFormatter();
+			formatter.printUsage(new PrintWriter(System.out, true), HelpFormatter.DEFAULT_WIDTH, scriptname, options);
+			System.exit(-1);
+		}
+		
+        // Run application
+        try{
+        	for(String file: files){
+        		run(new File(file), iterations, autoclose, nogui);
+        	}
+        	
+    		// Close application automatically if autoclose option is set (and visualizations are specified)
+    		if(nogui || autoclose ){	
+    			System.exit(0);
+    		}
+    		
+        }
+		catch(Exception ee){
+			System.out.println("Acquisition failed due to: "+ee.getMessage());
+			logger.log(Level.SEVERE, "Acquisition failed due to: ", ee); // Do not print stack trace
+			System.exit(-1);
+		}
+
+	}
+	
+	/**
+	 * Run scan
+	 * @param file			Scan file
+	 * @param iterations	Number of iterations
+	 * @param autoclose		Flag whether to close the application automatically after the scan
+	 * @param nogui			Flag whether to run the scan with a GUI
+	 */
+	public static void run(final File file, Integer iterations, boolean autoclose, boolean nogui){
+		
+		// Initialize application
+		new ApplicationConfigurator().initializeApplication();
+		
+		// Basic services
+		final ChannelService cservice = new DefaultChannelService();
+        ExecutorService executor = Executors.newSingleThreadExecutor();
+		EventBus b = new AsyncEventBus(executor);
+		Injector injector = Guice.createInjector(new InjectionModule(cservice));
+		
+
+		EDescriptor edescriptor = null;
+		VDescriptor vdescriptor = null;
+		ServiceLoader<DescriptorProvider> providers = ServiceLoader.load(DescriptorProvider.class);
+        for (DescriptorProvider provider : providers) {
+        	try{
+        		provider.load(file);
+        		edescriptor = provider.getEDescriptor();
+        		vdescriptor = provider.getVDescriptor();
+        		break;
+        	}
+        	catch(Exception e){
+        		logger.log(Level.INFO, provider.getClass().getName()+ " is not able to read provided descriptor files", e);
+        	}
+        }
+		
+
+        EContainer ec = null;
+		ServiceLoader<EContainerFactory> factories = ServiceLoader.load(EContainerFactory.class);
+        for (EContainerFactory factory : factories) {
+        	if(factory.supportsEDescriptor(edescriptor)){
+        		injector.injectMembers(factory);
+        		ec = factory.getEContainer(edescriptor, b);
+        		break;
+        	}
+        }
+        final EContainer econtainer = ec;
+		
+		
+		econtainer.initialize();
+		
+		Visualizer visualizer = null;
+		
+			
+		// Only register data visualization task/processor if there are visualizations
+		if(vdescriptor.getPlots().size()>0 && !nogui){
+			visualizer = new Visualizer(vdescriptor);
+			b.register(visualizer);
+		}
+		
+		
+		
+		// GUI GUI GUI GUI GUI GUI GUI
+		ProgressPanel progressPanel = null;
+		if(visualizer != null){ // Only bring up GUI if there are some plots ...
+			// Visualizations
+			JPanel opanel = new ScrollableFlowPanel();
+	        opanel.setLayout(new FlowLayout());
+	        
+	        JScrollPane spane = new JScrollPane(opanel, ScrollPaneLayout.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneLayout.HORIZONTAL_SCROLLBAR_NEVER);
+	        JTabbedPane tpane = new JTabbedPane();
+	        tpane.addTab("Overview", spane);
+	        
+	        for(JPanel p: visualizer.getPlotPanels()){
+				opanel.add(p);
+			}
+	        
+				final JFrame frame = new JFrame("FDA: "+file.getName());
+				frame.setSize(1200,800);
+				
+				// Create progress panel
+				progressPanel = new ProgressPanel();
+	            progressPanel.addActionListener(new ActionListener() {
+					
+					@Override
+					public void actionPerformed(ActionEvent e) {
+						try {
+							econtainer.abort();
+						} catch (Exception e1) {
+							logger.log(Level.SEVERE, "Exception occured while aborting scan", e1);
+						}
+						
+					}
+				});
+				
+				
+				JSplitPane splitPane = new JSplitPane();
+				splitPane.setLeftComponent(progressPanel);
+				splitPane.setRightComponent(tpane);
+				
+				frame.add(splitPane);
+				frame.addWindowListener(new WindowAdapter(){
+					@Override
+					public void windowClosing(WindowEvent we){
+						if(econtainer.isActive()){
+							// Abort acquisition
+							econtainer.abort();
+						}
+						
+						// Wait until acquisition is aborted. Maximum wait 10*100milliseconds before forcefully
+						// terminate application
+						int count=0;
+						while(econtainer.isActive()){
+							if(count == 10){
+								break;
+							}
+							
+							// Sleep 100 milliseconds
+							try {
+								Thread.sleep(100);
+							} catch (InterruptedException e) {
+								// TODO Auto-generated catch block
+								e.printStackTrace();
+							}
+							count++;
+						}
+						
+						// Terminate program
+						System.exit(0);
+					}
+				});
+				frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);//.DO_NOTHING_ON_CLOSE);
+//				frame.setVisible(true);
+				
+				java.awt.EventQueue.invokeLater(new Runnable() {
+		            public void run() {
+		                frame.setVisible(true);
+		            }
+		        });		
+		}
+		// GUI GUI GUI GUI GUI GUI GUI
+		
+		// CLI CLI CLI CLI
+		// Register the scan engine as Signal Handler
+		Signal.handle(new Signal("INT"), new SignalHandler() {
+			/**
+			 * Thread save signal counter
+			 */
+			private AtomicInteger signalCount= new AtomicInteger(0);
+			
+			/**
+			 * Testing signal handler (in Eclipse) use this after starting scan:
+			 *
+			 * SL5: A=`ps -ef | tail -10 | grep jav[a] | awk '{printf $2}'`;kill -2 $A
+			 * MacOS X: A=`ps -ef | grep AcquisitionMai[n] | awk '{printf $2}'`;kill -2 $A
+			 * 
+			 * on the command line use CTRL-C
+			 */
+			@Override
+			public void handle(Signal signal) {
+				
+				logger.finest("Received signal: "+signal);
+				
+				int count = signalCount.incrementAndGet();
+				
+				// If signal is received more than 1 time forcefully abort application
+				if(count>1){
+					logger.info("Terminate application");
+					System.exit(2);
+				}
+
+				// Abort acquisition engine
+				if(econtainer.isActive()){
+					// Abort acquisition
+					econtainer.abort();
+				}
+			}
+		});
+		// CLI CLI CLI CLI
+		
+		
+		// Run acquisition engine
+//		try {
+			if(visualizer != null){
+				// Start visualization
+				visualizer.configure();
+			}
+			
+			econtainer.execute();
+			econtainer.destroy();
+		
+			cservice.destroy();
+			executor.shutdownNow();
+		
+		// GUI GUI GUI GUI GUI GUI GUI
+		// Set progress panel to done
+		if(progressPanel != null){
+			// Can this be done via a Listener?
+			progressPanel.done();
+		}
+		// GUI GUI GUI GUI GUI GUI GUI
+		
+	}
+	
+	
+
+}

src/main/java/ch/psi/fda/ui/ApplicationConfigurator.java

@@ -0,0 +1,324 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.net.InetAddress;
+import java.net.InterfaceAddress;
+import java.net.NetworkInterface;
+import java.net.SocketException;
+import java.net.URISyntaxException;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.logging.Logger;
+
+public class ApplicationConfigurator {
+	
+	private static final Logger logger = Logger.getLogger(ApplicationConfigurator.class.getName());
+	
+	public final static String FDA_HOME_ARGUMENT = "ch.psi.fda.home";
+	
+	private final File home;
+	private final File configdir;
+	private final File datadir;
+	private final File logdir;
+	private final File scandir;
+	
+	private final File jcaeProperties;
+	private final File fdaProperties;
+	private final File loggingProperties;
+	
+	/**
+	 * Constructor: The constructor will determine the home directory based on the
+	 * System property fda.home passed via the VM option -Dfda.home=dir or, if not present,
+	 * via the source code (jar) location (this will fail if the source code is not loaded from a file source).
+	 */
+	public ApplicationConfigurator(){
+		this.home = determineHome();
+		this.configdir = new File(home, "config");
+		this.datadir = new File(home, "data");
+		this.logdir = new File(home, "logs");
+		this.scandir = new File(home, "scans");
+		
+		this.jcaeProperties = new File(configdir, "jcae.properties");
+		this.fdaProperties = new File(configdir, "fda.properties");
+		this.loggingProperties = new File(configdir, "logging.properties");
+	}
+	
+	
+	public void initializeApplication(){
+		
+		// Overwrite system property
+		System.setProperty(FDA_HOME_ARGUMENT, this.home.getAbsolutePath());
+		
+		createApplicationHome();
+		createDefaultConfigurationFiles();
+		
+		// Set FDA configuration argument -Dch.psi.fda.config.file=...
+		
+		final String configFile = "ch.psi.fda.xscan.config.file"; 
+		String property = System.getProperty(configFile);
+		if(property==null){
+			System.setProperty(configFile, fdaProperties.getAbsolutePath());
+		}
+		
+		// Set jcae.properties file
+		property = System.getProperty("ch.psi.jcae.config.file");
+		if(property==null){
+			System.setProperty("ch.psi.jcae.config.file", jcaeProperties.getAbsolutePath());
+		}
+	}
+	
+	/**
+	 * Function to determine home directory. This function assumes that the application directories are 
+	 * ordered as follows:
+	 * HOME
+	 * |-version
+	 * | |-lib
+	 * | | |-jars
+	 * | |-bin
+	 * |-config
+	 * |-logs
+	 * |-data
+	 * |-scans
+	 * | |-templates
+	 * | |-users   
+	 * @return file
+	 */
+	public File determineHome(){
+		File home = null;
+		
+		// Check whether fda.home System property is set
+		String s = System.getProperty(FDA_HOME_ARGUMENT);
+		if(s!=null){
+			// A system property is specified
+			home = new File(s);
+		}
+		else{
+			// No system property is specified
+			
+			// Try to determine home location based on the location of the sourcecode
+			try {
+				// Note: Obviously, this will do odd things if you class was loaded from a non-file location.
+				// http://stackoverflow.com/questions/320542/how-to-get-the-path-of-a-running-jar-file
+				// Get path where the jar is located
+				File f = new File(ApplicationConfigurator.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath());
+				
+				// Check whether class was loaded from a jar file
+				if(f.isDirectory()){
+					// Loaded from a directory
+					home = f.getParentFile().getParentFile();
+				}
+				else{
+					// Jar file
+					// Assume that the jar file is located in a <version>/lib directory
+					home = f.getParentFile().getParentFile().getParentFile();
+				}
+			} catch (URISyntaxException e) {;
+			}
+		}
+		return(home);
+	}
+	
+	/**
+	 * Initialize fda home directory
+	 * Will create the home directory directory structure
+	 */
+	public void createApplicationHome(){
+		
+		// Create directories
+		if(!home.exists()){
+			logger.info("Create home directory: "+home.getAbsolutePath());
+			home.mkdirs();
+		}
+		
+		// Configuration directory
+		if(!configdir.exists()){
+			logger.info("Create configuration directory: "+configdir.getAbsolutePath());
+			configdir.mkdir();
+		}
+		
+		// Data directory
+		if(!datadir.exists()){
+			logger.info("Create data directory: "+datadir.getAbsolutePath());
+			datadir.mkdir();
+		}
+		
+		// Log directory
+		if(!logdir.exists()){
+			logger.info("Create log directory: "+logdir.getAbsolutePath());
+			logdir.mkdir();
+		}
+		
+		// Scan directories
+		if(!scandir.exists()){
+			logger.info("Create scan directory: "+scandir.getAbsolutePath());
+			scandir.mkdir();
+		}
+		File sdir = new File(scandir, "templates");
+		if(!sdir.exists()){
+			logger.info("Create template scan directory: "+sdir.getAbsolutePath());
+			sdir.mkdir();
+		}
+		sdir = new File(scandir, "users");
+		if(!sdir.exists()){
+			logger.info("Create user scan directory: "+sdir.getAbsolutePath());
+			sdir.mkdir();
+		}
+		
+	}
+
+	/**
+	 * Create required configuration files
+	 */
+	public void createDefaultConfigurationFiles() {
+		try{
+	
+			if(!jcaeProperties.exists()){
+				logger.info("Create jcae.properties file: "+jcaeProperties.getAbsolutePath());
+				// jca.properties
+				String addresses = getLocalBroadcastAddresses();
+				
+				BufferedWriter writer = new BufferedWriter(new FileWriter(jcaeProperties));
+				PrintWriter w = new PrintWriter(writer);
+				// Set address list
+				w.println("ch.psi.jcae.ContextFactory.addressList="+addresses);
+				// Timeout for creating channels
+				w.println("ch.psi.jcae.ChannelFactory.timeout=2000");
+				w.println("ch.psi.jcae.ChannelFactory.retries=4");
+				// Get/set timeout of a ChannelBean
+				w.println("ch.psi.jcae.ChannelBeanFactory.timeout=10000");
+				// Set default wait time for wait operations of a ChannelBean (30 minutes)
+				w.println("ch.psi.jcae.ChannelBeanFactory.waitTimeout=1800000");
+				// Set wait retry period for wait operations of a ChannelBean (1 minutes)
+				w.println("ch.psi.jcae.ChannelBeanFactory.waitRetryPeriod=60000");
+				// Set retries for operations on a ChannelBean
+				w.println("ch.psi.jcae.ChannelBeanFactory.retries=4");
+				writer.close();
+			}
+	
+			if(!fdaProperties.exists()){
+				logger.info("Create fda.properties file: "+fdaProperties.getAbsolutePath());
+				// fda.properties
+				BufferedWriter writer = new BufferedWriter(new FileWriter(fdaProperties));
+				PrintWriter w = new PrintWriter(writer);
+				
+				w.println("ch.psi.fda.aq.data.dir=../data");
+				w.println("ch.psi.fda.aq.data.filePrefix=${yyyy_MM}/${yyyyMMdd}/${yyyyMMddHHmmss}_${name}/${yyyyMMddHHmm}_");
+				
+				w.println();
+				w.println("# Global Error Notification (uncomment if needed)");
+				w.println("#ch.psi.fda.aq.notification.recipients=mail.address@psi.ch smsnumber");
+				
+				w.println();
+				w.println("# OTFSCAN Configuration (uncomment if needed)");
+				w.println("#ch.psi.fda.aq.otf.channelPrefix=X-X-OTFX");
+				w.println("#ch.psi.fda.aq.otf.nfsServer=beamlineFileServer.psi.ch");
+				w.println("#ch.psi.fda.aq.otf.nfsShare=/usr/local/nfsshare");
+				w.println("#ch.psi.fda.aq.otf.smbShare=smb://:@beamlineFileServer.psi.ch/otftemp/");
+		
+				writer.close();
+			}
+		
+			if(!loggingProperties.exists()){
+				logger.info("Create logging.properties file: "+loggingProperties.getAbsolutePath());
+				// logging.properties
+				BufferedWriter writer = new BufferedWriter(new FileWriter(loggingProperties));
+				PrintWriter w = new PrintWriter(writer);
+				
+				w.println("# Specify the handlers to create in the root logger");
+				w.println("handlers = java.util.logging.ConsoleHandler, java.util.logging.FileHandler");
+				w.println("");
+				w.println("# Set the default logging level for the root logger");
+				w.println(".level=INFO");
+				w.println("");
+				w.println("# Set the default logging level for new ConsoleHandler instances");
+				w.println("java.util.logging.ConsoleHandler.level=ALL");
+				w.println("");
+				w.println("# Set the default formatter for new ConsoleHandler instances");
+				w.println("java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter");
+				w.println("");
+				w.println("# Set the default logging level for new FileHandler instances");
+				w.println("java.util.logging.FileHandler.level=ALL");
+				w.println("");
+				w.println("# Set the default formatter for new ConsoleHandler instances");
+				w.println("java.util.logging.FileHandler.formatter=java.util.logging.SimpleFormatter");
+				w.println("");
+				w.println("# Naming of the output file:");
+				w.println("java.util.logging.FileHandler.pattern="+logdir.getAbsolutePath()+"/fda-%u.%g.log");
+				w.println("");
+				w.println("# Limiting size of output file in bytes (10000kb):");
+				w.println("java.util.logging.FileHandler.limit=10000000");
+				w.println("");
+				w.println("# Number of output files to cycle through, by appending an");
+				w.println("# integer to the base file name:");
+				w.println("java.util.logging.FileHandler.count=10");
+				w.println("");
+				w.println("# Set the default logging level for the logger named com.mycompany");
+				w.println("ch.psi.fda.level=ALL");
+				writer.close();
+			}
+		}
+		catch(IOException e){
+			throw new RuntimeException("Cannot create default configuration files",e);
+		}
+		
+	}
+	
+	/**
+	 * Determine local broadcast addresses of the available network interfaces
+	 * @return
+	 */
+	private String getLocalBroadcastAddresses(){
+		StringBuffer bAddressList = new StringBuffer();
+
+        // Loop host interfaces
+        Enumeration<NetworkInterface> networkInterfaces;
+		try {
+			networkInterfaces = NetworkInterface.getNetworkInterfaces();
+		} catch (SocketException e) {
+			// Something went wrong while determining the network interfaces of the current machine.
+			// As there is nothing a user can do, turn this exception into a unchecked RuntimeException.
+			throw new RuntimeException("Unable to determine network interfaces of the machine", e);
+		}
+        while (networkInterfaces.hasMoreElements()) {
+            NetworkInterface networkInterface = networkInterfaces.nextElement();
+
+            // Loop IP addresses of interface
+            List<InterfaceAddress> interfaceAddresses = networkInterface.getInterfaceAddresses();
+            
+            for(InterfaceAddress interfaceAddress: interfaceAddresses){
+				InetAddress broadcastAddress = interfaceAddress.getBroadcast();
+				if (broadcastAddress != null) {
+					if(bAddressList.length()>0){
+						bAddressList.append(" ");
+					}
+					// Use of .substring(1) to remove leading "/" character
+					bAddressList.append(broadcastAddress.toString().substring(1));
+				}
+            }
+        }
+        return(bAddressList.toString());
+	}
+}

src/main/java/ch/psi/fda/ui/ConversionMain.java

@@ -0,0 +1,237 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui;
+
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.deserializer.DataDeserializer;
+import ch.psi.fda.deserializer.DataDeserializerMDA;
+import ch.psi.fda.deserializer.DataDeserializerTXT;
+import ch.psi.fda.serializer.SerializerMAT;
+import ch.psi.fda.serializer.SerializerMAT2D;
+import ch.psi.fda.serializer.SerializerMAT2DZigZag;
+import ch.psi.fda.serializer.SerializerMDA;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT2D;
+import ch.psi.fda.serializer.SerializerTXTSplit;
+
+/**
+ * Converter to convert the format of datafiles
+ */
+public class ConversionMain {
+
+	private static Logger logger = Logger.getLogger(ConversionMain.class.getName());
+	
+	public enum Writer {TXT, TXT_2D, TXT_SPLIT, MAT, MAT_2D, MDA, MAT_2D_Z};
+	public enum Reader {TXT, MDA};
+	
+	
+	public void convert(File input, File output, Reader reader, Writer writer) throws InterruptedException{
+		
+		// Check existence input file
+		if(input==null){
+			throw new IllegalArgumentException("Input file not specified (is null)");
+		}
+		else if(!input.exists()){
+			throw new IllegalArgumentException("Input file ["+input.getAbsolutePath()+"] does not exist");
+		}
+		
+		// Check existence output file
+		if(output==null){
+			throw new IllegalArgumentException("Output file not specified (is null)");
+		}
+		else if(output.exists()){
+			throw new IllegalArgumentException("Output file ["+output.getAbsolutePath()+"] already exists");
+		}
+
+		
+		EventBus bus = new EventBus();
+		
+		// Create deserializer
+		DataDeserializer deserializer;
+		if(reader.equals(Reader.TXT)){
+		 deserializer = new DataDeserializerTXT(bus, input);
+		}
+		else if(reader.equals(Reader.MDA)){
+			deserializer = new DataDeserializerMDA(bus, input);
+		}
+		else{
+			throw new IllegalArgumentException("Reader of type "+reader+" not supported.");
+		}
+
+		if(writer.equals(Writer.MAT)){
+			bus.register(new SerializerMAT(output));
+		}
+		else if(writer.equals(Writer.MAT_2D)){
+			bus.register(new SerializerMAT2D(output));
+		}
+		else if(writer.equals(Writer.TXT)){
+			bus.register(new SerializerTXT(output, false));
+		}
+		else if(writer.equals(Writer.TXT_2D)){
+			bus.register(new SerializerTXT2D(output));
+		}
+		else if(writer.equals(Writer.TXT_SPLIT)){
+			bus.register(new SerializerTXTSplit(output));
+		}
+		else if(writer.equals(Writer.MDA)){
+			bus.register(new SerializerMDA(output));
+		}
+		else if(writer.equals(Writer.MAT_2D_Z)){
+			bus.register(new SerializerMAT2DZigZag(output));
+		}
+		else{
+			throw new IllegalArgumentException("Writer of type "+writer+" not supported.");
+		}
+
+		// Start conversion
+		deserializer.read();
+	}	
+	
+	/**
+	 * This method accepts a data file and an option (-file) specifying the scan configuration file
+	 * used for creating the data file. If no option is specified the configuration file is derived by the 
+	 * data file name.
+	 * 
+	 * @param args	Command line arguments
+	 */
+	public static void main(String[] args) {
+		String scriptname = "fda_convert";
+		
+		File outfile = null;
+		File infile = null;
+		Reader reader = Reader.TXT;
+		Writer writer = Writer.TXT;
+		
+		
+		OptionBuilder.hasArg();
+        OptionBuilder.withArgName("writer");
+        OptionBuilder.withDescription("Output format");
+        OptionBuilder.withType(new String());
+        Option o_writer = OptionBuilder.create( "writer");
+        
+        OptionBuilder.hasArg();
+        OptionBuilder.withArgName("reader");
+        OptionBuilder.withDescription("Input format");
+        OptionBuilder.withType(new String());
+        Option o_reader = OptionBuilder.create( "reader");
+        
+        Options options = new Options();
+        options.addOption(o_writer);
+        options.addOption(o_reader);
+        
+        CommandLineParser parser = new GnuParser();
+        // Parse the command line arguments
+        try {
+			CommandLine line = parser.parse( options, args );
+			
+			// Check whether exactly one file is specified
+			if(line.getArgs().length != 2){
+				throw new ParseException("Two arguments required");
+			}
+			
+			infile = new File(line.getArgs()[0]);
+			outfile= new File(line.getArgs()[1]);
+			
+			if( line.hasOption(o_reader.getOpt() )){
+				String wr = line.getOptionValue(o_reader.getOpt());
+				try{
+					Reader r = Reader.valueOf(wr.toUpperCase());
+					reader = r;
+				}
+				catch(IllegalArgumentException e){
+					throw new ParseException("Data type "+ wr + " not supported");
+				}
+            }
+			else{
+				String suffix = infile.getName().replaceAll("^.*\\.", "");
+				try{
+					Reader r = Reader.valueOf(suffix.toUpperCase());
+					reader = r;
+				}
+				catch(IllegalArgumentException e){
+					throw new ParseException("Data type "+ suffix + " not supported");
+				}
+			}
+			
+			
+			if( line.hasOption(o_writer.getOpt() )){
+				String wr = line.getOptionValue(o_writer.getOpt());
+				try{
+					Writer v = Writer.valueOf(wr.toUpperCase());
+					writer = v;
+				}
+				catch(IllegalArgumentException e){
+					throw new ParseException("Data type "+ wr + " not supported");
+				}
+            }
+			else{
+				String suffix = outfile.getName().replaceAll("^.*\\.", "");
+				try{
+					Writer v = Writer.valueOf(suffix.toUpperCase());
+					writer = v;
+				}
+				catch(IllegalArgumentException e){
+					throw new ParseException("Data type "+ suffix + " not supported");
+				}
+			}
+			
+			// Debug output
+			logger.finest("Using writer: "+writer);
+		
+        } catch (ParseException e) {
+			System.err.println(e.getMessage());
+			HelpFormatter formatter = new HelpFormatter();
+			formatter.printUsage(new PrintWriter(System.out, true), HelpFormatter.DEFAULT_WIDTH, scriptname, options);
+			StringBuffer b = new StringBuffer();
+			for(Writer w: Writer.values()){
+				b.append(" ");
+				b.append(w.toString().toLowerCase());
+			}
+			System.out.println("Supported writer(s):"+ b);
+			System.exit(-1);
+		}
+		
+		ConversionMain e = new ConversionMain();
+		try{
+			e.convert(infile, outfile, reader, writer);
+		}
+		catch(Exception ee){
+			System.out.println("Conversion failed due to: "+ee.getMessage());
+			logger.log(Level.WARNING, "Conversion failed due to Exception:", ee);
+			System.exit(-1);
+		}
+	}
+
+}

src/main/java/ch/psi/fda/ui/RemoteAcquisitionMain.java

@@ -0,0 +1,293 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui;
+
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.ServiceLoader;
+import java.util.UUID;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.ScrollPaneLayout;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+import com.google.common.eventbus.AsyncEventBus;
+import com.google.common.eventbus.EventBus;
+import com.google.common.eventbus.Subscribe;
+
+import sun.misc.Signal;
+import sun.misc.SignalHandler;
+import ch.psi.fda.DescriptorProvider;
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.fda.gui.ProgressPanel;
+import ch.psi.fda.gui.ScrollableFlowPanel;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.ui.visualizer.Visualizer;
+import ch.psi.fda.vdescriptor.VDescriptor;
+
+@SuppressWarnings("restriction")
+public class RemoteAcquisitionMain {
+
+	private static Logger logger = Logger.getLogger(RemoteAcquisitionMain.class.getName());
+
+	StreamClient streamClient = null;
+	private String trackingId;
+	
+	/**
+	 * Main Program Process exit code: -1 if wrong number of arguments are
+	 * passed Process exit code: 3 if aborted via Ctrl+C
+	 * 
+	 * @param args
+	 *            Arguments of the program
+	 */
+	public static void main(String[] args) {
+
+		String scriptname = "scan";
+
+		String server = null;
+		boolean nogui = false;
+		List<File> files = new ArrayList<>();
+
+		OptionBuilder.hasArg();
+		OptionBuilder.isRequired();
+		OptionBuilder.withArgName("hostname");
+		OptionBuilder.withDescription("Hostname server");
+		OptionBuilder.withType(new String());
+		Option o_server = OptionBuilder.create("server");
+
+		Option o_nogui = new Option("nogui", "Do not show scan GUI");
+
+		Options options = new Options();
+		options.addOption(o_server);
+		options.addOption(o_nogui);
+
+		CommandLineParser parser = new GnuParser();
+		try {
+			CommandLine line = parser.parse(options, args);
+
+			if (line.getArgs().length < 1) {
+				throw new ParseException("One argument is required");
+			}
+
+			if (line.hasOption(o_server.getOpt())) {
+				server = line.getOptionValue(o_server.getOpt());
+			}
+
+			if (line.hasOption(o_nogui.getOpt())) {
+				nogui = true;
+			}
+
+			for (String f : line.getArgs()) {
+				File file = new File(f);
+				if (!file.exists()) {
+					throw new RuntimeException("File " + file.getAbsolutePath() + " does not exist");
+				}
+				files.add(file);
+			}
+
+		} catch (ParseException e) {
+			System.err.println(e.getMessage());
+			HelpFormatter formatter = new HelpFormatter();
+			formatter.printUsage(new PrintWriter(System.out, true), HelpFormatter.DEFAULT_WIDTH, scriptname, options);
+			System.exit(-1);
+		}
+
+		try {
+			for (File file : files) {
+				RemoteAcquisitionMain m = new RemoteAcquisitionMain();
+				m.execute(server, file, nogui);
+			}
+		} catch (Exception ee) {
+			logger.log(Level.SEVERE, "Acquisition failed due to: ", ee);
+			System.exit(-1);
+		}
+	}
+
+	
+	public void execute(final String server, File file, boolean nogui) {
+
+		trackingId = UUID.randomUUID().toString(); 
+		logger.info("TrackingID of job: " + trackingId);
+		
+		
+		EDescriptor edescriptor = null;
+		VDescriptor vdescriptor = null;
+		ServiceLoader<DescriptorProvider> providers = ServiceLoader.load(DescriptorProvider.class);
+        for (DescriptorProvider provider : providers) {
+        	try{
+        		provider.load(file);
+        		edescriptor = provider.getEDescriptor();
+        		vdescriptor = provider.getVDescriptor();
+        		break;
+        	}
+        	catch(Exception e){
+        		logger.log(Level.INFO, provider.getClass().getName()+ " is not able to read provided descriptor files", e);
+        	}
+        }
+
+
+		EventBus b = new AsyncEventBus(Executors.newSingleThreadExecutor());
+		final RestClient client = new RestClient(server, 8080); // TODO hardcoded server port
+		 
+
+		
+		if (!nogui && vdescriptor.getPlots().size() > 0) {
+		
+			streamClient = new StreamClient(b);
+
+			Visualizer visualizer = new Visualizer(vdescriptor);
+			visualizer.configure();
+			b.register(visualizer);
+
+			JPanel opanel = new ScrollableFlowPanel();
+			opanel.setLayout(new FlowLayout());
+
+			JScrollPane spane = new JScrollPane(opanel, ScrollPaneLayout.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneLayout.HORIZONTAL_SCROLLBAR_NEVER);
+			JTabbedPane tpane = new JTabbedPane();
+			tpane.addTab("Overview", spane);
+
+			for (JPanel p : visualizer.getPlotPanels()) {
+				opanel.add(p);
+			}
+
+			final JFrame frame = new JFrame("FDA: " + file);
+			frame.setSize(1200, 800);
+
+			final ProgressPanel progressPanel = new ProgressPanel();
+			progressPanel.addActionListener(new ActionListener() {
+
+				@Override
+				public void actionPerformed(ActionEvent e) {
+					try {
+						client.terminate(trackingId);
+					} catch (Exception e1) {
+						logger.log(Level.SEVERE, "Exception occured while aborting scan", e1);
+					} finally {
+						progressPanel.done();
+					}
+
+				}
+			});
+			
+			b.register(new Object(){
+				@Subscribe
+				public void onMessage(EndOfStreamMessage m){
+					progressPanel.done();
+				}
+			});
+
+			JSplitPane splitPane = new JSplitPane();
+			splitPane.setLeftComponent(progressPanel);
+			splitPane.setRightComponent(tpane);
+
+			frame.add(splitPane);
+			frame.addWindowListener(new WindowAdapter() {
+				@Override
+				public void windowClosing(WindowEvent we) {
+					client.terminate(trackingId);
+
+					int count = 0;
+					while (client.isActive(trackingId)) {
+						if (count == 10) {
+							break;
+						}
+
+						try {
+							Thread.sleep(100);
+						} catch (InterruptedException e) {
+						}
+						count++;
+					}
+
+					System.exit(0);
+				}
+			});
+			frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); // .DO_NOTHING_ON_CLOSE);
+
+			java.awt.EventQueue.invokeLater(new Runnable() {
+				public void run() {
+					frame.setVisible(true);
+				}
+			});
+		}
+
+		
+		
+		Signal.handle(new Signal("INT"), new SignalHandler() {
+
+			private AtomicInteger signalCount = new AtomicInteger(0);
+
+			@Override
+			public void handle(Signal signal) {
+
+				logger.finest("Received signal: " + signal);
+
+				try{
+					client.terminate(trackingId);
+				}
+				catch(Exception e){
+					logger.log(Level.WARNING, "Stopping scan failed with exception", e);
+				}
+				
+				if (signalCount.incrementAndGet() > 1) {
+					logger.info("Terminate application");
+					System.exit(2);
+				}
+			}
+		});
+
+		
+		
+		if(streamClient!=null){
+			streamClient.filterTrackingId(trackingId);
+			Executors.newSingleThreadExecutor().execute(new Runnable() {
+				@Override
+				public void run() {
+					streamClient.listen("tcp://"+server+":10000");
+				}
+			});
+		}
+		
+		client.acquire(trackingId, edescriptor);
+	}
+}

src/main/java/ch/psi/fda/ui/RestClient.java

@@ -0,0 +1,56 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.ui;
+
+import javax.ws.rs.client.Client;
+import javax.ws.rs.client.ClientBuilder;
+import javax.ws.rs.client.Entity;
+import javax.ws.rs.client.WebTarget;
+import javax.ws.rs.core.MediaType;
+
+import org.glassfish.jersey.jackson.JacksonFeature;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+
+public class RestClient {
+	
+	private final Client client;
+	private final WebTarget target;
+	
+	public RestClient(String servername, int port){
+		client = ClientBuilder.newClient().register(JacksonFeature.class);
+		target = client.target("http://"+servername+":"+port).path("fda");
+	}
+	 
+	public String acquire(String trackingId, EDescriptor edescriptor){
+		return target.path(trackingId).request().put(Entity.entity(edescriptor, MediaType.APPLICATION_XML), String.class);
+	}
+	
+	public void terminate(String trackingId){
+		target.path(trackingId).request().delete();
+	}
+	
+	public void terminateAll(){
+		target.request().delete();
+	}
+	
+	public boolean isActive(String trackingId){
+		return target.path(trackingId).path("running").request().get(Boolean.class);
+	}
+}

src/main/java/ch/psi/fda/ui/StreamClient.java

@@ -0,0 +1,98 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.ui;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.ObjectInput;
+import java.io.ObjectInputStream;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.codehaus.jackson.JsonFactory;
+import org.codehaus.jackson.map.ObjectMapper;
+import org.codehaus.jackson.type.TypeReference;
+import org.zeromq.ZMQ;
+
+import com.google.common.eventbus.EventBus;
+
+public class StreamClient {
+
+	private static final Logger logger = Logger.getLogger(StreamClient.class.getName());
+	private ObjectMapper mapper = new ObjectMapper(new JsonFactory());
+	
+	
+	private final EventBus bus;
+	private String trackingIdFilter = null;
+
+	public StreamClient(EventBus bus) {
+		this.bus = bus;
+	}
+	
+	public void listen(String endpoint) {
+		ZMQ.Context context = ZMQ.context(1);
+//		zmq.ZError.clear(); // Clear error code
+		ZMQ.Socket socket = context.socket(ZMQ.SUB);
+		socket.connect(endpoint);
+		socket.subscribe("".getBytes()); // SUBSCRIBE !
+
+		while (true) {
+			String tid = null;
+			
+			byte[] content = null;
+			byte[] header = socket.recv(); // header
+			if(trackingIdFilter!=null){
+				try {
+					Map<String,Object> m = mapper.readValue(header, new TypeReference<HashMap<String,Object>>(){});
+					tid = (String) m.get("trackingId");
+				} catch (IOException e) {
+				}
+			}
+			while (socket.hasReceiveMore()) {
+				content = socket.recv();
+			}
+			if (content == null) { // we lost something discard read messages
+				logger.warning("Lost some message - discard and continue");
+				continue;
+			}
+
+			if(tid!=null && !tid.matches(trackingIdFilter)){
+				continue;
+			}
+			
+			try (ByteArrayInputStream bis = new ByteArrayInputStream(content); ObjectInput in = new ObjectInputStream(bis);) {
+				Object o = in.readObject();
+				bus.post(o);
+			} catch (IOException | ClassNotFoundException e) {
+				logger.log(Level.WARNING, "Unable to deserialize message", e);
+			}
+
+		}
+	}
+
+	public String getTrackingIdFilter() {
+		return trackingIdFilter;
+	}
+
+	public void filterTrackingId(String trackingId) {
+		this.trackingIdFilter = trackingId;
+	}
+}

src/main/java/ch/psi/fda/ui/VisualizationMain.java

@@ -0,0 +1,221 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui;
+
+import java.awt.FlowLayout;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.ServiceLoader;
+import java.util.concurrent.Executors;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.ScrollPaneLayout;
+import javax.xml.bind.JAXBException;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.xml.sax.SAXException;
+
+import com.google.common.eventbus.AsyncEventBus;
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.DescriptorProvider;
+import ch.psi.fda.deserializer.DataDeserializer;
+import ch.psi.fda.deserializer.DataDeserializerTXT;
+import ch.psi.fda.gui.ScrollableFlowPanel;
+import ch.psi.fda.ui.visualizer.Visualizer;
+import ch.psi.fda.vdescriptor.VDescriptor;
+
+/**
+ * Visualize data according to the scan description
+ */
+public class VisualizationMain {
+
+	private static Logger logger = Logger.getLogger(VisualizationMain.class.getName());
+	
+	/**
+	 * Default constructor
+	 */
+	public VisualizationMain(){
+	}
+	
+	// Visualize data based on the configuration file
+	public void visualize(File configuration, File data) throws InterruptedException{
+		
+		if(configuration==null){
+			throw new IllegalArgumentException("Configuration file is null");
+		}
+		else if(!configuration.exists()){
+			throw new IllegalArgumentException("Configuration file ["+configuration.getAbsolutePath()+"] does not exist");
+		}
+		
+		VDescriptor vdescriptor = null;
+		ServiceLoader<DescriptorProvider> providers = ServiceLoader.load(DescriptorProvider.class);
+        for (DescriptorProvider provider : providers) {
+        	try{
+        		provider.load(configuration);
+        		vdescriptor = provider.getVDescriptor();
+        		break;
+        	}
+        	catch(Exception e){
+        		logger.log(Level.INFO, provider.getClass().getName()+ " is not able to read provided descriptor files", e);
+        	}
+        }
+		
+		// Visualize data
+		visualize(vdescriptor, data);
+	}
+	
+	public void visualize(VDescriptor vdescriptor, File data) throws InterruptedException{
+		
+		if(data==null){
+			throw new IllegalArgumentException("Data file is null");
+		}
+		else if(!data.exists()){
+			throw new IllegalArgumentException("Data file ["+data.getAbsolutePath()+"] does not exist");
+		}
+		
+		EventBus bus = new AsyncEventBus(Executors.newCachedThreadPool());
+		// Create deserializer
+		DataDeserializer deserializer = new DataDeserializerTXT(bus, data);
+		
+		// Create Visualizer
+		Visualizer visualizer = new Visualizer(vdescriptor);
+		
+//		visualizer.setTerminateAtEOS(true);
+		// Adapt default visualizer behavior to optimize performance for visualization
+		visualizer.setUpdateAtStreamElement(false);
+		visualizer.setUpdateAtStreamDelimiter(false);
+		visualizer.setUpdateAtEndOfStream(true);
+                
+		JPanel opanel = new ScrollableFlowPanel();
+		opanel.setLayout(new FlowLayout());
+
+		JScrollPane spane = new JScrollPane(opanel, ScrollPaneLayout.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneLayout.HORIZONTAL_SCROLLBAR_NEVER);
+		JTabbedPane tpane = new JTabbedPane();
+		tpane.addTab("Overview", spane);
+
+		for (JPanel p : visualizer.getPlotPanels()) {
+			opanel.add(p);
+		}
+		
+		final JFrame frame = new JFrame();
+		frame.setSize(1200,800);
+		frame.add(tpane);
+//		frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
+		frame.addWindowListener(new WindowAdapter(){
+			@Override
+			public void windowClosing(WindowEvent we){
+				System.exit(0);
+			}
+		});
+		frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);//.DO_NOTHING_ON_CLOSE);
+		
+		java.awt.EventQueue.invokeLater(new Runnable() {
+            public void run() {
+                frame.setVisible(true);
+            }
+        });
+		
+		// Start deserializer and visualizer
+		
+		bus.register(visualizer);
+		visualizer.configure();
+		deserializer.read();
+		
+		logger.info("Deserializer finished");
+//		visualizer.stopVisualization();
+	}	
+	
+	/**
+	 * This method accepts a data file and an option (-file) specifying the scan configuration file
+	 * used for creating the data file. If no option is specified the configuration file is derived by the 
+	 * data file name.
+	 * 
+	 * @param args	Command line arguments
+	 */
+	public static void main(String[] args) {
+		String scriptname = "fda_vis";
+		File dfile = null;
+		File cfile = null;
+		
+		OptionBuilder.hasArg();
+        OptionBuilder.withArgName("file");
+        OptionBuilder.withDescription("Scan configuration file");
+        OptionBuilder.withType(new String());
+        Option o_cfile = OptionBuilder.create( "file");
+        
+        Options options = new Options();
+        options.addOption(o_cfile);
+        
+        CommandLineParser parser = new GnuParser();
+        // Parse the command line arguments
+        try {
+			CommandLine line = parser.parse( options, args );
+			
+			// Check whether exactly one file is specified
+			if(line.getArgs().length!=1){
+				throw new ParseException("Only up to one argument is supported");
+			}
+			dfile= new File(line.getArgs()[0]);
+			
+			if( line.hasOption(o_cfile.getOpt() )){
+            	cfile = new File(line.getOptionValue(o_cfile.getOpt()));
+            }
+			else{
+				// Try to determine configuration file from data file name
+				File dir = dfile.getParentFile();
+				String name = dfile.getName();
+				name = name.replaceAll("_[0-9]*.txt$", "");
+				cfile = new File(dir, name+".xml");
+			}
+		
+        } catch (ParseException e) {
+			System.err.println(e.getMessage());
+			HelpFormatter formatter = new HelpFormatter();
+			formatter.printUsage(new PrintWriter(System.out, true), HelpFormatter.DEFAULT_WIDTH, scriptname, options);
+			System.exit(-1);
+		}
+		
+		VisualizationMain e = new VisualizationMain();
+		try{
+			e.visualize(cfile, dfile);
+		}
+		catch(Exception ee){
+			System.out.println("Visualization failed due to: "+ee.getMessage());
+			logger.log(Level.WARNING, "Visualization failed due to Exception:", ee);
+			System.exit(-1);
+		}
+	}
+
+}

src/main/java/ch/psi/fda/ui/VisualizationZMQMain.java

@@ -0,0 +1,179 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui;
+
+import java.awt.FlowLayout;
+import java.awt.Label;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.ScrollPaneLayout;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+import com.google.common.eventbus.EventBus;
+import com.google.common.eventbus.Subscribe;
+
+import ch.psi.fda.gui.ScrollableFlowPanel;
+import ch.psi.fda.ui.visualizer.Visualizer;
+import ch.psi.fda.vdescriptor.VDescriptor;
+
+/**
+ * Visualize data according to the descriptor streamed via ZMQ
+ */
+public class VisualizationZMQMain {
+
+	private static Logger logger = Logger.getLogger(VisualizationZMQMain.class.getName());
+	
+	private Visualizer visualizer;
+	private String source;;
+	
+	public VisualizationZMQMain(String source){
+		this.source = source;
+	}
+	
+	
+	public void visualize() throws InterruptedException{
+		
+		final JPanel opanel = new ScrollableFlowPanel();
+		opanel.setLayout(new FlowLayout());
+
+		opanel.add(new Label());
+		
+		JScrollPane spane = new JScrollPane(opanel, ScrollPaneLayout.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneLayout.HORIZONTAL_SCROLLBAR_NEVER);
+		JTabbedPane tpane = new JTabbedPane();
+		tpane.addTab("Overview", spane);
+
+		
+		
+		final JFrame frame = new JFrame();
+		frame.setSize(1200,800);
+		frame.add(tpane);
+		frame.addWindowListener(new WindowAdapter(){
+			@Override
+			public void windowClosing(WindowEvent we){
+				System.exit(0);
+			}
+		});
+		frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);//.DO_NOTHING_ON_CLOSE);
+		
+		java.awt.EventQueue.invokeLater(new Runnable() {
+            public void run() {
+                frame.setVisible(true);
+            }
+        });
+		
+		// Start receiving messages
+		final EventBus bus = new EventBus();
+		
+		bus.register(new Object(){
+			@Subscribe
+			public void onMessage(VDescriptor vdescriptor){
+				
+				logger.info("Build up new visualization");
+				
+				// De-register old visualizer
+				if(visualizer!=null){
+					bus.unregister(visualizer);
+				}
+				
+				visualizer = new Visualizer(vdescriptor);
+				visualizer.setUpdateAtStreamElement(true);
+				visualizer.setUpdateAtStreamDelimiter(true);
+				visualizer.setUpdateAtEndOfStream(true);
+				
+				
+				opanel.removeAll();
+				for (JPanel p : visualizer.getPlotPanels()) {
+					opanel.add(p);
+				}
+				frame.repaint();
+				
+				bus.register(visualizer);
+				visualizer.configure();
+			}
+		});
+		
+		
+		
+		new StreamClient(bus).listen(source);
+	}	
+	
+	/**
+	 * This method accepts a data file and an option (-file) specifying the scan configuration file
+	 * used for creating the data file. If no option is specified the configuration file is derived by the 
+	 * data file name.
+	 * 
+	 * @param args	Command line arguments
+	 */
+	public static void main(String[] args) {
+		
+		int port = 10000;
+		String hostname = "localhost";
+		Options options = new Options();
+		options.addOption("h", false, "Help");
+		options.addOption("p", true, "Server port (default: "+port+")");
+		options.addOption("s", true, "Server address (default: "+hostname+")");
+
+		GnuParser parser = new GnuParser();
+		
+		try {
+			CommandLine line = parser.parse(options, args);
+			
+			if (line.hasOption("p")) {
+				port = Integer.parseInt(line.getOptionValue("p"));
+			}
+			if (line.hasOption("s")) {
+				hostname = line.getOptionValue("s");
+			}
+			if (line.hasOption("h")) {
+				HelpFormatter f = new HelpFormatter();
+				f.printHelp("viewer", options);
+				return;
+			}
+		} catch (ParseException e1) {
+			System.err.println("Wrong arguments: "+ e1.getMessage());
+			System.exit(-1);
+		}
+
+		
+		
+		try{
+			VisualizationZMQMain e = new VisualizationZMQMain("tcp://"+hostname+":"+port);
+			e.visualize();
+		}
+		catch(Exception ee){
+			System.out.println("Visualization failed due to: "+ee.getMessage());
+			logger.log(Level.WARNING, "Visualization failed due to Exception:", ee);
+			System.exit(-1);
+		}
+	}
+
+}

src/main/java/ch/psi/fda/ui/visualizer/DataVisualization.java

@@ -0,0 +1,51 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui.visualizer;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.psi.plot.Plot;
+
+public class DataVisualization {
+
+	private final Plot plot;
+	private final List<XYSeriesDataFilter> series;
+	
+	public DataVisualization(Plot plot){
+		this.plot = plot;
+		this.series = new ArrayList<XYSeriesDataFilter>();
+	}
+
+	/**
+	 * @return the plot
+	 */
+	public Plot getPlot() {
+		return plot;
+	}
+
+	/**
+	 * @return the series
+	 */
+	public List<XYSeriesDataFilter> getSeries() {
+		return series;
+	}
+	
+}

src/main/java/ch/psi/fda/ui/visualizer/SeriesDataFilter.java

@@ -0,0 +1,32 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui.visualizer;
+
+import ch.psi.plot.Plot;
+import ch.psi.plot.PlotSeries;
+
+public interface SeriesDataFilter {
+	/**
+	 * Get the plot for the filter
+	 * @return Plot
+	 */
+	public Plot getPlot();
+        public PlotSeries getSeries();
+}

src/main/java/ch/psi/fda/ui/visualizer/Visualizer.java

@@ -0,0 +1,415 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui.visualizer;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+import ch.psi.fda.vdescriptor.Series;
+import ch.psi.fda.vdescriptor.VDescriptor;
+import ch.psi.fda.vdescriptor.XYSeries;
+import ch.psi.fda.vdescriptor.XYZSeries;
+import ch.psi.fda.vdescriptor.YSeries;
+import ch.psi.fda.vdescriptor.YZSeries;
+import ch.psi.plot.LinePlot;
+import ch.psi.plot.LinePlotBase;
+import ch.psi.plot.LinePlotSeries;
+import ch.psi.plot.MatrixPlot;
+import ch.psi.plot.MatrixPlotBase;
+import ch.psi.plot.MatrixPlotSeries;
+import ch.psi.plot.Plot;
+import com.google.common.eventbus.Subscribe;
+import java.awt.Font;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+
+/**
+ * Visualizer for visualizing data
+ */
+public class Visualizer {
+	
+	private static Logger logger = Logger.getLogger(Visualizer.class.getName());
+	
+	private boolean updateAtStreamElement = true;
+	private boolean updateAtStreamDelimiter = true;
+	private boolean updateAtEndOfStream = false;
+	
+	private int ecount;
+	private boolean clearPlot;
+	private List<SeriesDataFilter> filters;
+        
+        int subsampling;
+        int subsamplingCounter=0;
+        
+        public static final Font TITLE_FONT =  new Font("Tahoma", Font.BOLD, 18);
+	
+	private boolean first = true;
+	public Visualizer(VDescriptor vdescriptor){            
+            this(vdescriptor,null);
+        }
+	public Visualizer(VDescriptor vdescriptor, String linePlotImpl){            
+                if (linePlotImpl==null){
+                    linePlotImpl="jfree";
+                }
+                String matrixPlotImpl="jfree";
+                
+		filters = new ArrayList<SeriesDataFilter>();
+		
+                try{
+                    for(ch.psi.fda.vdescriptor.Plot vplot: vdescriptor.getPlots()){
+                            if(vplot instanceof ch.psi.fda.vdescriptor.LinePlot){
+                                    ch.psi.fda.vdescriptor.LinePlot lp = (ch.psi.fda.vdescriptor.LinePlot) vplot;
+
+                                    // Create plot for visualization
+                                    LinePlot plot = LinePlotBase.newPlot(linePlotImpl);
+                                    plot.setTitle(lp.getTitle());
+                                    plot.getAxis(Plot.AxisId.X).setLabel(null);
+                                    plot.getAxis(Plot.AxisId.Y).setLabel(null);
+                                    plot.setTitleFont(TITLE_FONT);
+
+                                    for(Series s: lp.getData()){
+                                            if(s instanceof XYSeries){
+                                                    XYSeries sxy = (XYSeries)s;
+                                                    XYSeriesDataFilter filter = new XYSeriesDataFilter(sxy.getX(), sxy.getY(), plot);
+                                                    filter.setSeriesName(sxy.getY());
+                                                    if (sxy.getMaxItemCount()>=0)
+                                                        filter.setMaxNumberOfPoints(sxy.getMaxItemCount());
+                                                    filters.add(filter);
+                                            }
+                                            else if(s instanceof YSeries){
+                                                    YSeries sy = (YSeries)s;
+
+                                                    XYSeriesArrayDataFilter filter = new XYSeriesArrayDataFilter(sy.getY(), plot);
+    //						filter.setMaxSeries(lp.getMaxSeries()*lp.getY().size()); // Workaround - keep for each array max series
+    //						filter.setOffset(lp.getOffset());
+    //						filter.setSize(lp.getSize());
+                                                    filter.setMaxSeries(lp.getMaxSeries());
+                                                    filter.setOffset(lp.getMinX().intValue());
+                                                    filter.setSize(Double.valueOf(lp.getMaxX()-lp.getMinX()).intValue());
+                                                    filter.setSeriesName(sy.getY());
+                                                    filters.add(filter);
+                                            }
+                                    }
+
+                            }
+                            else if(vplot instanceof ch.psi.fda.vdescriptor.MatrixPlot){
+
+                                    // MatrixPlot does currently not support RegionPositioners because of the
+                                    // plotting problems this would cause. If regions of the positioner have different
+                                    // step sizes it is not easily possible (without (specialized) rasterization) to plot the data.
+
+                                    ch.psi.fda.vdescriptor.MatrixPlot lp = (ch.psi.fda.vdescriptor.MatrixPlot) vplot;
+                                    MatrixPlotSeries data = new MatrixPlotSeries("", lp.getMinX(), lp.getMaxX(), lp.getnX(), lp.getMinY(), lp.getMaxY(), lp.getnY());
+                                    if ("3D".equals(lp.getType()))
+                                        matrixPlotImpl="jzy3d";                                    
+                                    MatrixPlot plot = MatrixPlotBase.newPlot(matrixPlotImpl);
+                                    plot.setTitle(lp.getTitle());
+                                    plot.setTitleFont(TITLE_FONT);
+                                    plot.addSeries(data);                                
+
+                                    for(Series s: lp.getData()){
+                                            if(s instanceof XYZSeries){
+                                                    XYZSeries sxyz = (XYZSeries) s;
+                                                    XYZSeriesDataFilter filter=new XYZSeriesDataFilter(sxyz.getX(), sxyz.getY(), sxyz.getZ(), plot);
+                                                    filter.setSeries(data);
+                                                    filters.add(filter);
+
+                                            }
+                                            else if(s instanceof YZSeries){
+                                                    YZSeries syz = (YZSeries) s;
+                                                    XYZSeriesArrayDataFilter filter = new XYZSeriesArrayDataFilter(syz.getY(), syz.getZ(), 0, 0, plot);
+                                                    filter.setSeries(data);
+                                                    filters.add(filter);
+
+                                            }
+                                    }
+                            }
+                    }
+		}
+                catch (Exception ex) {
+                        // Ignore if something goes wrong while adding a datapoint
+                        logger.log(Level.SEVERE, null, ex);
+                }
+                    
+	}
+	
+	
+	@Subscribe
+	public void onDataMessage(final DataMessage message){
+		
+			if(first){
+				first=false;
+//				filters = VisMapper.mapVisualizations(visualizations);
+				// TODO somehow handle dimension / clear
+			}
+		
+			// Clear is here as the plot should not be cleared after the last point is plotted
+			// but just before the first point of the next plot (cycle)
+			if (clearPlot) {
+				for (SeriesDataFilter f: filters) {
+					Plot plot = f.getPlot();
+					if(plot instanceof MatrixPlot){
+						f.getSeries().clear();
+					}
+				}
+				clearPlot = false;
+			}
+                        
+                        if (subsampling>1){
+                            if ((subsamplingCounter++) > subsampling) {
+                                subsamplingCounter=0;
+                            }
+                            else{
+                                return;
+                            }
+                        }
+
+			for(SeriesDataFilter filter: filters){
+				if(filter instanceof XYSeriesDataFilter){
+					XYSeriesDataFilter xyfilter = (XYSeriesDataFilter) filter;
+					
+					if(xyfilter.getSeries()==null || xyfilter.isNewseries()){
+						// First series that is filled by this filter!
+						LinePlotSeries s = new LinePlotSeries(xyfilter.getSeriesName() + " " + ecount + "-" + xyfilter.getCount());                                                
+                                                if (xyfilter.getMaxNumberOfPoints()>=0)
+                                                    s.setMaxItemCount(xyfilter.getMaxNumberOfPoints());
+						((LinePlot)xyfilter.getPlot()).addSeries(s);
+						xyfilter.setSeries(s);
+						xyfilter.setNewseries(false);
+					}
+					
+					LinePlotSeries series = xyfilter.getSeries(); // TODO Does not work with multiple series filter per plot !!!!
+					
+					// There might be other values than double in the data, therefore we have to check for it
+					Object dX = message.getData(xyfilter.getIdX());
+					Object dY = message.getData(xyfilter.getIdY());
+					Double dataX = getDoubleValue (dX);
+					Double dataY = getDoubleValue (dY);
+                                        
+					// Add Data to the series
+                                        ((LinePlot)xyfilter.getPlot()).setUpdatesEnabled(updateAtStreamElement);
+                                        series.appendData(dataX , dataY);
+                                        ((LinePlot)xyfilter.getPlot()).setUpdatesEnabled(true);                                        
+				}
+				if(filter instanceof XYSeriesArrayDataFilter){
+					final XYSeriesArrayDataFilter xyfilter = (XYSeriesArrayDataFilter) filter;
+					
+					// Ensure that there is no concurrent modification exception or synchronization problems with the
+					// Swing update task
+					SwingUtilities.invokeLater(new Runnable(){
+
+						@Override
+						public void run() {
+							LinePlotSeries series = new LinePlotSeries(xyfilter.getSeriesName() + "-" + xyfilter.getCount()); // Series name must be unique
+							xyfilter.incrementCount();
+
+//								((LinePlot)xyfilter.getPlot()).getData().removeAllSeries(); // Remove all series from the data
+							// If we can agree only to display one series at a time also a clear() on the actual series is better
+                                                        ((LinePlot)xyfilter.getPlot()).addSeries(series);
+                                                        xyfilter.setSeries(series);
+							
+							// Remove outdated series
+							if(((LinePlot)xyfilter.getPlot()).getNumberOfSeries()>xyfilter.getMaxSeries()){
+								// Remove oldest series
+                                                                LinePlotSeries s = ((LinePlot)xyfilter.getPlot()).getSeries(0);
+								((LinePlot)xyfilter.getPlot()).removeSeries(s);
+							}
+							
+							double[] data = message.getData(xyfilter.getIdY());
+                                                        
+                                                        
+							// Copy data starting from offset to size
+							int size = data.length;
+							int offset = xyfilter.getOffset();
+							if(xyfilter.getSize()>0 && offset+xyfilter.getSize()<data.length){
+								size = offset + xyfilter.getSize();
+							}
+                                                        
+                                                        ((LinePlot)xyfilter.getPlot()).setUpdatesEnabled(updateAtStreamElement);
+							for(int i=offset;i<size;i++){
+								//series.add(i,data[i], false); // Do not fire change event - this would degrade performance drastically
+                                                            series.appendData(i,data[i]);
+							}
+                                                        ((LinePlot)xyfilter.getPlot()).setUpdatesEnabled(true);
+						}
+						
+					});
+				}
+				else if(filter instanceof XYZSeriesDataFilter){
+					XYZSeriesDataFilter xyzfilter = (XYZSeriesDataFilter) filter;
+					try{
+                                            xyzfilter.getPlot().setUpdatesEnabled(updateAtStreamElement);
+						xyzfilter.getSeries().appendData((Double) message.getData(xyzfilter.getIdX()),(Double) message.getData(xyzfilter.getIdY()), (Double) message.getData(xyzfilter.getIdZ()));
+                                                xyzfilter.getPlot().setUpdatesEnabled(true);
+					}
+					catch (Exception e) {
+						// Ignore if something goes wrong while adding a datapoint
+						logger.log(Level.WARNING, "Unable to plot datapoint in matrix plot", e);
+					}
+				}
+				else if(filter instanceof XYZSeriesArrayDataFilter){
+					XYZSeriesArrayDataFilter xyzfilter = (XYZSeriesArrayDataFilter) filter;
+					try{
+						double[] data = (double[]) message.getData(xyzfilter.getIdZ());
+						double y = (Double) message.getData(xyzfilter.getIdY());
+//						int offset = xyzfilter.getOffset();
+//						int size = xyzfilter.getSize();
+//						for(int i=offset;i<offset+size; i++){
+                                                xyzfilter.getPlot().setUpdatesEnabled(updateAtStreamElement);
+						for(int i=0;i<data.length; i++){	
+							((MatrixPlot)xyzfilter.getPlot()).getSeries("").appendData(i, y, data[i]);
+						}
+                                                xyzfilter.getPlot().setUpdatesEnabled(true);                                                
+					}
+					catch (Exception e) {
+						// Ignore if something goes wrong while adding a datapoint
+						logger.log(Level.WARNING, "Unable to plot datapoint in matrix plot", e);
+					}
+				}
+			}
+	}
+	
+        Double getDoubleValue(Object value){
+            if(value instanceof Double){
+                return (Double) value;
+            }
+            if(value instanceof Integer){
+                return (double)((Integer) value);
+            }
+            else if(value instanceof Short){
+                return (double)((Short) value);
+            }
+            else if(value instanceof Long){
+                return (double)((Long) value);
+            }
+            else if(value instanceof Float){
+                return (double)((Float) value);
+            }
+            else if(value instanceof Boolean){
+                return ((Boolean) value)?1.0:0.0;
+            }
+            return Double.NaN;
+        }
+	
+	@Subscribe
+	public void onStreamDelimiterMessage(StreamDelimiterMessage message){
+			for(SeriesDataFilter filter: filters){
+				if(filter instanceof XYSeriesDataFilter){
+					// Create new series
+					XYSeriesDataFilter xyfilter = (XYSeriesDataFilter) filter;
+//					if (message.getNumber() == xyfilter.getDimensionX()) {
+						if (message.getNumber() == 0) { // TODO need to check this - here we assume that always at the lowest level we create a new series 
+						// Indicate to create new series at the next message
+						xyfilter.setCount(xyfilter.getCount()+1); // Increment count of the filter
+						xyfilter.setNewseries(true);
+					}
+				}
+			}
+
+			// Update matrix plot at the end of each line
+			if(updateAtStreamDelimiter){
+                            for (Plot plot:getPlots()) {
+                                    plot.update(true);
+				}
+			}
+
+			// Clear matrix plot if iflag is encountered
+			// TODO: One need to check whether the iflag belongs to a delimiter
+			// of a higher dimension than the highest dimension (axis) that
+			// is involved in the plot
+			if (message.isIflag()) {
+				clearPlot = true;
+			}
+	}
+	
+	@Subscribe
+	public void onEndOfStreamMessage(EndOfStreamMessage message){
+		ecount++;
+		
+		// Update plots if updateAtEndOfStream flag is set
+		if(updateAtEndOfStream){
+			// Update matrix plots
+                        for (Plot plot:getPlots()) {
+                                plot.update(true);
+                            }
+		}
+	}
+	
+	public void configure(){
+		ecount = 0;
+		clearPlot = false;
+	}
+	
+	/**
+	 * Get the plot panels for the visualizations
+	 * @return	List of configured JPanels
+	 */
+	public List<JPanel> getPlotPanels(){
+		List<JPanel> panels = new ArrayList<JPanel>();
+		for(SeriesDataFilter f: filters){
+                    JPanel panel=(JPanel) f.getPlot();
+                    if ((panel!=null) &&(!panels.contains(panel)))
+			panels.add(panel);
+		}
+		
+		return panels;
+	}
+
+	public List<Plot> getPlots(){
+		List<Plot> plots = new ArrayList<Plot>();
+		for(SeriesDataFilter f: filters){
+                    Plot plot=f.getPlot();
+                    if ((plot!=null) &&(!plots.contains(plot)))
+			plots.add(plot);
+		}		
+		return plots;
+	}
+
+        public boolean isUpdateAtStreamElement() {
+		return updateAtStreamElement;
+	}
+	public void setUpdateAtStreamElement(boolean updateAtStreamElement) {
+		this.updateAtStreamElement = updateAtStreamElement;
+	}
+	public boolean isUpdateAtStreamDelimiter() {
+		return updateAtStreamDelimiter;
+	}
+	public void setUpdateAtStreamDelimiter(boolean updateAtStreamDelimiter) {
+		this.updateAtStreamDelimiter = updateAtStreamDelimiter;
+	}
+	public boolean isUpdateAtEndOfStream() {
+		return updateAtEndOfStream;
+	}
+	public void setUpdateAtEndOfStream(boolean updateAtEndOfStream) {
+		this.updateAtEndOfStream = updateAtEndOfStream;
+	}
+
+        public int getSubsampling() {
+		return subsampling;
+	}
+	public void setSubsampling(int factor) {
+		this.subsampling = factor;
+                subsamplingCounter=subsampling;//To plot first point
+	}	
+}

src/main/java/ch/psi/fda/ui/visualizer/XYSeriesArrayDataFilter.java

@@ -0,0 +1,157 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui.visualizer;
+
+import ch.psi.plot.LinePlotSeries;
+import ch.psi.plot.Plot;
+
+/**
+ * Metadata of a group of XYSeries.
+ * This metadata holds the information needed by the DataVisualizer
+ * to plot series.
+ */
+public class XYSeriesArrayDataFilter implements SeriesDataFilter {
+	
+	private final String idY;
+	
+	// Name of the series generated by this filter
+	private String seriesName = "";
+	
+	// Number of series generated for this filter 
+	private int count = 0;
+	
+	private int maxSeries = 10;
+
+	// Offset of the array to plot
+	private int offset = 0;
+	// Size of the array to plot - size 0 means the complete array
+	private int size = 0;
+	
+	// Plot the data of this filter goes to
+	private final Plot plot;
+	
+	public XYSeriesArrayDataFilter(String idY, Plot plot){
+		this.idY = idY;
+		this.plot = plot;
+	}
+	
+	/**
+	 * @return the yId
+	 */
+	public String getIdY() {
+		return idY;
+	}
+
+	/**
+	 * @return the seriesName
+	 */
+	public String getSeriesName() {
+		return seriesName;
+	}
+
+	/**
+	 * @param seriesName the seriesName to set
+	 */
+	public void setSeriesName(String seriesName) {
+		this.seriesName = seriesName;
+	}
+
+	private LinePlotSeries series = null;
+        
+        @Override
+        public LinePlotSeries getSeries(){
+            return series;
+        }        
+        
+        public void setSeries(LinePlotSeries series){
+            this.series=series;
+        }        
+
+        /**
+	 * @return the count
+	 */
+	public int getCount() {
+		return count;
+	}
+
+	/**
+	 * @param count the count to set
+	 */
+	public void setCount(int count) {
+		this.count = count;
+	}
+
+	/**
+	 * @return the plot
+	 */
+	public Plot getPlot() {
+		return plot;
+	}
+
+	/**
+	 * Increment series count
+	 */
+	public void incrementCount(){
+		count++;
+	}
+
+	/**
+	 * @param maxSeries the maxSeries to set
+	 */
+	public void setMaxSeries(int maxSeries) {
+		this.maxSeries = maxSeries;
+	}
+
+	/**
+	 * @return the maxSeries
+	 */
+	public int getMaxSeries() {
+		return maxSeries;
+	}
+
+	/**
+	 * @return the offset
+	 */
+	public int getOffset() {
+		return offset;
+	}
+
+	/**
+	 * @param offset the offset to set
+	 */
+	public void setOffset(int offset) {
+		this.offset = offset;
+	}
+
+	/**
+	 * @return the size
+	 */
+	public int getSize() {
+		return size;
+	}
+
+	/**
+	 * @param size the size to set
+	 */
+	public void setSize(int size) {
+		this.size = size;
+	}
+	
+}

src/main/java/ch/psi/fda/ui/visualizer/XYSeriesDataFilter.java

@@ -0,0 +1,98 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui.visualizer;
+
+import ch.psi.plot.LinePlot;
+import ch.psi.plot.LinePlotSeries;
+import ch.psi.plot.PlotSeries;
+
+/**
+ * Metadata of a group of XYSeries.
+ * This metadata holds the information needed by the DataVisualizer
+ * to plot series.
+ */
+public class XYSeriesDataFilter implements SeriesDataFilter{
+	
+	private final String idX;
+	private final String idY;
+	
+	// Name of the series generated by this filter
+	private String seriesName = "";
+	
+	// Number of series generated for this filter 
+	private int count = 0;
+        
+        // Max number of points per series (additional appends make oldest value to be )
+        private int maxNumberOfPoints=-1;
+	
+	// Plot the data of this filter goes to
+	private final LinePlot plot;
+		
+	private boolean newseries = false;
+        
+        private LinePlotSeries series = null;
+        @Override
+        public LinePlotSeries getSeries(){
+            return series;
+        }
+        public void setSeries(LinePlotSeries series){
+            this.series=series;
+        }        
+	
+	public XYSeriesDataFilter(String idX, String idY, LinePlot plot){
+		this.idX = idX;
+		this.idY = idY;
+		this.plot = plot;
+	}
+
+	public String getIdX() {
+		return idX;
+	}
+	public String getIdY() {
+		return idY;
+	}
+	public String getSeriesName() {
+		return seriesName;
+	}
+	public void setSeriesName(String seriesName) {
+		this.seriesName = seriesName;
+	}
+	public int getCount() {
+		return count;
+	}
+	public void setCount(int count) {
+		this.count = count;
+	}
+	public LinePlot getPlot() {
+		return plot;
+	}
+	public boolean isNewseries() {
+		return newseries;
+	}
+	public void setNewseries(boolean newseries) {
+		this.newseries = newseries;
+	}
+	public int getMaxNumberOfPoints() {
+		return maxNumberOfPoints;
+	}
+	public void setMaxNumberOfPoints(int count) {
+		this.maxNumberOfPoints = count;
+	}	
+}

src/main/java/ch/psi/fda/ui/visualizer/XYZSeriesArrayDataFilter.java

@@ -0,0 +1,95 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui.visualizer;
+
+import ch.psi.plot.MatrixPlotSeries;
+import ch.psi.plot.Plot;
+
+public class XYZSeriesArrayDataFilter implements SeriesDataFilter {
+
+	private final String idY;
+	private final String idZ;
+	
+	// Name of the series generated by this filter
+	private String seriesName = "";
+
+	// Number of series generated for this filter 
+	private int count = 0;
+	
+	// Plot the data of this filter goes to
+	private final Plot plot;
+	
+	private boolean newseries = false;
+	
+	private final int size;
+	private final int offset;
+	
+	public XYZSeriesArrayDataFilter(String idY, String idZ, int offset, int size, Plot plot){
+		this.idY = idY;
+		this.idZ = idZ;
+		this.offset = offset;
+		this.size = size;
+		this.plot = plot;
+	}
+
+	public String getIdZ() {
+		return idZ;
+	}
+	public String getSeriesName() {
+		return seriesName;
+	}
+	public void setSeriesName(String seriesName) {
+		this.seriesName = seriesName;
+	}
+	private MatrixPlotSeries series = null;
+        
+        @Override
+        public MatrixPlotSeries getSeries(){
+            return series;
+        }        
+        
+        public void setSeries(MatrixPlotSeries series){
+            this.series=series;
+        }               
+	public int getCount() {
+		return count;
+	}
+	public void setCount(int count) {
+		this.count = count;
+	}
+	public boolean isNewseries() {
+		return newseries;
+	}
+	public void setNewseries(boolean newseries) {
+		this.newseries = newseries;
+	}
+	public String getIdY() {
+		return idY;
+	}
+	public int getOffset() {
+		return offset;
+	}
+	public int getSize() {
+		return size;
+	}
+	public Plot getPlot() {
+		return plot;
+	}
+}

src/main/java/ch/psi/fda/ui/visualizer/XYZSeriesDataFilter.java

@@ -0,0 +1,91 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui.visualizer;
+
+import ch.psi.plot.MatrixPlotSeries;
+import ch.psi.plot.Plot;
+
+public class XYZSeriesDataFilter implements SeriesDataFilter {
+
+	private final String idX;
+	private final String idY;
+	private final String idZ;
+	
+	// Name of the series generated by this filter
+	private String seriesName = "";
+	
+	// Number of series generated for this filter 
+	private int count = 0;
+	
+	// Plot the data of this filter goes to
+	private final Plot plot;
+	
+	private boolean newseries = false;
+	
+	
+	public XYZSeriesDataFilter(String idX, String idY, String idZ, Plot plot){
+		this.idX = idX;
+		this.idY = idY;
+		this.idZ = idZ;
+		this.plot = plot;
+	}
+
+	public String getIdZ() {
+		return idZ;
+	}
+	public String getSeriesName() {
+		return seriesName;
+	}
+	public void setSeriesName(String seriesName) {
+		this.seriesName = seriesName;
+	}
+        
+	private MatrixPlotSeries series = null;
+        
+        @Override
+        public MatrixPlotSeries getSeries(){
+            return series;
+        }        
+        public void setSeries(MatrixPlotSeries series){
+            this.series=series;
+        }              
+	public int getCount() {
+		return count;
+	}
+	public void setCount(int count) {
+		this.count = count;
+	}
+	public boolean isNewseries() {
+		return newseries;
+	}
+	public void setNewseries(boolean newseries) {
+		this.newseries = newseries;
+	}
+	public String getIdX() {
+		return idX;
+	}
+	public String getIdY() {
+		return idY;
+	}
+	public Plot getPlot() {
+		return plot;
+	}
+	
+}

src/test/java/ch/psi/fda/deserializer/DataDeserializerMDATest.java

@@ -0,0 +1,109 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.deserializer;
+
+import java.io.File;
+import java.net.URI;
+import java.net.URL;
+import java.util.logging.Logger;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import com.google.common.eventbus.EventBus;
+import com.google.common.eventbus.Subscribe;
+
+import ch.psi.fda.messages.ControlMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+
+/**
+ * For testing whether the created MDA file is correct use following 
+ * program on a SLS SL5 beamline console (or slslc05/06)
+ */
+public class DataDeserializerMDATest {
+	
+	private static Logger logger = Logger.getLogger(DataDeserializerMDATest.class.getName());
+
+	private EventBus bus;
+	private DataDeserializerMDA deserializer;
+	
+	@Before
+	public void setUp() throws Exception {
+		bus = new EventBus();
+		URL url = this.getClass().getClassLoader().getResource("testdata/mda/mdadata7.mda");
+		deserializer = new DataDeserializerMDA(bus, new File(new URI(url.toString())));
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testRead() throws InterruptedException {
+		
+		
+		
+		
+		// Do "read" data
+		bus.register(new Object(){
+			boolean first = true;
+			
+			@Subscribe
+			public void onMessage(Message m){
+				if(m instanceof DataMessage){
+					DataMessage x = (DataMessage) m;
+					
+					if(first){
+						first=false;
+						// Visualize metadata
+						StringBuilder b = new StringBuilder();
+						b.append("[");
+						StringBuilder b1 = new StringBuilder();
+						b1.append("[");
+						for(Metadata cm : x.getMetadata()){
+							b.append(" ");
+							b.append(cm.getId());
+							b1.append(" ");
+							b1.append(cm.getDimension());
+						}
+						b.append(" ]");
+						b1.append(" ]");
+						
+						logger.info("Metadata "+b.toString());
+						logger.info("Metadata "+b1.toString());
+					}
+					
+					
+					logger.info( x.toString() );
+				}
+				else if(m instanceof ControlMessage){
+					logger.info("---- "+m.toString()+" ----");
+				}
+			}
+		});
+		deserializer.read();
+		
+		
+	}
+
+}

src/test/java/ch/psi/fda/deserializer/DataDeserializerTest.java

@@ -0,0 +1,85 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.deserializer;
+
+import java.io.File;
+import java.net.URI;
+import java.net.URL;
+import java.util.logging.Logger;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import com.google.common.eventbus.EventBus;
+import com.google.common.eventbus.Subscribe;
+
+import ch.psi.fda.deserializer.DataDeserializer;
+import ch.psi.fda.deserializer.DataDeserializerTXT;
+import ch.psi.fda.messages.ControlMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
+
+public class DataDeserializerTest {
+	
+	private static Logger logger = Logger.getLogger(DataDeserializerTest.class.getName());
+	
+	private DataDeserializer deserializer;
+	private EventBus bus;
+	
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@Before
+	public void setUp() throws Exception {
+		bus = new EventBus();
+		URL url = this.getClass().getClassLoader().getResource("testdata/text/textdata2.txt");
+		deserializer = new DataDeserializerTXT(bus, new File(new URI(url.toString())));
+	}
+
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	/**
+	 * Test method for {@link ch.psi.fda.deserializer.DataDeserializerTXT#run()}.
+	 * @throws InterruptedException 
+	 */
+	@Test
+	public void testRun() throws InterruptedException {
+		
+		bus.register(new Object(){
+			@Subscribe
+			public void onMessage(Message m){
+				if(m instanceof DataMessage){
+					DataMessage x = (DataMessage) m;
+					logger.info( x.toString() );
+				}
+				else if(m instanceof ControlMessage){
+					logger.info("---- "+m.toString()+" ----");
+				}
+			}
+		});
+		deserializer.read();
+	}
+}

src/test/java/ch/psi/fda/serializer/SerializerTest.java

@@ -0,0 +1,225 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.serializer;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+import ch.psi.fda.serializer.SerializerMAT;
+import ch.psi.fda.serializer.SerializerMAT2D;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT2D;
+import ch.psi.fda.serializer.SerializerTXTSplit;
+
+
+public class SerializerTest {
+
+	private static final String tmpDirectory = "target/tmp";
+	
+	private EventBus bus;
+	
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@Before
+	public void setUp() throws Exception {
+		new File(tmpDirectory).mkdirs();
+		bus = new EventBus();
+	}
+	
+	/**
+	 * Generate 1D data
+	 * @throws InterruptedException
+	 */
+	private void generate1DData() throws InterruptedException{
+		List<Metadata> metadata = new ArrayList<>();
+		metadata.add(new Metadata("id0", 0));
+		metadata.add(new Metadata("id1", 0));
+		metadata.add(new Metadata("id2", 0));
+		
+		// Dimension
+		DataMessage m = new DataMessage(metadata);
+		m.getData().add(0.000000000000000001);
+		m.getData().add(0.1);
+		m.getData().add(1d); // have this value as double
+		bus.post(m);
+		
+		m = new DataMessage(metadata);
+		m.getData().add(0.02);
+		m.getData().add(0.2);
+		m.getData().add(2d); // have this value as double
+		bus.post(m);
+		bus.post(new EndOfStreamMessage());
+	}
+	
+	/**
+	 * Generate 2D test data
+	 * @throws InterruptedException
+	 */
+	private void generate2DData() throws InterruptedException{
+		List<Metadata> metadata = new ArrayList<>();
+		metadata.add(new Metadata("id0", 1));
+		metadata.add(new Metadata("id1", 0));
+		metadata.add(new Metadata("id2", 0));
+		
+		for(double i=0;i<5;i++){
+			for(double t=0.1; t<10; t=t+0.1){
+				// Dimension
+				DataMessage m = new DataMessage(metadata);
+				m.getData().add(i);
+				m.getData().add(t);
+				m.getData().add(Math.log(t)); // have this value as double
+				bus.post(m);
+			}
+			bus.post(new StreamDelimiterMessage(0));
+		}
+		bus.post(new StreamDelimiterMessage(1));
+		
+		
+		bus.post(new EndOfStreamMessage());
+	}
+	
+	/**
+	 * Generate 3d test data
+	 * @throws InterruptedException
+	 */
+	private void generate3DData() throws InterruptedException{
+		List<Metadata> metadata = new ArrayList<>();
+		metadata.add(new Metadata("id0", 2));
+		metadata.add(new Metadata("id1", 1));
+		metadata.add(new Metadata("id2", 0));
+		metadata.add(new Metadata("id3", 0));
+		
+		for(double z=30;z<36;z++){
+			for(double i=0;i<6;i++){
+				for(double t=0.1; t<1.1; t=t+0.1){
+					// Dimension
+					DataMessage m = new DataMessage(metadata);
+					m.getData().add(z);
+					m.getData().add(i);
+					m.getData().add(t);
+					m.getData().add(Math.log(t)); // have this value as double
+					bus.post(m);
+				}
+				bus.post(new StreamDelimiterMessage(0));
+			}
+			bus.post(new StreamDelimiterMessage(1));
+		}
+		bus.post(new StreamDelimiterMessage(2));
+		
+		bus.post(new EndOfStreamMessage());
+	}
+
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	/**
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
+	 * @throws InterruptedException 
+	 */
+	@Test
+	public void testRunTXT() throws InterruptedException {
+		SerializerTXT serializer = new SerializerTXT(new File(tmpDirectory+"/test.txt"), true);
+		bus.register(serializer);
+		generate1DData();
+	}
+
+	/**
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
+	 * @throws InterruptedException 
+	 */
+	@Test
+	public void testRunMAT() throws InterruptedException {
+		
+		SerializerMAT serializer = new SerializerMAT(new File(tmpDirectory+"/test.mat"));
+		bus.register(serializer);
+		generate1DData();
+	}
+	
+	/**
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
+	 * @throws InterruptedException 
+	 */
+	@Test
+	public void testRunMAT2D() throws InterruptedException {
+		SerializerMAT2D serializer = new SerializerMAT2D(new File(tmpDirectory+"/test-2d.mat"));
+		bus.register(serializer);
+		generate2DData();
+	}
+	
+	/**
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
+	 * @throws InterruptedException 
+	 */
+	@Test
+	public void testRunTXT2D() throws InterruptedException {
+		SerializerTXT2D serializer = new SerializerTXT2D(new File(tmpDirectory+"/test-2d.txt"));
+		bus.register(serializer);
+		generate2DData();
+	}
+	
+	/**
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
+	 * @throws InterruptedException 
+	 */
+	@Test
+	public void testRunSplitTXT() throws InterruptedException {
+		SerializerTXTSplit serializer = new SerializerTXTSplit(new File(tmpDirectory+"/test-2d-split.txt"));
+		bus.register(serializer);
+		generate2DData();
+	}
+	
+	/**
+	 * Test method for {@link ch.psi.fda.serializer.SerializerMDA#run()}.
+	 * @throws InterruptedException 
+	 */
+	@Test
+	public void testRun2D() throws InterruptedException {
+		SerializerMDA serializer = new SerializerMDA(new File(tmpDirectory+"/test-2d.mda"));
+		bus.register(serializer);
+		generate2DData();
+	}
+
+	/**
+	 * Test method for {@link ch.psi.fda.serializer.SerializerMDA#run()}.
+	 * @throws InterruptedException 
+	 */
+	@Test
+	public void testRun3D() throws InterruptedException {
+		SerializerMDA serializer = new SerializerMDA(new File(tmpDirectory+"/test-3d.mda"));
+		bus.register(serializer);
+		generate3DData();
+	}
+}

src/test/java/ch/psi/fda/ui/AcquisitionMainTest.java

@@ -0,0 +1,38 @@
+/**
+ * 
+ * Copyright 2011 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.ui;
+
+import org.junit.Ignore;
+import org.junit.Test;
+
+import ch.psi.fda.ui.AcquisitionMain;
+
+public class AcquisitionMainTest {
+
+	/**
+	 * Test method for {@link ch.psi.fda.ui.AcquisitionMain#main(java.lang.String[])}.
+	 */
+	@Ignore
+	@Test
+	public void testMain() {
+		System.setProperty("ch.psi.fda.home","src/test/resources/home");
+		AcquisitionMain.main(new String[]{"src/test/resources/home/scans/templates/scan1d-waitError.xml"});
+	}
+
+}

src/test/java/ch/psi/fda/ui/ApplicationConfiguratorTest.java

@@ -0,0 +1,41 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui;
+
+import java.io.IOException;
+
+import org.junit.Ignore;
+import org.junit.Test;
+
+import ch.psi.fda.ui.ApplicationConfigurator;
+
+public class ApplicationConfiguratorTest {
+
+	private ApplicationConfigurator configurator;
+	
+	@Ignore
+	@Test
+	public void testInitializeApplication() throws IOException{
+		System.setProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT, "target/tmp/home");
+		configurator = new ApplicationConfigurator();
+		configurator.initializeApplication();
+	}
+
+}

src/test/java/ch/psi/fda/ui/VisualizationMainTest.java

@@ -0,0 +1,122 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui;
+
+import java.io.File;
+import java.net.URI;
+import java.net.URL;
+
+import javax.xml.bind.JAXBException;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.xml.sax.SAXException;
+
+import ch.psi.fda.ui.VisualizationMain;
+
+/**
+ * Testcase for visualization engine
+ */
+public class VisualizationMainTest {
+
+	private VisualizationMain engine;
+	private String configurationFile;
+	private String dataFile;
+	
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@Before
+	public void setUp() throws Exception {
+		URL url = this.getClass().getClassLoader().getResource("testdata/scan/scan1d.xml");
+		configurationFile = new File(new URI(url.toString())).getAbsolutePath();
+		
+		url = this.getClass().getClassLoader().getResource("testdata/scan/scan1d_0000.txt");
+		dataFile = new File(new URI(url.toString())).getAbsolutePath();
+		
+		engine = new VisualizationMain();
+	}
+
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	/**
+	 * Test method for {@link ch.psi.fda.ui.VisualizationMain#visualize(java.io.File, java.io.File)}.
+	 * Test whether a null data parameter is handled correctly
+	 * @throws InterruptedException 
+	 * @throws SAXException 
+	 * @throws JAXBException 
+	 */
+	@Test(expected=RuntimeException.class)
+	public void testVisualizeFileFileDataNull() throws InterruptedException {
+		engine.visualize(new File(configurationFile), null);
+	}
+	
+	/**
+	 * Test method for {@link ch.psi.fda.ui.VisualizationMain#visualize(java.io.File, java.io.File)}.
+	 * Test whether a non existing data file is handled correctly
+	 * @throws InterruptedException 
+	 * @throws SAXException 
+	 * @throws JAXBException 
+	 */
+	@Test(expected=RuntimeException.class)
+	public void testVisualizeFileFileDataNoExist() throws InterruptedException {
+		engine.visualize(new File(configurationFile), new File(""));
+	}
+
+	/**
+	 * Test method for {@link ch.psi.fda.ui.VisualizationMain#visualize(java.io.File, java.io.File)}.
+	 * Check whether null configuration file is handled correctly
+	 * @throws InterruptedException 
+	 * @throws SAXException 
+	 * @throws JAXBException 
+	 */
+	@Test(expected=RuntimeException.class)
+	public void testVisualizeFileFileConfigNull() throws InterruptedException {
+		engine.visualize(new File(""), new File(dataFile));
+	}
+	
+	/**
+	 * Test method for {@link ch.psi.fda.ui.VisualizationMain#visualize(java.io.File, java.io.File)}.
+	 * Test correct visualization
+	 * @throws InterruptedException 
+	 * @throws SAXException 
+	 * @throws JAXBException 
+	 */
+	@Test
+	public void testVisualizeFileFile() throws InterruptedException {
+		engine.visualize(new File(configurationFile), new File(dataFile));
+	}
+	
+	/**
+	 * Test whether main can automatically determine the configuration file for a given data file
+	 * Test method for {@link ch.psi.fda.ui.VisualizationMain#main(String[])}
+	 */
+	@Test
+	public void testMain(){
+		// ATTENTION - This test will never fail because possible exceptions are caught in the main method !!!!
+		VisualizationMain.main(new String[]{dataFile});
+	}
+}

src/test/java/ch/psi/fda/ui/visualizer/DataVisualizerTest.java

@@ -0,0 +1,222 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.ui.visualizer;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import org.junit.Ignore;
+import org.junit.Test;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+import ch.psi.fda.ui.visualizer.Visualizer;
+import ch.psi.fda.vdescriptor.VDescriptor;
+import ch.psi.fda.vdescriptor.XYSeries;
+import ch.psi.fda.vdescriptor.XYZSeries;
+import ch.psi.fda.vdescriptor.YSeries;
+
+/**
+ * All test cases in this test class are meant to be executed manually Remove @Ignore
+ * in front of the test function to be able to run it.
+ */
+public class DataVisualizerTest {
+
+	private static final Logger logger = Logger.getLogger(DataVisualizerTest.class.getName());
+
+	@Ignore
+	@Test
+	public void testRun() throws InterruptedException {
+		List<Metadata> metadata = new ArrayList<>();
+		metadata.add(new Metadata("id1"));
+		metadata.add(new Metadata("id2"));
+		metadata.add(new Metadata("id3"));
+		
+		EventBus bus = new EventBus();
+		
+		VDescriptor vdescriptor = new VDescriptor();
+		
+		ch.psi.fda.vdescriptor.LinePlot plot = new ch.psi.fda.vdescriptor.LinePlot("One");
+		plot.getData().add(new XYSeries("id1", "id2"));
+		vdescriptor.getPlots().add(plot);
+		
+		plot = new ch.psi.fda.vdescriptor.LinePlot("Two");
+		plot.getData().add(new XYSeries("id1", "id3"));
+		vdescriptor.getPlots().add(plot);
+
+		// Create visualizer
+		Visualizer visualizer = new Visualizer(vdescriptor);
+		bus.register(visualizer);
+
+		JFrame f = new JFrame();
+		f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+		f.setSize(600, 400);
+		JPanel pan = new JPanel();
+		for (JPanel pp : visualizer.getPlotPanels()) {
+			pan.add(pp);
+		}
+		f.add(pan);
+		f.setVisible(true);
+
+		DataMessage m;
+		for (double t = 0; t < 4; t++) {
+			for (double i = 0; i < 100; i = i + 0.1) {
+				m = new DataMessage(metadata);
+				m.getData().add(i);
+				m.getData().add(t + Math.sin(i));
+				m.getData().add(t + Math.cos(i));
+				bus.post(m);
+
+				Thread.sleep(5);
+			}
+			bus.post(new StreamDelimiterMessage(0));
+		}
+
+		bus.post(new EndOfStreamMessage());
+
+		Thread.sleep(10000);
+	}
+
+	@Ignore
+	@Test
+	public void testRunArray() throws InterruptedException {
+
+		List<Metadata> metadata = new ArrayList<>();
+		metadata.add(new Metadata("id1"));
+
+		EventBus bus = new EventBus();
+
+		VDescriptor vdescriptor = new VDescriptor();
+		
+		ch.psi.fda.vdescriptor.LinePlot plot = new ch.psi.fda.vdescriptor.LinePlot("One");
+		plot.getData().add(new YSeries("id1"));
+		vdescriptor.getPlots().add(plot);
+		
+		// Create visualizer
+		Visualizer visualizer = new Visualizer(vdescriptor);
+		bus.register(visualizer);
+
+		JFrame f = new JFrame();
+		f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+		f.setSize(600, 400);
+		JPanel pan = new JPanel();
+		for (JPanel pp : visualizer.getPlotPanels()) {
+			pan.add(pp);
+		}
+		f.add(pan);
+		f.setVisible(true);
+
+		DataMessage m;
+		int npoints = 10000;
+		for (double t = 0; t < 10; t++) {
+			double[] values = new double[npoints];
+
+			for (int i = 0; i < npoints; i++) {
+				values[i] = Math.sin(i * 0.01) + Math.cos(t);
+			}
+
+			m = new DataMessage(metadata);
+			m.getData().add(values);
+			bus.post(m);
+
+			Thread.sleep(500);
+		}
+		bus.post(new StreamDelimiterMessage(0));
+		bus.post(new EndOfStreamMessage());
+
+		Thread.sleep(10000);
+	}
+
+	@Ignore
+	@Test
+	public void testRun2D() throws InterruptedException {
+
+		double nx = 1000;
+		double ny = 1000;
+
+		List<Metadata> metadata = new ArrayList<>();
+		metadata.add(new Metadata("id1"));
+		metadata.add(new Metadata("id2"));
+		metadata.add(new Metadata("id3"));
+
+		// EventBus bus = new AsyncEventBus(Executors.newFixedThreadPool(1));
+		EventBus bus = new EventBus();
+
+		VDescriptor vdescriptor = new VDescriptor();
+		
+		ch.psi.fda.vdescriptor.LinePlot lplot = new ch.psi.fda.vdescriptor.LinePlot("One");
+		lplot.getData().add(new XYSeries("id2", "id3"));
+		vdescriptor.getPlots().add(lplot);
+		
+		ch.psi.fda.vdescriptor.MatrixPlot mplot = new ch.psi.fda.vdescriptor.MatrixPlot("One");
+		mplot.setMinX(1.0);
+		mplot.setMaxX(nx);
+		mplot.setnX((int)nx);
+		mplot.setMinY(1.0);
+		mplot.setMaxY(ny);
+		mplot.setnY((int)ny);
+		mplot.getData().add(new XYZSeries("id1", "id2", "id3"));
+		vdescriptor.getPlots().add(mplot);
+		
+		// Create visualizer
+		Visualizer visualizer = new Visualizer(vdescriptor);
+		bus.register(visualizer);
+
+		JFrame f = new JFrame();
+		f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+		f.setSize(600, 400);
+		// f.add(plot.getPlotPanel());
+		JPanel pan = new JPanel();
+		for (JPanel pp : visualizer.getPlotPanels()) {
+			pan.add(pp);
+		}
+		f.add(pan);
+		f.setVisible(true);
+
+		DataMessage m;
+		for (double t = 1; t <= nx; t++) {
+			for (double i = 1; i <= ny; i++) {
+				m = new DataMessage(metadata);
+				m.getData().add(t);
+				m.getData().add(i);
+				m.getData().add(t + Math.cos(i));
+				bus.post(m);
+
+				// Thread.sleep(5);
+			}
+			bus.post(new StreamDelimiterMessage(0));
+		}
+
+		bus.post(new EndOfStreamMessage());
+
+		logger.info("Generation done");
+
+		Thread.sleep(100000);
+	}
+
+}

src/test/resources/cdump.properties

@@ -0,0 +1,4 @@
+ch.psi.fda.cdump.dataChannel=CDUMP:WAVE
+ch.psi.fda.cdump.controlChannel=CDUMP:CONTROL
+ch.psi.fda.cdump.samplingRateChannel=CDUMP:SAMPLING
+ch.psi.fda.cdump.nelements=4

src/test/resources/fdaq.properties

@@ -0,0 +1 @@
+ch.psi.fda.fdaq.hostname=localhost

src/test/resources/home/.gitignore

@@ -0,0 +1,2 @@
+/data
+/logs

src/test/resources/home/config/fda.properties

@@ -0,0 +1,15 @@
+# Serialization properties
+ch.psi.fda.aq.data.dir=../data
+ch.psi.fda.aq.data.filePrefix=${yyyy_MM}/${yyyyMMdd}/${yyyyMMddHHmmss}_${name}/${yyyyMMddHHmm}_
+
+# OTF scan related configuration
+ch.psi.fda.aq.otf.channelPrefix=MTEST-HW3-OTFX
+ch.psi.fda.aq.otf.nfsServer=yoke.psi.ch
+ch.psi.fda.aq.otf.nfsShare=/usr/nfs
+ch.psi.fda.aq.otf.smbShare=smb://:@yoke.psi.ch/nfs/
+
+ch.psi.fda.aq.otf.useCrlogic=true
+ch.psi.fda.aq.otf.crlogicPrefix=MTEST-HW3-CRL
+ch.psi.fda.aq.otf.scalerPrefix=MTEST-HW3:JS
+
+ch.psi.fda.aq.notification.recipients=simon.ebner@psi.ch

src/test/resources/home/config/jcae.properties

@@ -0,0 +1,6 @@
+ch.psi.jcae.ContextFactory.addressList=129.129.130.188 129.129.130.255 129.129.130.37 129.129.145.26 129.129.130.88 129.129.130.142
+ch.psi.jcae.ChannelFactory.timeout=2000
+ch.psi.jcae.ChannelFactory.retries=4
+ch.psi.jcae.ChannelBeanFactory.timeout=10000
+ch.psi.jcae.ChannelBeanFactory.waitTimeout=3600000
+ch.psi.jcae.ChannelBeanFactory.retries=4

src/test/resources/home/config/logging.properties

@@ -0,0 +1,14 @@
+# Specify the handlers to create in the root logger
+handlers = java.util.logging.ConsoleHandler
+
+# Set the default logging level for the root logger
+.level=INFO
+
+# Set the default logging level for new ConsoleHandler instances
+java.util.logging.ConsoleHandler.level=ALL
+
+# Set the default formatter for new ConsoleHandler instances
+java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
+
+# Set the default logging level for the logger named com.mycompany
+ch.psi.level=ALL

src/test/resources/home/scans/templates/Co_EXAFS_GeD.xml

@@ -0,0 +1,97 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="1" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 http://www.psi.ch/~ebner/models/scan/1.0">
+  <data format="txt"/>
+  <scan id="">
+	<preAction xsi:type="ChannelAction" channel="X10DA-ES1:START-CSMPL"  value="0" delay="0.1" /> <!-- continuous=OFF -->
+	<preAction xsi:type="ChannelAction" channel="X10DA-OP-MO1:KohzuModeBO.VAL"   value="Auto" delay="0.1" /> 
+	
+	<dimension>
+<!--		<positioner id="posX" name="X10DA-OP-MO1:BraggEAO" readback="X10DA-OP-MO1:BraggERdbkAO" settlingTime="0.4" xsi:type="RegionPositioner">
+-->
+		<positioner id="posX" name="X10DA-OP-MO1:BraggEAO" readback="X10DA-OP-MO1:BraggERdbkAO" settlingTime="0.4" xsi:type="RegionPositioner">
+<!--	REGIONS		-->
+            <region>
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="5" type="Integer" />
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal" value="1" type="Integer" />
+                <start>7.7</start>
+                <end>7.71</end>
+				<stepSize>0.005</stepSize>
+            </region>
+		    <region>
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="5" type="Integer" />
+ 	    	   <preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal" value="1" type="Integer" />
+                <start>7.71</start>
+                <end>7.732</end>
+				<stepSize>0.001</stepSize>
+            </region>
+		   <region>
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="5" type="Integer" />
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal" value="1" type="Integer" />
+                <start>7.732</start>
+                <end>7.75</end>
+				<stepSize>0.0005</stepSize>
+            </region>
+		   <region>
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="5" type="Integer" />
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal" value="1" type="Integer" />
+                <start>7.75</start>
+                <end>7.8</end>
+				<stepSize>0.001</stepSize>
+            </region>
+		   <region>
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="10" type="Integer" />
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal" value="2" type="Integer" />
+                <start>7.8</start>
+                <end>7.9</end>
+				<stepSize>0.0015</stepSize>
+            </region>
+			<region>
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="15" type="Integer" />
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal" value="3" type="Integer" />
+                <start>7.9</start>
+                <end>8.0</end>
+				<stepSize>0.002</stepSize>
+            </region>
+			<region>
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="20" type="Integer" />
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal" value="4" type="Integer" />
+                <start>8.0</start>
+                <end>8.1</end>
+				<stepSize>0.0025</stepSize>
+            </region>
+			<region>
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="20" type="Integer" />
+	    	   <preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal" value="4" type="Integer" />
+                <start>8.1</start>
+                <end>8.2</end>
+				<stepSize>0.003</stepSize>
+            </region>
+						
+		</positioner>
+        <detector id="SAI01-MEAN" xsi:type="ScalarDetector" name="X10DA-ES1-SAI_01:MEAN"/> 
+	   	<detector id="SAI02-MEAN" xsi:type="ScalarDetector" name="X10DA-ES1-SAI_02:MEAN"/> 
+	   	<detector id="SAI03-MEAN" xsi:type="ScalarDetector" name="X10DA-ES1-SAI_03:MEAN"/> 
+		
+ 		<detector id="Ring-current" xsi:type="ScalarDetector" name="ARIDI-PCT:CURRENT"/>
+		
+   		<detector id="IntegrTimeSet" xsi:type="ScalarDetector" name="X10DA-ES1:TOTAL-CYCLES"/>
+   		<detector id="IntegrTimeGet" xsi:type="ScalarDetector" name="X10DA-ES1:INTR-COUNT"/> 
+		<detector id="Timestamp" xsi:type="Timestamp"/> 
+
+		
+		<detector id="GeD_avg_corr" xsi:type="ScalarDetector" name="X10DA-GeD:CNT_Average">
+			<preAction xsi:type="ChannelAction" channel="X10DA-GeD:EraseStart" value="1" delay="0.1" operation="putq"/>   
+			<preAction xsi:type="ChannelAction" channel="X10DA-GeD:Acquiring" value="Acquiring" operation="wait"/>   
+			<preAction xsi:type="ChannelAction" channel="X10DA-ES1:SMPL" value="1" delay="0.1"/>                      
+			<preAction xsi:type="ChannelAction" channel="X10DA-ES1:SMPL-DONE" type="Integer" value="1" delay="0.3" operation="wait"/>
+			<!--<preAction xsi:type="ChannelAction" channel="X10DA-GeD:StopAll" value="1" delay="0.1" />  -->
+			<preAction xsi:type="ChannelAction" channel="X10DA-GeD:Acquiring" value="Done" operation="wait"/>   
+		</detector>
+		
+	</dimension>
+</scan>
+	<visualization xsi:type="LinePlot" x="posX" y="SAI01-MEAN" title="SAI01-MEAN" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="SAI02-MEAN" title="SAI02-MEAN" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="SAI03-MEAN" title="SAI03-MEAN" />  
+	<visualization xsi:type="LinePlot" x="posX" y="GeD_avg_corr" title="Ge detector" />
+</configuration>

src/test/resources/home/scans/templates/GUI_testing_extMot_otf.xml

@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" numberOfExecution="1" failOnSensorError="true">
+    <data format="txt" fileName="FDA_OTF_calc_test1_extMot"/>
+    <scan>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X10DA-TEST1-TMP-SC.CNT" value="0" operation="put" delay="0.1"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X10DA-TEST1-TMP-SC.G1" value="0" operation="put" delay="0.1"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X10DA-TEST1-TMP-SC.CONT" value="0" operation="put" delay="0.1"/>
+        <cdimension>
+            <positioner name="X10DA-ES2-PP2:MOT1" readback="X10DA-TEST1-TMP:EC1" id="id0">
+                <start>0.0</start>
+                <end>0.5</end>
+                <stepSize>0.0020</stepSize>
+                <integrationTime>0.05</integrationTime>
+            </positioner>
+            <detector name="X10DA-TEST1-TMP:EC1" id="Encoder"/>
+            <detector name="X10DA-TEST1-OTFX:FCNT" id="line"/>
+            <detector name="X10DA-TST-SAI_01:MEAN" id="SAI01-MEAN"/>
+            <detector name="X10DA-TST-SAI_02:MEAN" id="SAI02-MEAN"/>
+            <detector name="X10DA-TST-SAI_03:MEAN" id="SAI03-MEAN"/>
+            <detector name="ARIDI-PCT:CURRENT" id="Ring-current"/>
+            <detector name="X10DA-VME-TEST1:LOAD" id="VMELoad"/>
+            <detector name="X10DA-TST:INTR-COUNT" id="IntegrTimeGet"/>
+            <!--<detector name="X10DA-TEST1-OMS:MOT8.SPMG" id="id758511"/>-->
+            <scaler channel="0" id="id01"/>
+            <scaler channel="1" id="id02"/>
+            <timestamp id="Timestamp"/>
+        </cdimension>
+        <dimension zigzag="false">
+            <positioner xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="PseudoPositioner" id="id1">
+                <counts>10</counts>
+            </positioner>
+            <guard>
+                <condition channel="X10DA-TEST1-OMS:MOT8.SPMG" value="Go" type="Integer"/>
+            </guard>
+        </dimension>
+        <manipulation xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ScriptManipulation" id="idM1">
+            <mapping xsi:type="IDParameterMapping" refid="id0" variable="a"/>
+            <mapping xsi:type="IDParameterMapping" refid="Encoder" variable="b"/>
+            <script>
+import math
+def process(a,b):
+ return a + b
+    	</script>
+        </manipulation>
+        <manipulation xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ScriptManipulation" id="idM2">
+            <mapping xsi:type="IDParameterMapping" refid="Timestamp" variable="c"/>
+            <script>
+import math
+before=0.0
+first = True
+def process(c):
+ global before
+ global first
+ if first:
+  first=False
+  before=c
+  ret=0.0
+ else:
+  ret = c-before
+ return ret / 1000
+    	</script>
+        </manipulation>
+    </scan>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="Encoder" title="Encoder"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="idM1" title="Encoder-error"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="id01" title="Ref-scaler"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="MatrixPlot" x="id0" y="id1" z="idM1" title="Encoder-error"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="MatrixPlot" x="id0" y="id1" z="line" title="count-nr"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="idM2" title="Time-sec"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="VMELoad" title="VMELoad"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="MatrixPlot" x="id0" y="id1" z="id01" title="Reference"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="Ring-current" title=" ringcurrent"/>
+    <!--<visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="id758511" title=" guard"/>-->
+</configuration>

src/test/resources/home/scans/templates/StopGo_X10DA-DCM_Fl.xml

@@ -0,0 +1,156 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 http://www.psi.ch/~ebner/models/scan/1.0">
+  <data format="txt"/>
+  <scan id="">
+	<preAction xsi:type="ChannelAction" channel="X10DA-ES1:START-CSMPL"  value="0" delay="0.1" /> <!-- continuous=OFF -->
+	<preAction xsi:type="ChannelAction" channel="X10DA-GeD:StopAll"      value="0" delay="0.1" /> <!-- preset = 0, acquisition time defined by simultan --> 
+	<preAction xsi:type="ChannelAction" channel="X10DA-GeD:PresetReal"   value="0" delay="0.1" /> 
+	<preAction xsi:type="ChannelAction" channel="X10DA-OP-MO1:KohzuModeBO.VAL"   value="Auto" delay="0.1" /> 
+	
+	<dimension>
+		<positioner id="posX" name="X10DA-OP-MO1:BraggEAO" readback="X10DA-OP-MO1:BraggERdbkAO" settlingTime="0.4" xsi:type="RegionPositioner">
+    			  <!--<region>
+	    			  <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="5" type="Integer" />
+	    			  <start>     8.89 </start>
+	        		  <end>       8.9300 </end>
+	        		  <stepSize>   0.005 </stepSize>
+        		  </region>
+         		  <region>
+	    			  <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="5" type="Integer" />
+	    			  <start>     8.9300 </start>
+	        		  <end>       8.9700 </end>
+	        		  <stepSize>   0.001 </stepSize>
+        		  </region>  -->
+    			  <region>
+	    			  <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="10" type="Integer" />
+	    			  <start>     8.97 </start>
+	        		  <end>       9.000 </end>
+	        		  <stepSize>   0.0005 </stepSize>
+        		  </region>
+         		  <region>
+	    			  <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="10" type="Integer" />
+	    			  <start>     9.000 </start>
+	        		  <end>       9.170 </end>
+	        		  <stepSize>   0.001 </stepSize>
+        		  </region>  
+    			  <region>
+	    			  <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="15" type="Integer" />
+	    			  <start>     9.170 </start>
+	        		  <end>       9.320 </end>
+	        		  <stepSize>   0.002 </stepSize>
+        		  </region>
+         		  <region>
+	    			  <preAction xsi:type="ChannelAction" channel="X10DA-ES1:TOTAL-CYCLES" value="20" type="Integer" />
+	    			  <start>     9.320 </start>
+	        		  <end>       9.690 </end>
+	        		  <stepSize>   0.003 </stepSize>
+        		  </region>  
+
+		</positioner>
+		                   
+        <detector id="SAI01-MEAN" xsi:type="ScalarDetector" name="X10DA-ES1-SAI_01:MEAN"/> 
+	   	<detector id="SAI02-MEAN" xsi:type="ScalarDetector" name="X10DA-ES1-SAI_02:MEAN"/> 
+	   	<detector id="SAI03-MEAN" xsi:type="ScalarDetector" name="X10DA-ES1-SAI_03:MEAN"/> 
+		
+		<detector id="mca1.R0" xsi:type="ScalarDetector" name="X10DA-GeD:mca1.R0"/> 
+		<detector id="R1_Fast_peaks" xsi:type="ScalarDetector" name="X10DA-GeD:dxp1.FAST_PEAKS"/> 		
+		<detector id="R1_Slow_peaks" xsi:type="ScalarDetector" name="X10DA-GeD:dxp1.SLOW_PEAKS"/> 
+		<detector id="R1_ELTM" xsi:type="ScalarDetector" name="X10DA-GeD:mca1.ELTM"/> 
+		<detector id="GeD_elapsed_real" xsi:type="ScalarDetector" name="X10DA-GeD:ElapsedReal"/> 		
+		<detector id="GeD_elapsed_live" xsi:type="ScalarDetector" name="X10DA-GeD:ElapsedLive"/> 	
+		
+		<detector id="GeD_corrected_1" xsi:type="ScalarDetector" name="X10DA-GeD:CNT1"/>
+		<detector id="GeD_corrected_2" xsi:type="ScalarDetector" name="X10DA-GeD:CNT2"/>
+		<detector id="GeD_corrected_3" xsi:type="ScalarDetector" name="X10DA-GeD:CNT3"/>
+		<detector id="GeD_corrected_4" xsi:type="ScalarDetector" name="X10DA-GeD:CNT4"/>
+		<detector id="GeD_corrected_5" xsi:type="ScalarDetector" name="X10DA-GeD:CNT5"/>
+		<detector id="GeD_corrected_6" xsi:type="ScalarDetector" name="X10DA-GeD:CNT6"/>
+		<detector id="GeD_corrected_7" xsi:type="ScalarDetector" name="X10DA-GeD:CNT7"/>
+		<detector id="GeD_corrected_8" xsi:type="ScalarDetector" name="X10DA-GeD:CNT8"/>
+		<detector id="GeD_corrected_9" xsi:type="ScalarDetector" name="X10DA-GeD:CNT9"/>
+		<detector id="GeD_corrected_10" xsi:type="ScalarDetector" name="X10DA-GeD:CNT10"/>
+		<detector id="GeD_corrected_11" xsi:type="ScalarDetector" name="X10DA-GeD:CNT11"/>
+		<detector id="GeD_corrected_12" xsi:type="ScalarDetector" name="X10DA-GeD:CNT12"/>
+		<detector id="sample_count" xsi:type="ScalarDetector" name="X10DA-ES1:INTR-COUNT"/>		
+		<detector id="GeD_corrected_avg" xsi:type="ScalarDetector" name="X10DA-GeD:CNT_Average"/>
+				
+		<detector id="energyRB" xsi:type="ScalarDetector" name="X10DA-OP-MO1:BraggERdbkAO"/>
+   		<!--<detector id="Ring-current" xsi:type="ScalarDetector" name="ARIDI-PCT:CURRENT"/>-->
+   		<detector id="IntegrTimeSet" xsi:type="ScalarDetector" name="X10DA-ES1:TOTAL-CYCLES"/>
+   		<detector id="IntegrTimeGet" xsi:type="ScalarDetector" name="X10DA-ES1:INTR-COUNT"/> 
+		<detector id="Timestamp" xsi:type="Timestamp"/> 
+
+
+		<detector id="ElapsedRT" xsi:type="ScalarDetector" name="X10DA-GeD:mca1.ERTM"> 
+			<preAction xsi:type="ChannelAction" channel="X10DA-GeD:EraseStart" value="1" delay="0.1" operation="putq"/>   <!-- was putq -->  
+			<preAction xsi:type="ChannelAction" channel="X10DA-GeD:Acquiring" value="Acquiring" operation="wait"/>   
+			<preAction xsi:type="ChannelAction" channel="X10DA-ES1:SMPL" value="1" delay="0.1"/>                      
+			<preAction xsi:type="ChannelAction" channel="X10DA-ES1:SMPL-DONE" type="Integer" value="1" delay="0.2" operation="wait"/>
+			
+			<preAction xsi:type="ChannelAction" channel="X10DA-GeD:StopAll" value="1" delay="0.1" />                   
+			<!--<preAction xsi:type="ChannelAction" channel="X10DA-ES1:SMPL" value="0" /> -->                  
+			<preAction xsi:type="ChannelAction" channel="X10DA-GeD:Acquiring" value="Done" operation="wait"/>   
+		</detector>
+
+	</dimension>
+	
+<manipulation id="idM_IF" xsi:type="ScriptManipulation">
+    <mapping xsi:type="IDParameterMapping" variable="a" refid="SAI01-MEAN"/>
+    <mapping xsi:type="IDParameterMapping" variable="b" refid="GeD_corrected_avg"/>
+    <script>
+import math
+def process(a,b):
+ return (b / a)
+    </script>
+</manipulation>
+
+<manipulation id="idM_It" xsi:type="ScriptManipulation">
+    <mapping xsi:type="IDParameterMapping" variable="c" refid="SAI01-MEAN"/>
+    <mapping xsi:type="IDParameterMapping" variable="d" refid="SAI02-MEAN"/>
+    <script>
+import math
+def process(c,d):
+ return math.log(c / d)
+    </script>
+</manipulation>
+
+<manipulation id="idM_C1_dtc" xsi:type="ScriptManipulation">
+    <mapping xsi:type="IDParameterMapping" variable="e" refid="mca1.R0"/>
+    <mapping xsi:type="IDParameterMapping" variable="f" refid="R1_Fast_peaks"/>
+    <mapping xsi:type="IDParameterMapping" variable="g" refid="R1_Slow_peaks"/>
+    <mapping xsi:type="IDParameterMapping" variable="h" refid="R1_ELTM"/>
+    <script>
+import math
+def process(e,f,g,h):
+ return (e / h / g * f)
+    </script>
+</manipulation>
+	
+  </scan>
+	<!--<visualization xsi:type="LinePlot" x="posX" y="FAST_PEAKS" title="FAST_PEAKS" />
+	<visualization xsi:type="LinePlot" x="posX" y="SLOW_PEAKS" title="SLOW_PEAKS" />
+	<visualization xsi:type="LinePlot" x="posX" y="ICR" title="ICR" />
+	<visualization xsi:type="LinePlot" x="posX" y="OCR" title="OCR" />-->
+	
+	<visualization xsi:type="LinePlot" x="posX" y="idM_IF" title="If_calculated" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="GeD_corrected_avg" title="GeD_corrected_avg" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="mca1.R0" title="mca1.R0" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="R1_Fast_peaks" title="R1_Fast_peaks" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="R1_Slow_peaks" title="R1_Slow_peaks" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="GeD_elapsed_real" title="GeD_elapsed_real" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="GeD_elapsed_live" title="GeD_elapsed_live" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="idM_C1_dtc" title="GeD_C1_deadtimecorrected" /> 	
+	<visualization xsi:type="LinePlot" x="posX" y="sample_count" title="actual sample count" /> 		
+	<!--<visualization xsi:type="LinePlot" x="posX" y="idM_It" title="It_calculated" /> 	
+					
+  	<visualization xsi:type="LinePlot" x="posX" y="energyRB" title="Energy Readback" /> 
+	
+	<visualization xsi:type="LinePlot" x="posX" y="ElapsedRT" title="ElapsedRT" /> 
+	
+	<visualization xsi:type="LinePlot" x="posX" y="SAI01-MEAN" title="SAI01-MEAN" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="SAI02-MEAN" title="SAI02-MEAN" /> 
+	<visualization xsi:type="LinePlot" x="posX" y="SAI03-MEAN" title="SAI03-MEAN" /> -->
+	<!--<visualization xsi:type="LinePlot" x="posX" y="Ring-current" title="Ring-current" /> -->
+	<visualization xsi:type="LinePlot" x="posX" y="Timestamp" title="Timestamp" />   
+
+</configuration>

src/test/resources/home/scans/templates/TestXY__OTF_2D_v01_small-map.xml

@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" numberOfExecution="1" failOnSensorError="true">
+    <data format="txt" fileName="TestXY__OTF_2D_v01_small-map"/>
+    <scan>
+        <cdimension dataGroup="false">
+            <positioner name="X10DA-TEST1-OMS:MOT8" id="id0">
+                <start>-1.0</start>
+                <end>1.0</end>
+                <stepSize>0.01</stepSize>
+                <integrationTime>0.0050</integrationTime>
+            </positioner>
+            <detector name="X10DA-TEST1-TMP:ai07" id="Diode"/>
+            <scaler channel="0" id="diodeS"/>
+            <scaler channel="11" id="refS"/>
+            <timestamp id="timestamp"/>
+        </cdimension>
+        <dimension zigzag="false" dataGroup="false">
+            <positioner xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinearPositioner" name="X10DA-TEST1-OMS:MOT7" id="scanY">
+                <start>-1.0</start>
+                <end>1.0</end>
+                <stepSize>0.25</stepSize>
+            </positioner>
+        </dimension>
+    </scan>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="MatrixPlot" x="id0" y="scanY" z="Diode" title=" Diode"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="Diode" title=" Diode"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="diodeS" title=" Diode Scaler"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="refS" title=" Reference Scaler"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="timestamp" y="diodeS" title=" Diode Scaler f (t)"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="timestamp" y="refS" title="  Ref Scaler f (t)"/>
+</configuration>

src/test/resources/home/scans/templates/cscan1d-crlogic-2.xml

@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../../src/model-v1.xsd">
+	<data format="txt" />
+	<scan id="">
+
+		<!-- Ensure that scaler is configured the correct way -->
+		<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.CONT" value="OneShot" operation="putq"/> <!-- Mode -->
+		<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.G1" value="0" /> <!-- Gate -->
+		<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.PR1" value="0" /> <!-- Preset Count -->
+
+		<cdimension zigzag="false">
+			
+			<!-- start scaler -->
+			<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.CNT" value="Count" operation="putq" />
+
+			<positioner id="id0" name="MTEST-HW3:MOT1" xsi:type="ContinuousPositioner">
+				<start>0.0</start>
+				<end>2.0</end>
+				<stepSize>0.01</stepSize>
+				<integrationTime>0.01</integrationTime>
+			</positioner>
+			<detector id="idD0" xsi:type="SimpleScalarDetector" name="TRIGGER0" />
+			<detector id="idD1" xsi:type="SimpleScalarDetector" name="TRIGGER1" />
+			<!-- <detector id="jsChannel2" xsi:type="SimpleScalarDetector" name="MTEST-HW3:JS.S2"/> -->
+
+			<scaler id="scaler0" channel="0" />
+			<scaler id="scaler1" channel="1" />
+			<!-- <scaler id="scaler2" channel="2"/> -->
+			<timestamp id="test" />
+
+			<!-- stop scaler -->
+			<postAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.CNT" value="Done" />
+		</cdimension>
+
+
+	</scan>
+
+	<visualization title="Scaler 0" xsi:type="LinePlot" x="id0" y="scaler0" />
+	<visualization title="Scaler 1" xsi:type="LinePlot" x="id0" y="scaler1" />
+	<visualization title="Trigger Count 1" xsi:type="LinePlot" x="id0" y="idD0"/>
+	<visualization title="Trigger Count 2" xsi:type="LinePlot" x="id0" y="idD1"/>
+	<visualization xsi:type="LinePlot" x="id0" y="test" title="Timestamp" />
+</configuration>

src/test/resources/home/scans/templates/cscan1d-crlogic.xml

@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../../src/model-v1.xsd">
+	<data format="txt" />
+	<scan id="">
+
+		<!-- Ensure that scaler is configured the correct way -->
+		<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.CONT" value="OneShot" operation="putq"/> <!-- Mode -->
+		<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.G1" value="0" /> <!-- Gate -->
+		<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.PR1" value="0" /> <!-- Preset Count -->
+
+		<cdimension zigzag="false">
+			
+			<!-- start scaler -->
+			<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.CNT" value="Count" operation="putq" />
+
+			<positioner id="id0" name="MTEST-HW3:MOT1" xsi:type="ContinuousPositioner">
+				<start>0.0</start>
+				<end>2.0</end>
+				<stepSize>0.01</stepSize>
+				<integrationTime>0.01</integrationTime>
+			</positioner>
+			<detector id="idD0" xsi:type="SimpleScalarDetector" name="TRIGGER0" />
+			<!-- <detector id="jsChannel2" xsi:type="SimpleScalarDetector" name="MTEST-HW3:JS.S2"/> -->
+
+			<scaler id="scaler0" channel="0" />
+			<scaler id="scaler1" channel="1" />
+			<!-- <scaler id="scaler2" channel="2"/> -->
+			<timestamp id="test" />
+
+			<!-- stop scaler -->
+			<postAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.CNT" value="Done" />
+		</cdimension>
+
+
+	</scan>
+
+	<visualization title="Scaler 0" xsi:type="LinePlot" x="id0" y="scaler0" />
+	<visualization title="Scaler 1" xsi:type="LinePlot" x="id0" y="scaler1" />
+	<visualization title="Trigger Count" xsi:type="LinePlot" x="id0" y="idD0"/>
+	<visualization xsi:type="LinePlot" x="id0" y="test" title="Timestamp" />
+</configuration>

src/test/resources/home/scans/templates/cscan1d-manipulation.xml

@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="1" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../src/model-v1.xsd">
+  <data format="txt"/>
+  <scan id="">
+  	<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.G1" value="0"/>
+    <cdimension zigzag="false">
+      <positioner id="id0" name="MTEST-HW3:MOT1">
+        <start>0.0</start>
+        <end>8.0</end>
+        <stepSize>0.5</stepSize>
+        <integrationTime>0.5</integrationTime>
+      </positioner>
+      
+      <detector name="MTEST-HW3:MOT1.RBV" id="id00"/>
+      <scaler id="idXX01" channel="0"/>
+      <timestamp id="test"/>
+    </cdimension>
+    
+    <manipulation id="idM1" xsi:type="ScriptManipulation">
+    	<!-- <mapping xsi:type="IDParameterMapping" variable="a" refid="id0"/> -->
+    	<mapping xsi:type="IDParameterMapping" variable="b" refid="idXX01"/>
+    	<mapping xsi:type="IDParameterMapping" variable="c" refid="id00"/>
+    	<script>
+import math
+def process(b,c):
+    print b
+    return math.cos(c)
+    	</script>
+    </manipulation>
+  </scan>
+  
+  <visualization title="Line Plot One" xsi:type="LinePlot" x="id0" y="idXX01"/>
+  <visualization xsi:type="LinePlot" x="id0" y="test" title="Timestamp" />
+  <visualization xsi:type="LinePlot" x="id0" y="idM1" title="Manipulation" />
+</configuration>

src/test/resources/home/scans/templates/cscan1d-maxv.xml

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../src/model-v1.xsd">
+  <data format="txt"/>
+  <scan id="">
+  	<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.G1" value="0"/>
+    <cdimension zigzag="false">
+      <positioner id="id0" name="MTEST-HW3:MMOT1" xsi:type="ContinuousPositioner">
+        <start>8.0</start>
+        <end>14.0</end>
+        <stepSize>0.5</stepSize>
+        <integrationTime>0.5</integrationTime>
+      </positioner>
+      <detector id="idD0" xsi:type="SimpleScalarDetector" name="MTEST-HW3:MMOT1.RRBV"/>
+      <detector id="jsChannel2" xsi:type="SimpleScalarDetector" name="MTEST-HW3:JS.S2"/>
+      
+      <scaler id="scaler0" channel="0"/>
+      <scaler id="scaler1" channel="1"/>
+      <scaler id="scaler2" channel="2"/>
+      <timestamp id="test"/>
+    </cdimension>
+  </scan>
+  
+  <visualization title="Scaler 0" xsi:type="LinePlot" x="id0" y="scaler0"/>
+  <visualization title="Scaler 1" xsi:type="LinePlot" x="id0" y="scaler1"/>
+  <visualization title="Scaler 1 Count via CA" xsi:type="LinePlot" x="id0" y="jsChannel2"/>
+  <visualization xsi:type="LinePlot" x="id0" y="test" title="Timestamp" />
+</configuration>

src/test/resources/home/scans/templates/cscan1d-prePostAction.xml

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../src/model-v1.xsd">
+  <data format="txt"/>
+  <scan id="">
+  	<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.G1" value="0"/>
+    <cdimension zigzag="false">
+    
+     <preAction xsi:type="ShellAction" command="echo 'This is a continuous dimension pre action'"/>
+     
+      <positioner id="id0" name="MTEST-HW3:MOT1" xsi:type="ContinuousPositioner">
+        <start>0.0</start>
+        <end>8.0</end>
+        <stepSize>0.5</stepSize>
+        <integrationTime>0.5</integrationTime>
+      </positioner>
+      <detector id="idD0" xsi:type="SimpleScalarDetector" name="MTEST-HW3:MOT1.RRBV"/>
+      
+      <scaler id="idXX01" channel="0"/>
+      <timestamp id="test"/>
+      
+      <postAction xsi:type="ShellAction" command="echo 'This is a continuous dimension post action'"/>
+    </cdimension>
+  </scan>
+  
+  <visualization title="Line Plot One" xsi:type="LinePlot" x="id0" y="idXX01"/>
+  <visualization xsi:type="LinePlot" x="id0" y="test" title="Timestamp" />
+</configuration>

src/test/resources/home/scans/templates/cscan1d-scrlogic.xml

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../../src/model-v1.xsd">
+  <data format="txt"/>
+  <scan id="">
+  	<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.G1" value="0"/>
+    <cdimension zigzag="false">
+      <positioner id="id0" name="MTEST-HW3:MOT1" xsi:type="ContinuousPositioner">
+        <start>0.0</start>
+        <end>2.0</end>
+        <stepSize>0.01</stepSize>
+        <integrationTime>0.01</integrationTime>
+      </positioner>
+      <detector id="idD0" xsi:type="SimpleScalarDetector" name="TRIGGER0" />
+      
+      <!-- NORMAL CHANNEL -->
+      <detector id="idCD0" xsi:type="SimpleScalarDetector" name="MTEST-HW3:MOT1.RBV" scr="true"/>
+      
+      <scaler id="scaler0" channel="0"/>
+      <scaler id="scaler1" channel="1"/>
+      <!-- <scaler id="scaler2" channel="2"/>-->
+      <timestamp id="test"/>
+    </cdimension>
+  </scan>
+  
+  <visualization title="Scaler 0" xsi:type="LinePlot" x="id0" y="scaler0"/>
+  <visualization title="Scaler 1" xsi:type="LinePlot" x="id0" y="scaler1"/>
+  <!-- <visualization title="Scaler 1 Count via CA" xsi:type="LinePlot" x="id0" y="jsChannel2"/>-->
+  <visualization xsi:type="LinePlot" x="id0" y="test" title="Timestamp" />
+  <visualization xsi:type="LinePlot" x="id0" y="idCD0" title="Readback Channel Access" />
+</configuration>

src/test/resources/home/scans/templates/cscan1d.xml

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../src/model-v1.xsd">
+  <data format="txt"/>
+  <scan id="">
+  	<preAction xsi:type="ChannelAction" channel="MTEST-HW3:JS.G1" value="0"/>
+    <cdimension zigzag="false">
+      <positioner id="id0" name="MTEST-HW3:MOT1" xsi:type="ContinuousPositioner">
+        <start>0.0</start>
+        <end>8.0</end>
+        <stepSize>0.5</stepSize>
+        <integrationTime>0.5</integrationTime>
+      </positioner>
+      <detector id="idD0" xsi:type="SimpleScalarDetector" name="MTEST-HW3:MOT1.RRBV"/>
+      <detector id="jsChannel2" xsi:type="SimpleScalarDetector" name="MTEST-HW3:JS.S2"/>
+      
+      <scaler id="scaler0" channel="0"/>
+      <scaler id="scaler1" channel="1"/>
+      <scaler id="scaler2" channel="2"/>
+      <timestamp id="test"/>
+    </cdimension>
+  </scan>
+  
+  <visualization title="Scaler 0" xsi:type="LinePlot" x="id0" y="scaler0"/>
+  <visualization title="Scaler 1" xsi:type="LinePlot" x="id0" y="scaler1"/>
+  <visualization title="Scaler 1 Count via CA" xsi:type="LinePlot" x="id0" y="jsChannel2"/>
+  <visualization xsi:type="LinePlot" x="id0" y="test" title="Timestamp" />
+</configuration>

src/test/resources/home/scans/templates/cscan2d-crlogic-additional.xml

@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" numberOfExecution="1">
+    <data fileName="cscan2d-crlogic" format="txt"/>
+    <scan id="">
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" operation="putq" value="OneShot" channel="MTEST-HW3:JS.CONT"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" value="0" channel="MTEST-HW3:JS.G1"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" value="0" channel="MTEST-HW3:JS.PR1"/>
+        <cdimension zigzag="true">
+            <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" operation="putq" value="Count" channel="MTEST-HW3:JS.CNT"/>
+            <positioner name="MTEST-HW3:MOT1" id="id0">
+                <start>0.0</start>
+                <end>2.0</end>
+                <stepSize>0.01</stepSize>
+                <integrationTime>0.01</integrationTime>
+            </positioner>
+            <detector name="TRIGGER0" id="idD0"/>
+            <detector scr="true" name="MTEST-HW3:MOT1.RBV" id="id500224"/>
+            <scaler channel="0" id="scaler0"/>
+            <scaler channel="1" id="scaler1"/>
+            <timestamp id="test"/>
+            <postAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" value="Done" channel="MTEST-HW3:JS.CNT"/>
+        </cdimension>
+        <dimension>
+            <positioner xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="PseudoPositioner" id="p1">
+                <counts>30</counts>
+            </positioner>
+        </dimension>
+    </scan>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" y="scaler0" x="id0" title="Scaler 0"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" y="scaler1" x="id0" title="Scaler 1"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" y="test" x="id0" title="Timestamp"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" y="id500224" x="id0" title=" Readback"/>
+</configuration>

src/test/resources/home/scans/templates/cscan2d-crlogic.xml

@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" numberOfExecution="1">
+    <data format="txt" fileName="cscan2d-crlogic"/>
+    <scan id="">
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="MTEST-HW3:JS.CONT" value="OneShot" operation="putq"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="MTEST-HW3:JS.G1" value="0"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="MTEST-HW3:JS.PR1" value="0"/>
+        <cdimension zigzag="true">
+            <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="MTEST-HW3:JS.CNT" value="Count" operation="putq"/>
+            <positioner name="MTEST-HW3:MOT1" id="id0">
+                <start>0.0</start>
+                <end>2.0</end>
+                <stepSize>0.01</stepSize>
+                <integrationTime>0.01</integrationTime>
+            </positioner>
+            <detector name="TRIGGER0" id="idD0"/>
+            <scaler channel="0" id="scaler0"/>
+            <scaler channel="1" id="scaler1"/>
+            <timestamp id="test"/>
+            <postAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="MTEST-HW3:JS.CNT" value="Done"/>
+        </cdimension>
+        <dimension>
+            <positioner xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="PseudoPositioner" id="p1">
+                <counts>30</counts>
+            </positioner>
+        </dimension>
+    </scan>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="scaler0" title="Scaler 0"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="scaler1" title="Scaler 1"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="test" title="Timestamp"/>
+</configuration>

src/test/resources/home/scans/templates/cscan2d-zigzag.xml

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" numberOfExecution="1">
+    <data format="txt" fileName="cscan2d-zigzag"/>
+    <scan id="">
+        <cdimension zigzag="true">
+            <positioner name="MTEST-HW3:MOT1" id="id0">
+                <start>0.0</start>
+                <end>8.0</end>
+                <stepSize>0.5</stepSize>
+                <integrationTime>0.5</integrationTime>
+            </positioner>
+            <scaler channel="0" id="idD0"/>
+            <scaler channel="1" id="idD1"/>
+        </cdimension>
+        <dimension>
+            <positioner xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinearPositioner" name="MTEST-HW3:MOT2" settlingTime="1.0" id="id2">
+                <start>-1.0</start>
+                <end>-2.0</end>
+                <stepSize>0.1</stepSize>
+            </positioner>
+        </dimension>
+    </scan>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="idD0" title="Line Plot One"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="idD1" title="Line Plot One"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="id2" title="Line Plot Two"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="MatrixPlot" x="id0" y="id2" z="idD0" title="Matrix Plot"/>
+</configuration>

src/test/resources/home/scans/templates/cscan2d.xml

@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../src/model-v1.xsd">
+  <data format="txt"/>
+  <scan id="">
+    <cdimension>
+      <positioner id="id0" name="MTEST-HW3:MOT1">
+        <start>0.0</start>
+        <end>8.0</end>
+        <stepSize>0.5</stepSize>
+        <integrationTime>0.5</integrationTime>
+      </positioner>
+      <scaler id="idD0" channel="0"/>
+      <scaler id="idD1" channel="1"/>
+    </cdimension>
+    <dimension>
+    	<positioner id="id2" name="MTEST-HW3:MOT2" settlingTime="1" xsi:type="LinearPositioner">
+    		<start>-1.0</start>
+        	<end>-2.0</end>
+        	<stepSize>0.1</stepSize>
+    	</positioner>
+    </dimension>
+  </scan>
+  
+  <visualization title="Line Plot One" xsi:type="LinePlot" x="id0" y="idD0"/>
+  <visualization title="Line Plot One" xsi:type="LinePlot" x="id0" y="idD1"/>
+  <visualization title="Line Plot Two" xsi:type="LinePlot" x="id0" y="id2"/>
+  <visualization title="Matrix Plot" xsi:type="MatrixPlot" x="id0" y="id2" z="idD0"/>  
+  
+</configuration>

src/test/resources/home/scans/templates/scan0d-pseudo.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="1" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 http://www.psi.ch/~ebner/models/scan/1.0">
+  <data format="txt"/>
+  <scan id="">
+    <dimension>
+    	<positioner id="id2" xsi:type="PseudoPositioner">
+    		<counts>100</counts>
+    	</positioner>
+    	<detector id="x" xsi:type="ScalarDetector" name="CHANNEL-TO-TRIGGER">
+    	 	 <preAction xsi:type="ChannelAction" channel="CHANNEL-TO-TRIGGER" value="TRIGGER-VALUE"/>
+    	</detector>
+    </dimension>
+  </scan>
+</configuration>

src/test/resources/home/scans/templates/scan0d.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" numberOfExecution="1" failOnSensorError="true">
+    <data format="txt"/>
+    <scan>
+        <preAction xsi:type="ShellAction" command="testfiles/testscript.sh"/>
+    </scan>
+</configuration>

src/test/resources/home/scans/templates/scan1d-array.xml

@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../../src/model-v1.xsd">
+<!-- 
+1D scan reading out an array channel
+ -->
+  <data format="txt"/>
+  <scan id="">
+    <dimension>
+    	<positioner id="id0" name="MTEST-HW3:MOT1" settlingTime="0.1" xsi:type="LinearPositioner">
+    		<start>0.0</start>
+        	<end>8.0</end>
+        	<stepSize>0.5</stepSize>
+    	</positioner>
+    	<detector id="idD0" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RRBV"/>
+    	<detector id="idD2" xsi:type="ArrayDetector" name="MTEST-PC-SSCAN:scan2.P1PA" arraySize="10"/>
+    	<detector id="idD20" xsi:type="ArrayDetector" name="MTEST-PC-SSCAN:scan1.P1PA" arraySize="10"/>
+    	<detector id="idD1" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RBV"/>
+    </dimension>
+  </scan>
+  
+  <visualization title="Array" xsi:type="LinePlotArray" y="idD2 idD20" maxSeries="4"/>
+  <visualization title="Array Offset/Size" xsi:type="LinePlotArray" y="idD2" offset="2" size="4" maxSeries="4"/>
+  <visualization title="Array 2D" xsi:type="MatrixPlotArray" y="id0" z="idD2" offset="2" size="10"/>
+  
+</configuration>

src/test/resources/home/scans/templates/scan1d-arrayManipulation.xml

@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../../src/model-v1.xsd">
+<!-- 
+1D scan reading out an array channel
+ -->
+  <data format="txt"/>
+  <scan id="">
+    <dimension>
+    	<positioner id="id0" name="MTEST-HW3:MOT1" settlingTime="0.1" xsi:type="LinearPositioner">
+    		<start>0.0</start>
+        	<end>8.0</end>
+        	<stepSize>0.5</stepSize>
+    	</positioner>
+    	<detector id="idD0" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RRBV"/>
+    	<detector id="idD2" xsi:type="ArrayDetector" name="MTEST-PC-SSCAN:scan2.P1PA" arraySize="10"/>
+    	<detector id="idD20" xsi:type="ArrayDetector" name="MTEST-PC-SSCAN:scan1.P1PA" arraySize="10"/>
+    	<detector id="idD1" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RBV"/>
+    </dimension>
+    
+    <!-- <manipulation id="idM2" xsi:type="ScriptManipulation" returnArray="true">
+		<mapping xsi:type="IDParameterMapping" variable="a" refid="idD2"/>
+    	<script>
+import math
+def process(a):
+    return float(len(a))
+    	</script>
+    </manipulation> -->
+    <manipulation id="idM2" xsi:type="ScriptManipulation" returnArray="true">
+		<mapping xsi:type="IDParameterMapping" variable="a" refid="idD2"/>
+    	<script>
+import math
+import operator
+from jarray import array
+
+var = True
+
+def process(a):
+    global var
+    global ovalue
+    
+    if var:
+        ovalue = a
+        var = False
+        return a
+    ovalue = map(operator.add, ovalue, a)
+    return array(ovalue, 'd')
+    	</script>
+    </manipulation>
+    <!-- <manipulation id="idM2" xsi:type="ScriptManipulation" returnArray="true">
+		<mapping xsi:type="IDParameterMapping" variable="a" refid="idD2"/>
+    	<script>
+from jarray import array
+def process(a):
+    return array((1.0, 0.1), 'd')
+    	</script>
+    </manipulation> -->
+  </scan>
+  
+  
+  
+  <visualization title="Array" xsi:type="LinePlotArray" y="idD2 idD20" maxSeries="4"/>
+  <visualization title="Array Offset/Size" xsi:type="LinePlotArray" y="idD2" offset="2" size="4" maxSeries="4"/>
+  <visualization title="Array 2D" xsi:type="MatrixPlotArray" y="id0" z="idD2" offset="2" size="10"/>
+  <!-- <visualization xsi:type="LinePlot" x="id0" y="idM2"/> -->
+  <!-- <visualization title="Array Manipulated" xsi:type="LinePlotArray" y="idM2" maxSeries="10"/> -->
+  <visualization title="Array Manipulated 2D" xsi:type="MatrixPlotArray" y="id0" z="idM2" offset="2" size="10"/>
+  
+</configuration>

src/test/resources/home/scans/templates/scan1d-arrayManipulation2.xml

@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" numberOfExecution="1">
+    <data format="txt" fileName="scan1d-arrayManipulation2"/>
+    <description>hello wolrd</description>
+    <scan id="">
+        <dimension>
+            <positioner xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinearPositioner" name="MTEST-HW3:MOT1" settlingTime="0.1" id="id0">
+                <start>0.0</start>
+                <end>8.0</end>
+                <stepSize>0.5</stepSize>
+            </positioner>
+            <detector xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RRBV" id="idD0"/>
+            <detector xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ArrayDetector" arraySize="10" name="MTEST-PC-SSCAN:scan2.P1PA" id="idD2"/>
+            <detector xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ArrayDetector" arraySize="10" name="MTEST-PC-SSCAN:scan1.P1PA" id="idD20"/>
+            <detector xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RBV" id="idD1"/>
+        </dimension>
+        <manipulation xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ScriptManipulation" returnArray="true" id="idM2">
+            <mapping xsi:type="IDParameterMapping" refid="idD2" variable="a"/>
+            <script>import math
+import operator
+from jarray import array
+
+var = True
+
+def process(a):
+    global var
+    global ovalue
+    
+    if var:
+        ovalue = a
+        var = False
+        return a
+    ovalue = map(operator.add, ovalue, a)
+    return array(ovalue, 'd')</script>
+        </manipulation>
+    </scan>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlotArray" y="idD2 idD20" maxSeries="4" title="Array"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlotArray" y="idD2" maxSeries="4" offset="2" size="4" title="Array Offset/Size"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="MatrixPlotArray" y="id0" z="idD2" offset="2" size="10" title="Array 2D"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="MatrixPlotArray" y="id0" z="idM2" offset="2" size="10" title="Array Manipulated 2D"/>
+</configuration>

src/test/resources/home/scans/templates/scan1d-condition.xml

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" numberOfExecution="1" failOnSensorError="true" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../../src/model-v1.xsd">
+    <data format="txt" fileName="scan1d"/>
+    <scan>
+        <dimension zigzag="true">
+            <positioner xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinearPositioner" name="MTEST-HW3:MOT1" settlingTime="0.1" doneValue="1" doneDelay="0.0" id="id0">
+                <start>0.0</start>
+                <end>8.0</end>
+                <stepSize>0.5</stepSize>
+            </positioner>
+            <guard><condition channel="MTEST-PC-X10:AO" value="0" type="Integer"/></guard>
+            <detector xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RRBV" id="idD0"/>
+            <detector xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RBV" id="idD1"/>
+            <detector xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="Timestamp" id="timestamp"/>
+        </dimension>
+    </scan>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="idD1" title="Readback"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="idD0" title="Raw"/>
+    <visualization xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LinePlot" x="id0" y="timestamp idD0" title="Timestamp"/>
+</configuration>

src/test/resources/home/scans/templates/scan1d-dod.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../../src/model-v1.xsd">
+<!-- 
+1D Scan with a non motor positioner (one set channel and one channel indicating done)
+ -->
+  <data format="txt"/>
+  <scan id="">
+    <dimension>
+    	<positioner id="id0" name="MTEST-HW3:MOT1" settlingTime="0.1" xsi:type="LinearPositioner" done="MTEST-PC-X10:BO2" doneValue="1">
+    		<start>0.0</start>
+        	<end>8.0</end>
+        	<stepSize>0.5</stepSize>
+    	</positioner>
+    	<detector id="idm" xsi:type="DetectorOfDetectors" name=""/>
+    	<detector id="idD0" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RRBV"/>
+    	<detector id="idD1" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RBV"/>
+    	<detector xsi:type="Timestamp" id="timestamp"/>
+    </dimension>
+  </scan>
+
+	<visualization title="Line Plot One" xsi:type="LinePlot" x="id0" y="idD0"/>
+	<visualization title="Line Plot Two" xsi:type="LinePlot" x="id0" y="idD1"/>
+	<visualization xsi:type="LinePlot" x="id0" y="timestamp" title="Timestamp" />
+</configuration>