Added an release notes file

-- however still lots of bugs in there !

ch.psi.fda/.classpath

@@ -6,7 +6,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" path="target/generated-sources/xjc"/>
 	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

ch.psi.fda/ReleaseNotes.md

@@ -0,0 +1,2 @@
+# 3.0.0
+  * Update the fda.properties file and replace ch.psi.fda.aq.data.baseDirectory with ch.psi.fda.aq.data.dir.

ch.psi.fda/pom.xml

@@ -3,25 +3,49 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi</groupId>
 	<artifactId>fda</artifactId>
-	<version>2.1.1</version>
+	<version>2.4.3</version>
 
 	<dependencies>
 
 		<dependency>
 			<groupId>ch.psi</groupId>
 			<artifactId>ch.psi.fda.core</artifactId>
-			<version>0.0.1-SNAPSHOT</version>
+			<version>2.3.0</version>
 		</dependency>
 
+		<!-- These 3 libraries are just needed for testing -->
+		<dependency>
+			<groupId>ch.psi.fda</groupId>
+			<artifactId>ch.psi.fda.xscan</artifactId>
+			<version>2.3.2</version>
+		</dependency>
 		<dependency>
 			<groupId>ch.psi</groupId>
 			<artifactId>ch.psi.fda.cdump</artifactId>
-			<version>1.0.1</version>
+			<version>2.3.0</version>
 		</dependency>
 		<dependency>
 			<groupId>ch.psi</groupId>
 			<artifactId>ch.psi.fda.fdaq</artifactId>
-			<version>1.0.5</version>
+			<version>2.3.0</version>
+		</dependency>
+
+		<dependency>
+			<groupId>ch.psi</groupId>
+			<artifactId>jcae</artifactId>
+			<version>2.4.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>ch.psi</groupId>
+			<artifactId>plot</artifactId>
+			<version>1.1.31</version>
+		</dependency>
+
+		<dependency>
+			<groupId>com.google.inject</groupId>
+			<artifactId>guice</artifactId>
+			<version>3.0</version>
 		</dependency>
 
 		<dependency>
@@ -42,66 +66,31 @@
 			<version>2.5.1</version>
 		</dependency>
 
-
 		<dependency>
 			<groupId>org.jeromq</groupId>
 			<artifactId>jeromq</artifactId>
 			<version>0.2.0</version>
 		</dependency>
 
-		<dependency>
-			<groupId>ch.psi</groupId>
-			<artifactId>jcae</artifactId>
-			<version>2.1.11</version>
-		</dependency>
-		<!-- Plotting library -->
-		<dependency>
-			<groupId>ch.psi</groupId>
-			<artifactId>plot</artifactId>
-			<version>1.1.31</version>
-		</dependency>
-		<!-- Java SMB/CIFS library -->
-		<dependency>
-			<groupId>jcifs</groupId>
-			<artifactId>jcifs</artifactId>
-			<version>1.3.17</version>
-		</dependency>
-
-		<!-- JAXB implementation -->
-		<!-- <dependency> <groupId>com.sun.xml.bind</groupId> <artifactId>jaxb-impl</artifactId> 
-			<version>2.2.1</version> </dependency> <dependency> <groupId>com.sun.xml.bind</groupId> 
-			<artifactId>jaxb-xjc</artifactId> <version>2.2.1</version> </dependency> -->
-		<!-- Jython Library -->
-		<dependency>
-			<groupId>org.python</groupId>
-			<artifactId>jython</artifactId>
-			<version>2.5.3</version>
-		</dependency>
-		<!-- CLI Libraries -->
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>cli</artifactId>
 			<version>1.2</version>
 		</dependency>
+
 		<!-- Library to Read Matlab Files -->
 		<dependency>
 			<groupId>com.jmatio</groupId>
 			<artifactId>jmatio</artifactId>
 			<version>0.2u2psi1</version>
 		</dependency>
-		<!-- Mail Libraries -->
-		<dependency>
-			<groupId>com.sun.mail</groupId>
-			<artifactId>javax.mail</artifactId>
-			<version>1.5.0</version>
-		</dependency>
 		<!-- Library for reading/writing XDR Format (MDA) -->
 		<dependency>
 			<groupId>org.freehep</groupId>
 			<artifactId>freehep-xdr</artifactId>
 			<version>2.0.4</version>
 		</dependency>
-		<!-- JUnit test library -->
+
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
@@ -121,10 +110,12 @@
 					<target>1.7</target>
 				</configuration>
 			</plugin>
-			<!-- <plugin>
+			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
-				<version>2.8</version>
+				<configuration>
+					<additionalparam>-Xdoclint:none</additionalparam> <!-- Disable Java8 strict Javadoc checking -->
+				</configuration>
 				<executions>
 					<execution>
 						<id>attach-javadocs</id>
@@ -133,11 +124,10 @@
 						</goals>
 					</execution>
 				</executions>
-			</plugin> -->
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
-				<version>2.1.2</version>
 				<executions>
 					<execution>
 						<id>attach-sources</id>
@@ -147,111 +137,19 @@
 					</execution>
 				</executions>
 			</plugin>
-			<!-- Schema generation -->
-			<plugin>
-				<groupId>org.jvnet.jaxb2.maven2</groupId>
-				<artifactId>maven-jaxb2-plugin</artifactId>
-				<version>0.8.0</version>
-				<executions>
-					<execution>
-						<goals>
-							<goal>generate</goal>
-						</goals>
-					</execution>
-				</executions>
-				<configuration>
-					<generatePackage>ch.psi.fda.model.v1</generatePackage>
-				</configuration>
-			</plugin>
-			<!-- Schema Documentation Generation -->
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>xml-maven-plugin</artifactId>
-				<version>1.0</version>
-				<executions>
-					<execution>
-						<phase>transform</phase>
-						<goals>
-							<goal>transform</goal>
-						</goals>
-					</execution>
-				</executions>
-				<configuration>
-					<transformationSets>
-						<transformationSet>
-							<!-- <outputDir>target</outputDir> -->
-							<dir>src/main/resources</dir>
-							<stylesheet>src/main/documentation/xs3p.xsl</stylesheet>
-							<fileMappers>
-								<fileMapper
-									implementation="org.codehaus.plexus.components.io.filemappers.RegExpFileMapper">
-									<pattern>\.xsd$</pattern>
-									<replacement>.html</replacement>
-								</fileMapper>
-							</fileMappers>
-						</transformationSet>
-					</transformationSets>
-				</configuration>
-			</plugin>
 		</plugins>
-		<pluginManagement>
-			<plugins>
-				<!--This plugin's configuration is used to store Eclipse m2e settings 
-					only. It has no influence on the Maven build itself. -->
-				<plugin>
-					<groupId>org.eclipse.m2e</groupId>
-					<artifactId>lifecycle-mapping</artifactId>
-					<version>1.0.0</version>
-					<configuration>
-						<lifecycleMappingMetadata>
-							<pluginExecutions>
-								<pluginExecution>
-									<pluginExecutionFilter>
-										<groupId>
-											org.jvnet.jaxb2.maven2
-										</groupId>
-										<artifactId>
-											maven-jaxb2-plugin
-										</artifactId>
-										<versionRange>
-											[0.8.0,)
-										</versionRange>
-										<goals>
-											<goal>generate</goal>
-										</goals>
-									</pluginExecutionFilter>
-									<action>
-										<ignore></ignore>
-									</action>
-								</pluginExecution>
-							</pluginExecutions>
-						</lifecycleMappingMetadata>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-assembly-plugin</artifactId>
-					<configuration>
-						<descriptors>
-							<descriptor>src/main/assembly/assembly.xml</descriptor>
-						</descriptors>
-					</configuration>
-				</plugin>
-
-			</plugins>
-		</pluginManagement>
 	</build>
 
 	<distributionManagement>
 		<snapshotRepository>
 			<id>i.snapshots</id>
 			<name>Artifactory Snapshots</name>
-			<url>http://yoke/artifactory/libs-snapshots-local</url>
+			<url>http://yoke.psi.ch:8081/artifactory/libs-snapshots-local</url>
 		</snapshotRepository>
 		<repository>
 			<id>i.releases</id>
 			<name>Atrifactory Releases</name>
-			<url>http://yoke/artifactory/libs-releases-local</url>
+			<url>http://yoke.psi.ch:8081/artifactory/libs-releases-local</url>
 		</repository>
 	</distributionManagement>
 </project>

ch.psi.fda/src/main/assembly/bin/convert

@@ -37,4 +37,4 @@ do
 done
 
 # Execute java
-java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ConversionMain $ARGUMENTS
+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

ch.psi.fda/src/main/assembly/bin/scan

@@ -37,4 +37,4 @@ do
 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.AcquisitionMain $ARGUMENTS
+java -Xmx1024m -XX:MaxPermSize=128m -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS -cp $CLASSPATH ch.psi.fda.ui.RemoteAcquisitionMain $ARGUMENTS

ch.psi.fda/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

ch.psi.fda/src/main/assembly/bin/viewer

@@ -37,4 +37,4 @@ do
 done
 
 # Execute java
-java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ViewerMain $ARGUMENTS
+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

ch.psi.fda/src/main/assembly/bin/visualize

@@ -37,4 +37,4 @@ do
 done
 
 # Execute java
-java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.VisualizationMain $ARGUMENTS
+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

ch.psi.fda/src/main/assembly/www/css/main.css

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

ch.psi.fda/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>

ch.psi.fda/src/main/assembly/www/js/main.js

@@ -0,0 +1 @@
+

ch.psi.fda/src/main/java/ch/psi/fda/aq/AcquisitionConfiguration.java

@@ -1,251 +0,0 @@
-/**
- * 
- * 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.aq;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-import java.util.Properties;
-import java.util.logging.Logger;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class AcquisitionConfiguration {
-	
-	
-	private static final Logger logger = Logger.getLogger(AcquisitionConfiguration.class.getName());
-	
-	public final static String FDA_CONFIG_FILE = "ch.psi.fda.config.file";
-	
-	private String otfChannelPrefix;
-	private String otfNfsServer;
-	private String otfNfsShare;
-	private String otfSmbShare;
-	private String otfScalerPrefix;
-	private boolean otfUseCrlogic;
-	private String otfCrlogicPrefix;
-	private boolean otfCrlogicKeepTmpFiles;
-	
-	/**
-	 * Base directory for data. The directory may contain date macros. The string may contain any @see java.text.SimpleDateFormat
-	 * patterns within ${ } brackets. The macros are resolved with the actual time while the get method
-	 * of this property is called.
-	 */
-	private String dataBaseDirectory = System.getProperty("user.home");
-	/**
-	 * Prefix of the data file. The prefix may contain date macros. The string may contain any @see java.text.SimpleDateFormat
-	 * patterns within ${ } brackets. The macros are resolved with the actual time while the get method
-	 * of this property is called.
-	 */
-	private String dataFilePrefix = "";
-	
-	/**
-	 * Maximum time for a actor move
-	 */
-	private Long actorMoveTimeout = 600000l; // 10 Minutes maximum move time 
-	
-	private String smptServer;
-	
-	
-	/**
-	 * Default Constructor
-	 * The constructor will read the configuration from the /fda.properties file (resource) located in the classpath.
-	 */
-	public AcquisitionConfiguration(){
-		loadConfiguration(System.getProperty(FDA_CONFIG_FILE));
-	}
-	
-	/**
-	 * Load configuration from properties file
-	 */
-	public void loadConfiguration(String file) {
-		Properties properties = new Properties();
-		
-		File cfile = null;
-		// Only read in the property file if a file is specified
-		if(file != null){
-			cfile = new File(file);
-			try {
-				properties.load(new FileReader(cfile));
-			} catch (FileNotFoundException e) {
-				throw new RuntimeException("Configuration file "+file+" not found", e);
-			} catch (IOException e) {
-				throw new RuntimeException("Cannot read configuration file "+file, e);
-			}
-		}
-		else{
-			logger.warning("No configfile specified !");
-		}
-		
-		// The defaults are set here
-		otfChannelPrefix = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.channelPrefix", "");
-		otfScalerPrefix = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.scalerPrefix", "");
-		otfNfsServer = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.nfsServer", "");
-		otfNfsShare = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.nfsShare", "");
-		otfSmbShare = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.smbShare", "");
-		
-		otfUseCrlogic = new Boolean(properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.useCrlogic", "false"));
-		otfCrlogicPrefix = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.crlogicPrefix", "");
-		otfCrlogicKeepTmpFiles = new Boolean(properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.crlogicKeepTmpFiles", "false"));
-
-		
-		dataBaseDirectory = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".data.dir",".");
-		if(cfile!=null && dataBaseDirectory.matches("^\\.\\.?/.*")){ // if basedir starts with . or .. we assume the data directory to be relative to the directory of the configuration file
-			dataBaseDirectory = cfile.getParentFile().getAbsolutePath()+"/"+dataBaseDirectory; 
-		}
-		dataFilePrefix = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".data.filePrefix","");
-		
-		
-		actorMoveTimeout = new Long(properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".actorMoveTimeout","600000"));
-		
-		smptServer= properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".notification.host","mail.psi.ch");
-		
-	}
-	
-	/**
-	 * Replace ${name} and ${date} macro given string
-	 * @param string
-	 * @param date
-	 * @param name
-	 * @return
-	 */
-	public String replaceMacros(String string, Date date, String name){
-		String newString = string;
-		
-		// Replace scan name macros
-		newString = newString.replaceAll("\\$\\{name\\}", name);
-		
-		
-		// Replace date macros
-		Pattern pattern = Pattern.compile("\\$\\{[a-z,A-Z,-,_,:]*\\}");
-        Matcher matcher = pattern.matcher(newString);
-        while(matcher.find()){
-        	String datePattern = matcher.group();
-        	datePattern = datePattern.replaceAll("\\$\\{", "");
-        	datePattern = datePattern.replaceAll("\\}", "");
-        	SimpleDateFormat datef = new SimpleDateFormat(datePattern);
-        	newString = matcher.replaceFirst(datef.format(date));
-        	matcher = pattern.matcher(newString);
-        }
-		return newString;
-	}
-
-	// Getter and setter functions
-	
-	public String getOtfChannelPrefix() {
-		return otfChannelPrefix;
-	}
-
-	public void setOtfChannelPrefix(String otfChannelPrefix) {
-		this.otfChannelPrefix = otfChannelPrefix;
-	}
-
-	public String getOtfNfsServer() {
-		return otfNfsServer;
-	}
-
-	public void setOtfNfsServer(String otfNfsServer) {
-		this.otfNfsServer = otfNfsServer;
-	}
-
-	public String getOtfNfsShare() {
-		return otfNfsShare;
-	}
-
-	public void setOtfNfsShare(String otfNfsShare) {
-		this.otfNfsShare = otfNfsShare;
-	}
-
-	public String getOtfSmbShare() {
-		return otfSmbShare;
-	}
-
-	public void setOtfSmbShare(String otfSmbShare) {
-		this.otfSmbShare = otfSmbShare;
-	}
-
-	public String getOtfScalerPrefix() {
-		return otfScalerPrefix;
-	}
-
-	public void setOtfScalerPrefix(String otfScalerPrefix) {
-		this.otfScalerPrefix = otfScalerPrefix;
-	}
-
-	public boolean isOtfUseCrlogic() {
-		return otfUseCrlogic;
-	}
-
-	public void setOtfUseCrlogic(boolean otfUseCrlogic) {
-		this.otfUseCrlogic = otfUseCrlogic;
-	}
-
-	public String getOtfCrlogicPrefix() {
-		return otfCrlogicPrefix;
-	}
-
-	public void setOtfCrlogicPrefix(String otfCrlogicPrefix) {
-		this.otfCrlogicPrefix = otfCrlogicPrefix;
-	}
-
-	public boolean isOtfCrlogicKeepTmpFiles() {
-		return otfCrlogicKeepTmpFiles;
-	}
-
-	public void setOtfCrlogicKeepTmpFiles(boolean otfCrlogicKeepTmpFiles) {
-		this.otfCrlogicKeepTmpFiles = otfCrlogicKeepTmpFiles;
-	}
-
-	public String getDataBaseDirectory() {
-		return dataBaseDirectory;
-	}
-
-	public void setDataBaseDirectory(String dataBaseDirectory) {
-		this.dataBaseDirectory = dataBaseDirectory;
-	}
-
-	public String getDataFilePrefix() {
-		return dataFilePrefix;
-	}
-
-	public void setDataFilePrefix(String dataFilePrefix) {
-		this.dataFilePrefix = dataFilePrefix;
-	}
-
-	public Long getActorMoveTimeout() {
-		return actorMoveTimeout;
-	}
-
-	public void setActorMoveTimeout(Long actorMoveTimeout) {
-		this.actorMoveTimeout = actorMoveTimeout;
-	}
-
-	public String getSmptServer() {
-		return smptServer;
-	}
-
-	public void setSmptServer(String smptServer) {
-		this.smptServer = smptServer;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/Collector.java

@@ -1,102 +0,0 @@
-/**
- * 
- * 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.aq;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.google.common.eventbus.EventBus;
-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;
-
-/**
- * Collector class that is collecting and merging data from different Queues.
- */
-public class Collector {
-	
-	private EventBus bus;
-	private List<MessageListener> listeners = new ArrayList<>();
-	
-	private List<Metadata> metadata;
-	private boolean first = true;
-	
-	public Collector(EventBus b){
-		this.bus = b;
-	}
-	
-	public void addEventBus(EventBus b){
-		MessageListener l = new MessageListener();
-		listeners.add(l);
-		b.register(l);
-	}
-
-	
-	
-	private class MessageListener{
-		
-		private DataMessage message;
-		
-		@Subscribe
-		public void onMessage(Message message){
-			int level = listeners.indexOf(this);
-			if(message instanceof DataMessage){
-				this.message = (DataMessage) message;
-				
-				if(level==0){
-					if(first){
-						metadata = new ArrayList<>();
-						for(int i=listeners.size()-1;i>=0;i--){
-							// Correct/Add dimension information
-							for(Metadata m: listeners.get(i).getMessage().getMetadata()){
-								m.setDimension(i);
-							}
-							metadata.addAll(listeners.get(i).getMessage().getMetadata());
-						}
-						
-					}
-					DataMessage m = new DataMessage(metadata);
-					for(int i=listeners.size()-1;i>=0;i--){
-						m.getData().addAll(listeners.get(i).getMessage().getData());
-					}
-					bus.post(m);
-				}
-			}
-			if(message instanceof EndOfStreamMessage){
-				
-				StreamDelimiterMessage ddm = new StreamDelimiterMessage(level, ((EndOfStreamMessage)message).isIflag());
-				bus.post(ddm);
-				if(level==(listeners.size()-1)){ // if highest dimension then send end of stream
-					bus.post(new EndOfStreamMessage());
-				}
-			}
-		}
-		
-		public DataMessage getMessage(){
-			return message;
-		}
-	}
-	
-}
-

ch.psi.fda/src/main/java/ch/psi/fda/aq/Manipulator.java

@@ -1,77 +0,0 @@
-/**
- * 
- * 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.aq;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.google.common.eventbus.EventBus;
-import com.google.common.eventbus.Subscribe;
-
-import ch.psi.fda.core.Manipulation;
-import ch.psi.fda.messages.DataMessage;
-import ch.psi.fda.messages.Message;
-import ch.psi.fda.messages.Metadata;
-
-/**
- * Applies manipulations to the data stream
- */
-public class Manipulator {
-	
-	private EventBus bus;
-	
-	private final List<Manipulation> manipulations;
-	private boolean first = true;
-	private List<Metadata> metadata = new ArrayList<>();
-	
-	public Manipulator(EventBus b, List<Manipulation> manipulations){
-		this.bus = b;
-		this.manipulations = manipulations;
-	}
-
-	@Subscribe
-	public void onMessage(Message message){
-		if(message instanceof DataMessage){
-			if(first){
-				first=false;
-				
-				metadata.addAll(((DataMessage) message).getMetadata());
-				
-				for(Manipulation manipulation: this.manipulations){
-					manipulation.initialize(this.metadata);
-					
-					// Add manipulation id to metadata
-					this.metadata.add(new Metadata(manipulation.getId(),0)); // Calculated component always belongs to lowes dimension
-				}
-			}
-			
-			
-			DataMessage dm = (DataMessage) message;
-//			message = new DataMessage(metadata);
-			for(Manipulation manipulation: manipulations){
-//				((DataMessage)message).getData().add(manipulation.execute(dm));
-				dm.getData().add(manipulation.execute(dm));
-			}
-			// Need to update the metadata of the message
-			dm.setMetadata(this.metadata);
-		}
-		bus.post(message);
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/NotificationAgent.java

@@ -1,109 +0,0 @@
-/*
- *  Copyright (C) 2011 Paul Scherrer Institute
- * 
- *  This program is free software: you can redistribute it and/or modify
- *  it under the terms of the GNU General Public License as published by
- *  the Free Software Foundation, either version 3 of the License, or
- *  (at your option) any later version.
- * 
- *  This program 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 General Public License for more details.
- * 
- *  You should have received a copy of the GNU General Public License
- *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-package ch.psi.fda.aq;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import javax.mail.Message;
-import javax.mail.MessagingException;
-import javax.mail.Session;
-import javax.mail.Transport;
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
-
-import ch.psi.fda.model.v1.Recipient;
-
-/**
- * Agent to send out notifications to specified recipients.
- */
-public class NotificationAgent {
-
-    private final static String smsPostfix = "@sms.switch.ch";
-
-    private Properties properties;
-    private String fromAddress;
-    private final List<Recipient> recipients = new ArrayList<Recipient>();
-
-    /**
-     * Constructor
-     * @param host		SMTP server to send notifications to
-     * @param recipients	List of recipients
-     * @param from		Address string that will show up in the from field. For example: fda@psi.ch. This argument must not contain white spaces
-     */
-    public NotificationAgent(String host, String from){
-
-        fromAddress = from;
-
-        properties = new Properties();
-        properties.put("mail.smtp.host", host);
-    }
-
-    
-    
-    public void sendNotification(String aSubject, String aBody, boolean error, boolean success) {
-
-        for(Recipient recipient: recipients){
-        	
-        	if((error && recipient.isError()) || (success && recipient.isSuccess())){
-	        	String receiver;
-	        	
-	        	// Verify mail recipients
-	            if(recipient.getValue().matches("[0-9,\\\\.,-,a-z,A-Z]*@[0-9,\\\\.,a-z,A-Z]*")){
-	                receiver = recipient.getValue();
-	            }
-	            else if(recipient.getValue().matches("[0-9]+")){
-	                // Assume that it is a SMS number
-	                receiver = recipient.getValue() + smsPostfix;
-	            }
-	            else{
-	                Logger.getLogger(NotificationAgent.class.getName()).log(Level.WARNING, "Invalid email address");
-	                continue;
-	            }
-	        	
-	        	
-	        	Logger.getLogger(NotificationAgent.class.getName()).log(Level.INFO, "Send notification to " + receiver);
-	        	
-	            //Here, no Authenticator argument is used (it is null).
-	            //Authenticators are used to prompt the user for user
-	            //name and password.
-	            Session session = Session.getDefaultInstance(properties, null);
-	            MimeMessage message = new MimeMessage(session);
-	            try {
-	                //The "from" address may be set in code, or set in the
-	                //config file under "mail.from" ; here, the latter style is used
-	                message.setFrom( new InternetAddress(fromAddress) );
-	
-	                message.addRecipient(Message.RecipientType.TO, new InternetAddress(receiver));
-	                message.setSubject(aSubject);
-	                message.setText(aBody);
-	                Transport.send(message);
-	            } catch (MessagingException ex) {
-	                Logger.getLogger(NotificationAgent.class.getName()).log(Level.WARNING, "Failed to send notification to " + receiver, ex);
-	            }
-        	}
-        }
-    }
-
-    public List<Recipient> getRecipients() {
-        return recipients;
-    }
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/VisualizationMapper.java

@@ -1,273 +0,0 @@
-/**
- * 
- * 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.aq;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.psi.fda.model.v1.ArrayDetector;
-import ch.psi.fda.model.v1.ContinuousPositioner;
-import ch.psi.fda.model.v1.Detector;
-import ch.psi.fda.model.v1.LinearPositioner;
-import ch.psi.fda.model.v1.Positioner;
-import ch.psi.fda.model.v1.PseudoPositioner;
-import ch.psi.fda.model.v1.Visualization;
-import ch.psi.fda.visualizer.SeriesDataFilter;
-import ch.psi.fda.visualizer.XYSeriesArrayDataFilter;
-import ch.psi.fda.visualizer.XYSeriesDataFilter;
-import ch.psi.fda.visualizer.XYZSeriesArrayDataFilter;
-import ch.psi.fda.visualizer.XYZSeriesDataFilter;
-import ch.psi.plot.xyz.MatrixPlot;
-import ch.psi.plot.xyz.MatrixPlotData;
-
-public class VisualizationMapper {
-	
-	
-	/**
-	 * Retrieve id string of the passed object
-	 * @param object
-	 * @return	Id string of object
-	 */
-	private static String getId(Object object){
-		String id;
-		if(object instanceof Positioner){
-			id = ((Positioner)object).getId();
-		}
-		else if (object instanceof Detector){
-			id = ((Detector)object).getId();
-		}
-		else if (object instanceof ch.psi.fda.model.v1.Manipulation){
-			id = ((ch.psi.fda.model.v1.Manipulation)object).getId();
-		}
-		// For testing purposes
-		else if(object instanceof String){
-			id = (String) object;
-		}
-		else{
-			throw new RuntimeException("Unable to identify id of object reference "+object);
-		}
-		return id;
-	}
-	
-	/**
-	 * Converts a list of visualizations into a list of data filters which can be applied to the data stream
-	 * 
-	 * @param vl
-	 * @return
-	 */
-	public static List<SeriesDataFilter> mapVisualizations(List<Visualization> vl){
-		List<SeriesDataFilter> filters = new ArrayList<SeriesDataFilter>();
-		
-		for(Visualization v: vl){
-			if(v instanceof ch.psi.fda.model.v1.LinePlot){
-				ch.psi.fda.model.v1.LinePlot lp = (ch.psi.fda.model.v1.LinePlot) v;
-				
-				// Create plot for visualization
-				ch.psi.plot.xy.LinePlot plot = new ch.psi.plot.xy.LinePlot(lp.getTitle());
-				
-				// Create data filter for visualization
-				String idX = getId(lp.getX());
-				
-				List<Object> l = lp.getY();
-				for(Object o: l){
-					String idY = getId(o);
-					XYSeriesDataFilter filter = new XYSeriesDataFilter(idX, idY, plot);
-					filter.setSeriesName(idY);
-					filters.add(filter);
-				}
-			}
-			else if(v instanceof ch.psi.fda.model.v1.LinePlotArray){
-				// Array visualization
-				ch.psi.fda.model.v1.LinePlotArray lp = (ch.psi.fda.model.v1.LinePlotArray) v;
-				
-				// Create plot for visualization
-				ch.psi.plot.xy.LinePlot plot = new ch.psi.plot.xy.LinePlot(lp.getTitle());
-				
-				// Create data filter for visualization
-				List<Object> l = lp.getY();
-				for(Object o: l){
-					String idY = getId(o);
-					
-					XYSeriesArrayDataFilter filter = new XYSeriesArrayDataFilter(idY, plot);
-					filter.setMaxSeries(lp.getMaxSeries()*lp.getY().size()); // Workaround - keep for each array max series
-					filter.setOffset(lp.getOffset());
-					filter.setSize(lp.getSize());
-					filter.setSeriesName(idY);
-					filters.add(filter);
-				}
-			}
-			else if(v instanceof ch.psi.fda.model.v1.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.model.v1.MatrixPlot mp = (ch.psi.fda.model.v1.MatrixPlot) v;
-				
-
-				double minX, maxX;
-				int nX;
-				double minY, maxY;
-				int nY;
-				
-				String idX, idY, idZ;
-				
-				// X Axis
-				if(mp.getX() instanceof LinearPositioner){
-					LinearPositioner linp = ((LinearPositioner)mp.getX());
-					idX = linp.getId();
-					
-					minX = (Math.min(linp.getStart(), linp.getEnd()));
-					maxX = (Math.max(linp.getStart(), linp.getEnd()));
-					nX = ((int) Math.floor((Math.abs(maxX-minX))/linp.getStepSize()) + 1);
-				}
-				else if(mp.getX() instanceof PseudoPositioner){
-					PseudoPositioner pp = ((PseudoPositioner)mp.getX());
-					idX = pp.getId();
-					minX = (1); // Count starts at 1
-					maxX = (pp.getCounts());
-					nX = (pp.getCounts());
-				}
-				else if(mp.getX() instanceof ContinuousPositioner){
-					ContinuousPositioner conp = ((ContinuousPositioner)mp.getX());
-					idX = conp.getId();
-					
-					minX = (Math.min(conp.getStart(), conp.getEnd()));
-					maxX = (Math.max(conp.getStart(), conp.getEnd()));
-					nX = ((int) Math.floor((Math.abs(maxX-minX))/conp.getStepSize()) + 1);
-				}
-				else{
-					// Fail as we cannot determine the min, max and number of steps
-					throw new RuntimeException(mp.getX().getClass().getName()+" is not supported as x-axis of a MatrixPlot");
-				}
-				
-				// Y Axis
-				if(mp.getY() instanceof LinearPositioner){
-					LinearPositioner linp = ((LinearPositioner)mp.getY());
-					idY = linp.getId();
-					minY = (Math.min(linp.getStart(), linp.getEnd()));
-					maxY = (Math.max(linp.getStart(), linp.getEnd()));
-					nY = ((int) Math.floor((Math.abs(maxY-minY))/linp.getStepSize()) + 1);
-				}
-				else if(mp.getY() instanceof PseudoPositioner){
-					PseudoPositioner pp = ((PseudoPositioner)mp.getY());
-					idY = pp.getId();
-					minY = (1); // Count starts at 1
-					maxY = (pp.getCounts());
-					nY = (pp.getCounts());
-				}
-				else{
-					// Fail as we cannot determine the min, max and number of steps
-					throw new RuntimeException(mp.getY().getClass().getName()+" is not supported as y-axis of a MatrixPlot");
-				}
-				
-				// Z Dimension
-				idZ = getId(mp.getZ());
-
-				// Create plot for visualization
-				MatrixPlotData data = new MatrixPlotData(minX, maxX, nX, minY, maxY, nY);
-				MatrixPlot plot = new MatrixPlot(mp.getTitle(), data);
-				
-				XYZSeriesDataFilter filter = new XYZSeriesDataFilter(idX, idY, idZ, plot);
-				filters.add(filter);
-			}
-			else if(v instanceof ch.psi.fda.model.v1.MatrixPlotArray){
-				// Support for 2D waveform plots
-				ch.psi.fda.model.v1.MatrixPlotArray mp = (ch.psi.fda.model.v1.MatrixPlotArray) v;
-				
-				// Get size of the array detector
-				int arraySize = 0;
-				Object o = mp.getZ();
-				if(o instanceof ArrayDetector){
-					ArrayDetector ad = (ArrayDetector) o;
-					arraySize = ad.getArraySize();
-				}
-				else{
-					// Workaround
-					arraySize = mp.getSize(); // of array is from a manipulation the size is not known. Then the size will indicate the size of the array to display
-				}
-				
-				int offset = mp.getOffset();
-				// Determine size for array
-				int size = mp.getSize();
-				if(size>0 && offset+size<arraySize){
-					size = mp.getSize();
-				}
-				else{
-					size=arraySize-offset;
-				}
-				
-				
-				double minY, maxY;
-				int nY;
-				
-				double minX = offset;
-				double maxX = offset+size-1;
-				int nX = size;
-				
-				String idY, idZ;
-				
-				// Y Axis
-				if(mp.getY() instanceof LinearPositioner){
-					LinearPositioner linp = ((LinearPositioner)mp.getY());
-					idY = linp.getId();
-					
-					minY = (Math.min(linp.getStart(), linp.getEnd()));
-					maxY = (Math.max(linp.getStart(), linp.getEnd()));
-					nY = ((int) Math.floor((Math.abs(maxY-minY))/linp.getStepSize()) + 1);
-				}
-				else if(mp.getY() instanceof PseudoPositioner){
-					PseudoPositioner pp = ((PseudoPositioner)mp.getY());
-					idY = pp.getId();
-					minY = (1); // Count starts at 1
-					maxY = (pp.getCounts());
-					nY = (pp.getCounts());
-				}
-				else if(mp.getY() instanceof ContinuousPositioner){
-					ContinuousPositioner conp = ((ContinuousPositioner)mp.getY());
-					idY = conp.getId();
-					
-					minY = (Math.min(conp.getStart(), conp.getEnd()));
-					maxY = (Math.max(conp.getStart(), conp.getEnd()));
-					nY = ((int) Math.floor((Math.abs(maxY-minY))/conp.getStepSize()) + 1);
-				}
-				else{
-					// Fail as we cannot determine the min, max and number of steps
-					throw new RuntimeException(mp.getY().getClass().getName()+" is not supported as x-axis of a MatrixPlot");
-				}
-				
-				
-				// Z Dimension
-				idZ = getId(mp.getZ());
-
-				// Create plot for visualization
-				MatrixPlotData data = new MatrixPlotData(minX, maxX, nX, minY, maxY, nY);
-				MatrixPlot plot = new MatrixPlot(mp.getTitle(), data);
-				
-				XYZSeriesArrayDataFilter filter = new XYZSeriesArrayDataFilter(idY, idZ, offset, size, plot);
-				filters.add(filter);
-			}
-			else{
-				// Visualization type (currently) not supported
-				throw new RuntimeException(v.getClass().getName()+" is not supported as visualization type");
-			}
-		}
-		return filters;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/Action.java

@@ -1,33 +0,0 @@
-/**
- * 
- * 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.core;
-
-public interface Action {
-	
-	/**
-	 * Execute logic of the action
-	 */
-	public void execute() throws InterruptedException;
-	
-	/**
-	 * Abort the execution logic of the action
-	 */
-	public void abort();
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/ActionLoop.java

@@ -1,66 +0,0 @@
-/**
- * 
- * 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.core;
-
-import java.util.List;
-
-import com.google.common.eventbus.EventBus;
-
-/**
- * Loop of actions to accomplish a task. Depending on the loop
- * actions may be executed in a different way.
- */
-public interface ActionLoop extends Action {
-	
-	/**
-	 * Prepare ActionLoop for execution.
-	 */
-	public void prepare();
-	
-	/**
-	 * Cleanup resources used by this ActionLoop while it was executed.
-	 */
-	public void cleanup();
-	
-	/**
-	 * Get the pre actions of the Loop
-	 * @return	pre actions
-	 */
-	public List<Action> getPreActions();
-	
-	/**
-	 * Get the post actions of the loop
-	 * @return post actions
-	 */
-	public List<Action> getPostActions();
-	
-	/**
-	 * @return is a datagroup
-	 */
-	public boolean isDataGroup();
-
-	/**
-	 * Set whether data of the loop belongs to a own data group
-	 * @param dataGroup
-	 */
-	public void setDataGroup(boolean dataGroup);
-	
-	public EventBus getEventBus();
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/Actor.java

@@ -1,49 +0,0 @@
-/**
- * 
- * 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.core;
-
-public interface Actor {
-	/**
-	 * Set actor value
-	 */
-	public void set() throws InterruptedException;
-	
-	/**
-	 * Function to check whether the actor has a next set value
-	 * @return  Returns true if there is an actor value for the next iteration.
-	 * 			False if there is no actor value (i.e. this will be the last iteration in the ActionLoop)
-	 */
-	public boolean hasNext();
-	
-	/**
-	 * Initialize the actor to the start
-	 */
-	public void init();
-	
-	/**
-	 * Reverse the set values of the actor
-	 */
-	public void reverse();
-	
-	/**
-	 * Reset the actuator to its initial configuration
-	 */
-	public void reset();
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/ActorSetCallable.java

@@ -1,40 +0,0 @@
-/**
- * 
- * 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.core;
-
-import java.util.concurrent.Callable;
-
-/**
- * Callable used for parallel execution of the set method of an actor
- */
-public class ActorSetCallable implements Callable<Object> {
-
-	private Actor actor;
-	
-	public ActorSetCallable(Actor actor){
-		this.actor = actor;
-	}
-	
-	@Override
-	public Object call() throws Exception {
-		actor.set();
-		return null;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/Guard.java

@@ -1,41 +0,0 @@
-/**
- * 
- * 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.core;
-
-/**
- * Guard to protect specific activities. A guard can be used to check for environment changes while a
- * certain activity was executed. 
- * 
- * Example:
- * An Guard can be used to check whether an injection happened while the the detector were read. 
- */
-public interface Guard {
-	
-	/**
-	 * Initialize guard object and its internal state.
-	 */
-	public void init();
-	
-	/**
-	 * Check the status of the guard.
-	 * @return	Returns true if the guard condition was not constrainted since the last init call. False otherwise.
-	 */
-	public boolean check();
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/Manipulation.java

@@ -1,47 +0,0 @@
-/**
- * 
- * 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.core;
-
-import java.util.List;
-
-import ch.psi.fda.messages.DataMessage;
-import ch.psi.fda.messages.Metadata;
-
-public interface Manipulation {
-
-	/**
-	 * Get the id of the manipulation
-	 * @return	id of manipulation
-	 */
-	public String getId();
-	
-	/**
-	 * Initialize the manipulation
-	 * @param metadata	Metadata of the incomming data message
-	 */
-	public void initialize(List<Metadata> metadata);
-	
-	/**
-	 * Execute the manipulation on the passed data message
-	 * @param message Message to manipulate
-	 * @return	Result of the manipulation
-	 */
-	public Object execute(DataMessage message);
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/Sensor.java

@@ -1,39 +0,0 @@
-/**
- * 
- * 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.core;
-
-/**
- * The sensor interface describes an entity that can be read out like a
- * simple channel or (image) detector. Depending on the sensor type the
- * returned data is of a certain type.
- */
-public interface Sensor {
-	/**
-	 * Readout sensor. 
-	 * @return	Sensor value. The type of the returned value depends on the sensor type.
-	 */
-	public Object read() throws InterruptedException;
-	
-	/**
-	 * Get the global id of the sensor
-	 * @return	id of sensor
-	 */
-	public String getId();
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ChannelAccessCondition.java

@@ -1,124 +0,0 @@
-/**
- * 
- * 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.core.actions;
-
-import java.util.Comparator;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- */
-public class ChannelAccessCondition<E> implements Action {
-
-	private static Logger logger = Logger.getLogger(ChannelAccessCondition.class.getName());
-	
-	private final Channel<E> channel;
-	private final E expectedValue;
-	private final Comparator<E> comparator;
-	private final Long timeout;
-	
-	private volatile boolean abort = false;
-	private volatile Thread waitT = null;
-	
-	/**
-	 * @param channel		Channel to wait value for
-	 * @param expectedValue		Value to wait for
-	 * @param timeout			Timeout of the condition in milliseconds (null accepted - will take default wait timeout for channels ch.psi.jcae.ChannelBeanFactory.waitTimeout)
-	 * 
-	 * @throws	IllegalArgumentException	Timeout specified is not >=0
-	 */
-	public ChannelAccessCondition(Channel<E> channel, E expectedValue, Long timeout){
-
-		if(timeout != null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-		
-		this.channel = channel;
-		this.expectedValue = expectedValue;
-		this.comparator = null;
-		this.timeout = timeout;
-	}
-	
-	public ChannelAccessCondition(Channel<E> channel, E expectedValue, Comparator<E> comparator, Long timeout){
-
-		if(timeout != null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-		
-		this.channel = channel;
-		this.expectedValue = expectedValue;
-		this.comparator = comparator;
-		this.timeout = timeout;
-	}
-
-	
-	/**
-	 * @throws RuntimeException		Channel value did not reach expected value (within the specified timeout period)
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort=false;
-		logger.finest("Checking channel "+channel.getName()+" for value "+expectedValue+" [timeout: "+timeout+"]" );
-		try{
-			waitT = Thread.currentThread();
-			try {
-				if(comparator==null){
-					if(timeout == null){
-						channel.waitForValue(expectedValue);
-					}
-					else{
-						channel.waitForValue(expectedValue, timeout);
-					}
-				}
-				else{
-					if(timeout == null){
-						channel.waitForValue(expectedValue, comparator);
-					}
-					else{
-						channel.waitForValue(expectedValue, comparator, timeout);
-					}
-				}
-			} catch (ExecutionException | ChannelException | TimeoutException | InterruptedException e) {
-				if(abort && e instanceof InterruptedException){
-					return;
-				}
-				throw new RuntimeException("Channel [name:"+channel.getName()+"] did not reach expected value "+expectedValue+" ", e);
-			}
-		}
-		finally{
-			waitT=null;
-		}
-	}
-
-	@Override
-	public void abort() {
-		abort=true;
-		if(waitT!=null){
-			waitT.interrupt();
-		}
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ChannelAccessPut.java

@@ -1,94 +0,0 @@
-/**
- * 
- * 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.core.actions;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- */
-public class ChannelAccessPut<E> implements Action {
-	
-	private static Logger logger = Logger.getLogger(ChannelAccessPut.class.getName());
-
-	private final Channel<E> channel;
-	private final E value;
-	private final boolean asynchronous;
-	
-	private final Long timeout;
-	
-	/**
-	 * @param channel
-	 * @param value				Value to set
-	 * @param asynchronous		Flag whether to set the value synchronous (wait for response) or asynchronously (fire and forget)
-	 * @param timeout			Timeout used for set operation (time that set need to come back)
-	 */
-	public ChannelAccessPut(Channel<E> channel, E value, boolean asynchronous, Long timeout){
-
-		this.channel = channel;
-		this.value = value;
-		this.asynchronous = asynchronous;
-		this.timeout = timeout;
-	}
-	
-	/**
-	 * Additional constructor for convenience. This constructor defaults the operation type to synchronous put.
-	 * @param channel
-	 * @param value				Value to set
-	 */
-	public ChannelAccessPut(Channel<E> channel, E value){
-		this(channel, value, false, null);
-	}
-	
-	/**
-	 * @throws RuntimeException		Cannot set value on channel
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		logger.finest("Put to channel: "+channel.getName()+ " asynchronous: "+asynchronous);
-		try{
-			if(asynchronous){
-				channel.setValueNoWait(value);
-			}
-			else{
-				if(timeout==null){
-					channel.setValue(value);
-				}
-				else{
-					channel.setValueAsync(value).get(timeout, TimeUnit.MILLISECONDS);
-				}
-			}
-		} catch (ExecutionException | TimeoutException | ChannelException e) {
-			throw new RuntimeException("Unable to set channel [name:"+channel.getName()+"] to value "+value, e);
-		}
-	}
-
-	@Override
-	public void abort() {
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/Delay.java

@@ -1,52 +0,0 @@
-/**
- * 
- * 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.core.actions;
-
-import ch.psi.fda.core.Action;
-
-/**
- * Wait a specific time until executing the next action ...
- */
-public class Delay implements Action {
-
-	private final long time;
-	
-	/**
-	 * @param time		Time to wait in milliseconds
-	 */
-	public Delay(long time){
-		
-		// Check if delay time is positive and >0
-		if(time<=0){
-			throw new IllegalArgumentException("Wait time must be >0");
-		}
-		
-		this.time = time;
-	}
-	
-	@Override
-	public void execute() throws InterruptedException {
-		Thread.sleep(time);
-	}
-
-	@Override
-	public void abort() {
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/JythonAction.java

@@ -1,142 +0,0 @@
-/**
- * 
- * 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.core.actions;
-
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.logging.Logger;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.script.ScriptEngine;
-import javax.script.ScriptEngineManager;
-import javax.script.ScriptException;
-
-import ch.psi.fda.core.Action;
-
-/**
- * Executes a python script inside a Jython interpreter
- */
-public class JythonAction implements Action {
-
-	private static Logger logger = Logger.getLogger(JythonAction.class.getName());
-	
-	/**
-	 * Pattern of the entry function of the jython script
-	 */
-	private static final String entryFunction = "process";
-	private static final String entryFunctionPattern = "def "+entryFunction+"\\((.*)\\):";
-	
-	private ScriptEngine engine;
-	
-	private String jythonCall; // entry call to script - including all parameters, etc.
-	
-	private final Map<String,Object> globalObjects;
-	
-	public JythonAction(String script, Map<String, ?> mapping){
-		this(script, mapping, new HashMap<String,Object>());
-	}
-	
-	public JythonAction(String script, Map<String, ?> mapping, Map<String,Object> globalObjects){
-		
-		this.globalObjects = globalObjects;
-		
-		// Workaround for Jython memory leak 
-		// http://blog.hillbrecht.de/2009/07/11/jython-memory-leakout-of-memory-problem/
-		System.setProperty("python.options.internalTablesImpl","weak");
-		
-		// Create new script engine
-		this.engine = new ScriptEngineManager().getEngineByName("python");
-		
-		// Determine script entry function and the function parameters
-		Pattern pattern = Pattern.compile(entryFunctionPattern);
-		Matcher matcher = pattern.matcher(script);
-		String[] functionParameters = null;
-		if(matcher.find() && matcher.groupCount()==1){
-			logger.finest("Entry function '"+entryFunctionPattern+"' found - Identified parameters: "+matcher.group(1));
-			jythonCall = entryFunction+"("+matcher.group(1)+")";
-			if(matcher.group(1).matches(" *")){
-				functionParameters = new String[0];
-			}
-			else{
-				functionParameters = matcher.group(1).split(" *, *");
-			}
-		}
-		else{
-			throw new IllegalArgumentException("Cannot determine entry function: "+entryFunctionPattern);
-		}
-		
-		// Check whether all function parameters have a mapping
-		for(int i=0;i<functionParameters.length; i++){
-			String p = functionParameters[i];
-			p = p.trim();
-			boolean found = false;
-			for(String pm: mapping.keySet()){
-				if(pm.equals(p)){
-					found=true;
-					break;
-				}
-			}
-			if(!found){
-				throw new IllegalArgumentException("No mapping compontent found for parameter "+p);
-			}
-		}
-		
-		// Check whether more mappings are specified than function parameters
-		if(functionParameters.length<mapping.size()){
-			throw new IllegalArgumentException("More mappings than function parameters are specified");
-		}
-		
-		// Load manipulation script
-		try {
-			engine.eval(script);
-		} catch (ScriptException e) {
-			throw new RuntimeException("Unable to load manipulation script", e);
-		}
-		
-		for(String b: mapping.keySet()){
-			// Assign channel bean to variable
-			engine.put(b, mapping.get(b));
-		}
-	}
-	
-	@Override
-	public void execute() {
-		
-		// Set global objects
-		// This block is not in initialization as we want to assure that all invocations
-		// of this manipulation will get the same value (i.e. to prevent inconsistent behavior
-		// if variable was changed during an execution of the manipulation)
-		for(String k: globalObjects.keySet()){
-			engine.put(k, globalObjects.get(k));
-		}
-		
-		try {
-			engine.eval(jythonCall+"\n");
-		} catch (ScriptException e) {
-			throw new RuntimeException("Action failed while executing the Jython script",e);
-		}		
-	}
-
-	@Override
-	public void abort() {
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ShellAction.java

@@ -1,133 +0,0 @@
-/**
- * 
- * 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.core.actions;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-
-/**
- * Action that executes a specified command when it is executed.
- */
-public class ShellAction implements Action{
-	
-	private static Logger logger = Logger.getLogger(ShellAction.class.getName());
-
-	private volatile Process process;
-	private volatile boolean abort = false;
-	private boolean checkExitValue = true;
-	private int exitValue = 0;
-	
-	/**
-	 * Name (full path if it is not in the system path) of the script to execute when
-	 * the execute() function of this action is invoked.
-	 */
-	private final String script;
-	
-	/**
-	 * @param script	Name of the command to execute when this action is invoked
-	 * 
-	 * @throws IllegalArgumentException		Specified script does not exist
-	 */
-	public ShellAction(String script){
-		String[] scri = script.split("[ ,\t]");
-		File s = new File(scri[0]);
-		if(!s.exists()){
-			throw new IllegalArgumentException("Script "+script+" does not exist.");
-		}
-		this.script = script;
-	}
-	
-	@Override
-	public void execute() throws InterruptedException {
-		try{
-			abort = false;
-			logger.fine("Execute script "+script);
-			process = Runtime.getRuntime().exec(new String[]{"/bin/bash","-c",script});
-			int exitVal = process.waitFor();
-			
-			// Log output of the shell script if loglevel is finest
-			if(logger.isLoggable(Level.FINEST)){
-				logger.finest("STDOUT [BEGIN]");
-				// Ideally the readout of the stream should be in parallel to the processing of the script! I.e. the output appears in the log as it is generated by the script!
-				BufferedReader reader = new BufferedReader(new InputStreamReader(process.getInputStream()));
-				String line = null;
-				while((line=reader.readLine()) != null){
-					logger.finest(line);
-				}
-				logger.finest("STDOUT [END]");
-				
-				logger.finest("STDERR [BEGIN]");
-				// Ideally the readout of the stream should be in parallel to the processing of the script! I.e. the output appears in the log as it is generated by the script!
-				reader = new BufferedReader(new InputStreamReader(process.getErrorStream()));
-				line = null;
-				while((line=reader.readLine()) != null){
-					logger.finest(line);
-				}
-				logger.finest("STDERR [END]");
-			}
-			
-			logger.fine("Script ["+script+"] return value: "+exitVal);
-			
-			if(abort){
-				throw new RuntimeException("Script ["+script+"] was aborted");
-			}
-			else{
-				// Check script exit value to 0 if != 0 then throw an runtime exception
-				if(checkExitValue && exitVal != exitValue){
-					throw new RuntimeException("Script ["+script+"] returned with an exit value not equal to 0");
-				}
-			}
-			process = null;
-		}
-		catch(IOException e){
-			throw new RuntimeException("Unable to execute script: "+script,e);
-		}
-	}
-
-	@Override
-	public void abort() {
-		abort=true;
-		if(process!=null){
-			process.destroy();
-		}
-	}
-
-	public boolean isCheckExitValue() {
-		return checkExitValue;
-	}
-
-	public void setCheckExitValue(boolean checkExitValue) {
-		this.checkExitValue = checkExitValue;
-	}
-
-	public int getExitValue() {
-		return exitValue;
-	}
-
-	public void setExitValue(int exitValue) {
-		this.exitValue = exitValue;
-	}	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/ChannelAccessFunctionActuator.java

@@ -1,253 +0,0 @@
-/**
- * 
- * 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.core.actors;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Actor;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-
-public class ChannelAccessFunctionActuator<T> implements Actor {
-	
-	private static Logger logger = Logger.getLogger(ChannelAccessFunctionActuator.class.getName());
-
-	private boolean asynchronous = false;
-	private double start;
-	private double end;
-	private double stepSize;
-	private int direction; // Move direction (start&lt;end = 1, start&gt;end = -1)
-	
-	/**
-	 * Execution count of actuator. This variable is used to minimize the floating point
-	 * rounding errors for calculating the next step. 
-	 */
-	private int count;
-	
-	/**
-	 * Flag that indicates whether there is a next set value for the Actor
-	 */
-	private boolean next;
-	
-	/**
-	 * Value to set at next @see ch.psi.fda.engine.Actor#set() call
-	 */
-	private double value;
-	
-	/**
-	 * Level of accuracy the positioner need to have (e.g. if a positioner is set to 1 the readback set value
-	 * of the positioner need to have at lease 1+/-accuracy) 
-	 * Default is stepSize/2 
-	 */
-	private double accuracy;
-	
-	/**
-	 * Move timeout
-	 */
-	private Long timeout;
-	
-	private final T doneValue;
-	private final long doneDelay;
-	
-	private final double originalStart;
-	private final double originalEnd;
-	private final int originalDirection;
-	
-	private Channel<Double> channel;
-	private Channel<T> doneChannel = null;
-	
-	private final Function function;
-	private boolean checkActorSet = true;
-	
-	/**
-	 * Constructor - Initialize actor
-	 * @param channelName
-	 * @param start
-	 * @param end
-	 * @param stepSize
-	 * @param timeout 	Maximum move time (in milliseconds)
-	 */
-	public ChannelAccessFunctionActuator(Channel<Double> channel, Function function, double start, double end, double stepSize, Long timeout){
-		this(channel, null, null, 0, function, start, end, stepSize, timeout);
-	}
-	
-	/**
-	 * Constructor
-	 * @param channel
-	 * @param doneChannel	If null actor will not wait (for this channel) to continue
-	 * @param doneValue
-	 * @param doneDelay			Delay in seconds before checking the done channel
-	 * @param start
-	 * @param end
-	 * @param stepSize
-	 * @param timeout			Maximum move time (in milliseconds)
-	 */
-	public ChannelAccessFunctionActuator(Channel<Double> channel, Channel<T> doneChannel, T doneValue, double doneDelay,  Function function, double start, double end, double stepSize, Long timeout){
-		
-		this.doneValue = doneValue;
-		this.doneDelay = (long) Math.floor((doneDelay*1000));
-		this.start = start;
-		this.end = end;
-		
-		if(stepSize <= 0){
-			throw new IllegalArgumentException("Step size ["+stepSize+"] must be > 0");
-		}
-		this.stepSize = stepSize;
-		
-		this.accuracy = stepSize/2;
-		
-		// Validate and save timeout parameter
-		if(timeout!=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be >0 or null");
-		}
-		else{
-			this.timeout = timeout;
-		}
-		
-		if(function==null){
-			throw new IllegalArgumentException("Function must not be null");
-		}
-		this.function = function;
-		
-		
-		init();
-		
-		// Save original settings
-		this.originalStart = start;
-		this.originalEnd = end;
-		this.originalDirection = direction;
-		
-		this.channel = channel;
-		this.doneChannel = doneChannel;
-	}
-	
-	@Override
-	public void set() throws InterruptedException {
-		
-		// Throw an IllegalStateException in the case that set is called although there is no next step.
-		if(!next){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		// Set actuator channel
-		logger.finest("Set actuator channel "+channel.getName()+" to value: "+value);
-		try {
-			double fvalue = function.calculate(value);
-			
-			if(!asynchronous){
-				if(timeout==null){
-					channel.setValue(fvalue);
-				}
-				else{
-					channel.setValueAsync(fvalue).get(timeout, TimeUnit.MILLISECONDS); 
-				}
-			}
-			else{
-				channel.setValueNoWait(fvalue);
-			}
-			
-			if(doneChannel != null){
-				Thread.sleep(doneDelay);
-				doneChannel.waitForValue(doneValue); 
-			}
-			
-			// Check whether the set value is really on the value that was set before.
-			if(checkActorSet){
-				double c = channel.getValue(true);
-				double a = Math.abs( c - fvalue ); 
-				if ( a > accuracy ){
-					throw new RuntimeException("Actor could not be set to the value "+fvalue+" The readback of the set value does not match the value that was set [value: "+c+" delta: "+a+" accuracy: "+accuracy+"]");
-				}
-			}
-			
-		} catch (ExecutionException | TimeoutException | ChannelException e) {
-			throw new RuntimeException("Unable to move actuator [channel: "+channel.getName()+"] to value "+value,e);
-		}
-		
-		
-		count++;
-		double nextValue = start+(count*stepSize*direction); // Done like this to keep floating point rounding errors minimal
-		
-		if((direction==1&&nextValue<=end)||(direction==-1&nextValue>=end)){
-			
-			// Apply function
-//			nextValue = function.calculate(nextValue);
-			
-			logger.fine("Next actor value: "+nextValue);
-			value=nextValue;
-			this.next = true;
-		}
-		else{
-			// There is no next set value
-			this.next = false;
-		}
-	}
-
-	@Override
-	public boolean hasNext() {
-		return next;
-	}
-
-	@Override
-	public void init() {
-		this.count = 0;
-		
-		// Determine move direction
-		this.direction = 1;
-		if(start>end){
-			direction=-1; // Move in negative direction
-		}
-
-		// Set first set value to the start value
-		this.value = start;
-		this.next = true;
-	}
-
-	@Override
-	public synchronized void reverse() {
-		double oldStart = start;
-		this.start = this.end;
-		this.end = oldStart;
-		
-		// Determine move direction
-		this.direction = 1;
-		if(this.start>this.end){
-			direction=-1; // Move in negative direction
-		}
-		
-	}
-
-	@Override
-	public void reset() {
-		this.start = this.originalStart;
-		this.end = this.originalEnd;
-		this.direction = this.originalDirection;
-	}
-
-	public boolean isAsynchronous() {
-		return asynchronous;
-	}
-	public void setAsynchronous(boolean asynchronous) {
-		this.asynchronous = asynchronous;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/ChannelAccessLinearActuator.java

@@ -1,234 +0,0 @@
-/**
- * 
- * 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.core.actors;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Actor;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-
-/**
- * This actuator sets an Channel Access channel from a start to an end value by doing discrete steps.
- */
-public class ChannelAccessLinearActuator<T> implements Actor {
-	
-	private static Logger logger = Logger.getLogger(ChannelAccessLinearActuator.class.getName());
-
-	private boolean asynchronous = false;
-	
-	private double start;
-	private double end;
-	private double stepSize;
-	private int direction;
-	
-	/**
-	 * Execution count of actuator. This variable is used to minimize the floating point
-	 * rounding errors for calculating the next step. 
-	 */
-	private int count;
-	
-	/**
-	 * Flag that indicates whether there is a next set value for the Actor
-	 */
-	private boolean next;
-	
-	/**
-	 * Value to set at next @see ch.psi.fda.engine.Actor#set() call
-	 */
-	private double value;
-	
-	/**
-	 * Level of accuracy the positioner need to have (e.g. if a positioner is set to 1 the readback set value
-	 * of the positioner need to have at lease 1+/-accuracy) 
-	 * Default is stepSize/2 
-	 */
-	private double accuracy;
-	
-	
-	
-	private final T doneValue;
-	private final long doneDelay;
-	
-	private final double originalStart;
-	private final double originalEnd;
-	private final int originalDirection;
-	
-	private Long timeout; // Set timeout
-	
-	private final Channel<Double> channel;
-	private final Channel<T> doneChannel;
-	
-	private boolean checkActorSet = true;
-	
-	/**
-	 * Constructor
-	 * @param channel
-	 * @param doneChannel	If null actor will not wait (for this channel) to continue
-	 * @param doneValue
-	 * @param doneDelay			Delay in seconds before checking the done channel
-	 * @param start
-	 * @param end
-	 * @param stepSize
-	 * @param timeout			Maximum move time (in milliseconds)
-	 */
-	public ChannelAccessLinearActuator(Channel<Double> channel, Channel<T> doneChannel, T doneValue, double doneDelay,  double start, double end, double stepSize, Long timeout){
-		
-		this.doneValue = doneValue;
-		this.doneDelay = (long) Math.floor((doneDelay*1000));
-		this.start = start;
-		this.end = end;
-		
-		if(stepSize <= 0){
-			throw new IllegalArgumentException("Step size ["+stepSize+"] must be > 0");
-		}
-		this.stepSize = stepSize;
-		
-		this.accuracy = stepSize/2;
-		
-		// Validate and save timeout parameter
-		if(timeout!=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be >0 or null");
-		}
-		else{
-			this.timeout = timeout;
-		}
-		
-		
-		init();
-		
-		// Save original settings
-		this.originalStart = start;
-		this.originalEnd = end;
-		this.originalDirection = direction;
-		
-		this.channel = channel;
-		this.doneChannel = doneChannel;
-	}
-	
-	@Override
-	public void set() throws InterruptedException {
-		
-		// Throw an IllegalStateException in the case that set is called although there is no next step.
-		if(!next){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		// Set actuator channel
-		logger.finest("Set actuator channel "+channel.getName()+" to value: "+value);
-		try {
-			
-			if(!asynchronous){
-				if(timeout==null){
-					channel.setValue(value);
-				}
-				else{
-					channel.setValueAsync(value).get(timeout, TimeUnit.MILLISECONDS); 
-				}
-			}
-			else{
-				channel.setValueNoWait(value);
-			}
-			
-			if(doneChannel != null){
-				Thread.sleep(doneDelay);
-				doneChannel.waitForValue(doneValue); 
-			}
-			
-			// Check whether the set value is really on the value that was set before.
-			if(checkActorSet){
-				double c = channel.getValue(true);
-				double a = Math.abs( c - value ); 
-				if ( a > accuracy ){
-					throw new RuntimeException("Actor could not be set to the value "+value+" The readback of the set value does not match the value that was set [value: "+c+" delta: "+a+" accuracy: "+accuracy+"]");
-				}
-			}
-			
-		} catch (ExecutionException | TimeoutException | ChannelException e) {
-			throw new RuntimeException("Unable to move actuator [channel: "+channel.getName()+"] to value "+value,e);
-		}
-		
-		
-		count++;
-		double nextValue = start+(count*stepSize*direction); // Done like this to keep floating point rounding errors minimal
-		
-		if((direction==1&&nextValue<=end)||(direction==-1&nextValue>=end)){
-			logger.fine("Next actor value: "+nextValue);
-			value=nextValue;
-			this.next = true;
-		}
-		else{
-			// There is no next set value
-			this.next = false;
-		}
-	}
-
-	@Override
-	public boolean hasNext() {
-		return next;
-	}
-
-	@Override
-	public void init() {
-		this.count = 0;
-		
-		// Determine move direction
-		this.direction = 1;
-		if(start>end){
-			direction=-1; // Move in negative direction
-		}
-		
-		
-		// Set first set value to the start value
-		this.value = start;
-		this.next = true;
-	}
-
-	@Override
-	public synchronized void reverse() {
-		double oldStart = start;
-		this.start = this.end;
-		this.end = oldStart;
-		
-		// Determine move direction
-		this.direction = 1;
-		if(this.start>this.end){
-			direction=-1; // Move in negative direction
-		}
-		
-	}
-
-	@Override
-	public void reset() {
-		this.start = this.originalStart;
-		this.end = this.originalEnd;
-		this.direction = this.originalDirection;
-	}
-
-	public boolean isAsynchronous() {
-		return asynchronous;
-	}
-	public void setAsynchronous(boolean asynchronous) {
-		this.asynchronous = asynchronous;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/ChannelAccessTableActuator.java

@@ -1,238 +0,0 @@
-/**
- * 
- * 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.core.actors;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Actor;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-
-/**
- * This actuator sets an Channel Access channel by using the positions from the given table.
- * @author ebner
- *
- */
-public class ChannelAccessTableActuator<T> implements Actor {
-	
-	private static Logger logger = Logger.getLogger(ChannelAccessTableActuator.class.getName());
-
-	private boolean asynchronous = false;
-	
-	/**
-	 * Position table
-	 */
-	private final double[] table;
-	
-	/**
-	 * Level of accuracy the positioner need to have (e.g. if a positioner is set to 1 the readback set value
-	 * of the positioner need to have at lease 1+/-accuracy)
-	 */
-	private double accuracy = 0.1;
-	
-	/**
-	 * Execution count of actuator. This variable is used to minimize the floating point
-	 * rounding errors for calculating the next step. 
-	 */
-	private int count;
-	
-	/**
-	 * Flag that indicates whether there is a next set value for the Actor
-	 */
-	private boolean next;
-
-	
-	private Channel<Double> channel;
-	private Channel<T> doneChannel = null;
-	
-	private final T doneValue;
-	private final long doneDelay;
-	
-	/**
-	 * Flag that indicates whether the actor moves in the positive direction 
-	 */
-	private boolean positiveDirection = true;
-	private final boolean originalPositiveDirection;
-	
-	/**
-	 * Maximum move time (in milliseconds)
-	 */
-	private Long timeout = null;
-	
-	private boolean checkActorSet = true;
-	
-	/**
-	 * Constructor - Initialize actor
-	 * @param channelName	Name of the channel to set
-	 * @param table			Position table with the explicit positions for each step
-	 * @param timeout		Maximum move time (in milliseconds)
-	 */
-	public ChannelAccessTableActuator(Channel<Double> channel, double[] table, Long timeout){
-		this(channel, null, null, 0, table, timeout);
-	}
-	
-	/**
-	 * Constructor
-	 * @param channel
-	 * @param doneChannel
-	 * @param doneValue
-	 * @param doneDelay
-	 * @param table
-	 * @param timeout		Maximum move time (in milliseconds)
-	 */
-	public ChannelAccessTableActuator(Channel<Double> channel, Channel<T> doneChannel, T doneValue, double doneDelay, double[] table, Long timeout){
-		
-		this.doneValue = doneValue;
-		this.doneDelay = (long) Math.floor((doneDelay*1000));
-		
-		if(table==null){
-			throw new IllegalArgumentException("Null table is not accepted");
-		}
-		if(table.length==0){
-			throw new IllegalArgumentException("Position table need to have at least one position");
-		}
-		
-		this.table = table;
-		
-		// Validate and save timeout parameter
-		if(timeout!=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be >0 or null");
-		}
-		else{
-			this.timeout = timeout;
-		}
-		
-		init();
-		
-		// Save the initial direction
-		this.originalPositiveDirection = positiveDirection;
-		
-		this.channel = channel;
-		this.doneChannel = doneChannel;
-	}
-	
-	@Override
-	public void set() throws InterruptedException {
-		
-		// Throw an IllegalStateException in the case that set is called although there is no next step.
-		if(!next){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		// Set actuator channel
-		logger.finest("Set actuator channel "+channel.getName()+" to value: "+table[count]);
-		try {
-			if(!asynchronous){
-				if(timeout==null){
-					channel.setValue(table[count]);
-				}
-				else{
-					channel.setValueAsync(table[count]).get(timeout, TimeUnit.MILLISECONDS);
-				}
-			}
-			else{
-				channel.setValueNoWait(table[count]);
-			}
-			
-			
-			if(doneChannel != null){
-				Thread.sleep(doneDelay);
-				doneChannel.waitForValue(doneValue); 
-			}
-			
-			// Check whether the set value is really on the value that was set before.
-			if(doneChannel==null && !asynchronous && checkActorSet){
-				if ( Math.abs( channel.getValue() - table[count] ) > accuracy ){
-					throw new RuntimeException("Actor could not be set to the value "+table[count]+" The readback of the set value does not match the value that was set");
-				}
-			}
-			
-		} catch (ExecutionException | ChannelException | TimeoutException e) {
-			throw new RuntimeException("Move actuator [channel: "+channel.getName()+"] to value "+table[count],e);
-		}
-		
-		if(positiveDirection){
-			count++;
-			if(count<table.length){
-				this.next = true;
-			}
-			else{
-				// There is no next set value
-				this.next = false;
-			}
-		}
-		else{
-			count--;
-			if(count>=0){
-				this.next = true;
-			}
-			else{
-				// There is no next set value
-				this.next = false;
-			}
-		}
-	}
-
-	@Override
-	public boolean hasNext() {
-		return next;
-	}
-
-	@Override
-	public void init() {
-		
-		// Set first set value to the start value
-		if(positiveDirection){
-			this.count = 0; // Set count to the first element
-		}
-		else{
-			this.count = table.length-1; // Set count to the last element
-		}
-		
-		if(table.length>0){
-			this.next = true;
-		}
-	}
-
-	@Override
-	public void reverse() {
-		if(positiveDirection){
-			positiveDirection=false;
-		}
-		else{
-			positiveDirection=true;
-		}
-	}
-
-	@Override
-	public void reset() {
-		this.positiveDirection = this.originalPositiveDirection;
-	}
-
-	public boolean isAsynchronous() {
-		return asynchronous;
-	}
-	public void setAsynchronous(boolean asynchronous) {
-		this.asynchronous = asynchronous;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/ComplexActuator.java

@@ -1,201 +0,0 @@
-/**
- * 
- * 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.core.actors;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.Actor;
-
-/**
- * Complex actuator that consists of a list of other actuators. The steps of this actor are composed out of the
- * steps of the actors that this actuator consists of.
- * First all the steps of the first actor are used, after that the steps of the next actor are done.
- * Before the first step of an actor pre actions are available and after the last step of an actor a post action is available.
- */
-public class ComplexActuator implements Actor {
-
-	private static Logger logger = Logger.getLogger(ComplexActuator.class.getName());
-	
-	/**
-	 * List of actors this actor is made of
-	 */
-	private final List<Actor> actors;
-	
-	/**
-	 * Actions that are executed directly before the first step of this actor
-	 */
-	private final List<Action> preActions;
-	
-	/**
-	 * Actions that are executed directly after the last step of this actor
-	 */
-	private final List<Action> postActions;
-	
-	/**
-	 * Flag that indicates whether there is a next set value for the Actor
-	 */
-	private boolean next;
-	
-	/**
-	 * Index of the actor currently used
-	 */
-	private int actualActorCount;
-	
-	/**
-	 * Actor currently used to perform steps
-	 */
-	private Actor actualActor;
-	
-	/**
-	 * Flag to indicate the first set() execution of this actor.
-	 * This flag is used to decide whether to execute the pre actions.
-	 */
-	private boolean firstrun;
-	
-	public ComplexActuator(){
-		this.actors = new ArrayList<Actor>();
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		
-		this.next = false;
-		this.actualActorCount = 0;
-		
-		this.firstrun = true;
-	}
-	
-	@Override
-	public void set() throws InterruptedException {
-		if(!next){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		// PRE actions
-		if(firstrun){
-			this.firstrun = false;
-			
-			// Execute pre actions
-			logger.finest("Execute pre actions");
-			for(Action action: preActions){
-				action.execute();
-			}
-		}
-		
-		actualActor.set(); // If the actor has no next step then something is wrong in the init/next step logic
-		
-		// If the last point of the actual actuator is set take the next actuator in the list if there is one available
-		while(!actualActor.hasNext()&&actualActorCount<actors.size()){
-			actualActorCount++;
-			if(actualActorCount<actors.size()){
-				actualActor = actors.get(actualActorCount);
-			}
-			else{
-				break;
-			}
-		}
-		
-		if(actualActor.hasNext()){
-			this.next = true;
-		}
-		else{
-			this.next = false;
-			
-			// Execute post actions
-			logger.finest("Execute post actions");
-			for(Action action: postActions){
-				action.execute();
-			}
-		}
-		
-	}
-
-	@Override
-	public boolean hasNext() {
-		return next;
-	}
-
-	@Override
-	public void init() {
-		// Initialize all actors this actor consist of
-		for(Actor a: actors){
-			a.init();
-		}
-		
-		// Set the actual actor to the first actor in the list
-		actualActorCount=0;
-		if(actualActorCount<actors.size()){
-			actualActor = actors.get(actualActorCount);
-			
-			// Check whether the actor has a next step, if not increase to the next one
-			// This is needed because the first actor might not have any step ... (very unlikely but bad things happens some time)
-			while(!actualActor.hasNext()&&actualActorCount<actors.size()){
-				actualActorCount++;
-				if(actualActorCount<actors.size()){
-					actualActor = actors.get(actualActorCount);
-				}
-				else{
-					break;
-				}
-			}
-			
-			if(actualActor.hasNext()){
-				this.next = true;
-			}
-			else{
-				this.next = false;
-			}
-			
-		}
-		else{
-			actualActor=null;
-			this.next=false;
-		}
-		
-		this.firstrun = true;
-	}
-
-	@Override
-	public void reverse() {
-		// Reverse all actors this actor consist of
-		for(Actor a: actors){
-			a.reverse();
-		}
-	}
-	
-	@Override
-	public void reset() {
-		// Reset all actors this actor consist of
-		for(Actor a: actors){
-			a.reset();
-		}
-	}
-	
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-	public List<Actor> getActors() {
-		return actors;
-	}
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/Function.java

@@ -1,24 +0,0 @@
-/**
- * 
- * 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.core.actors;
-
-public interface Function {
-	public double calculate(double parameter);
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/JythonFunction.java

@@ -1,106 +0,0 @@
-/**
- * 
- * 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.core.actors;
-
-import java.util.Map;
-import java.util.logging.Logger;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.script.ScriptEngine;
-import javax.script.ScriptEngineManager;
-import javax.script.ScriptException;
-
-import ch.psi.fda.core.scripting.JythonGlobalVariable;
-
-public class JythonFunction implements Function {
-	
-	private static final Logger logger = Logger.getLogger(JythonFunction.class.getName());
-
-	public static final String ENTRY_FUNCTION_NAME = "calculate";
-	private static final String ENTRY_FUNCTION_PATTERN = "def "+ENTRY_FUNCTION_NAME+"\\((.*)\\):";
-	
-	private ScriptEngine engine;
-	private String additionalParameter = "";
-	
-	
-	public JythonFunction(String script, Map<String, JythonGlobalVariable> map){
-		
-		// Workaround for Jython memory leak 
-		// http://blog.hillbrecht.de/2009/07/11/jython-memory-leakout-of-memory-problem/
-		System.setProperty("python.options.internalTablesImpl","weak");
-		
-		this.engine = new ScriptEngineManager().getEngineByName("python");
-		
-		// Determine script entry function and the function parameters
-		String[] parameter;
-		Pattern pattern = Pattern.compile(ENTRY_FUNCTION_PATTERN);
-		Matcher matcher = pattern.matcher(script);
-		if(matcher.find() && matcher.groupCount()==1){
-			if(!matcher.group(1).trim().equals("")){
-				logger.finest("Entry function '"+ENTRY_FUNCTION_PATTERN+"' found - Identified parameters: "+matcher.group(1));
-				parameter = matcher.group(1).split(" *, *");
-			}
-			else{
-				parameter = new String[0];
-			}
-		}
-		else{
-			throw new IllegalArgumentException("Cannot determine entry function: "+ENTRY_FUNCTION_PATTERN);
-		}
-		
-		// Check whether all parameters are mapped
-		StringBuilder b = new StringBuilder();
-		for(int i=1;i<parameter.length; i++){ // Starting at 1 because first argument is implicit.
-			if(!map.containsKey(parameter[i])){
-				throw new IllegalArgumentException("Function parameter "+parameter[i]+" is not mapped");
-			}
-			b.append(",");
-			b.append(parameter[i]);
-		}
-		additionalParameter = b.toString();
-		
-		// Set variables in Jython engine
-		for(String k: map.keySet()){
-			engine.put(k, map.get(k));
-		}
-		
-		// Load manipulation script
-		try {
-			engine.eval(script);
-		} catch (ScriptException e) {
-			throw new RuntimeException("Unable to load manipulation script", e);
-		}
-	}
-	
-	@Override
-	public double calculate(double parameter) {
-		logger.fine("Function called");
-		
-		try {
-			logger.info("calculate( "+parameter+""+additionalParameter+" )");
-			return ((Double) engine.eval("calculate( "+parameter+""+additionalParameter+" )"));
-		} catch (ScriptException e) {
-			throw new RuntimeException("Calculating actuator step failed while executing the Jython script",e);
-		}
-		
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/PseudoActuatorSensor.java

@@ -1,93 +0,0 @@
-/**
- * 
- * 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.core.actors;
-
-import ch.psi.fda.core.Actor;
-import ch.psi.fda.core.Sensor;
-
-/**
- * Pseudo actor that is literally doing nothing for n times
- */
-public class PseudoActuatorSensor implements Actor, Sensor {
-
-	/**
-	 * Execution count of actuator.
-	 */
-	private int count;
-	
-	/**
-	 * Number of counts for this actuator
-	 */
-	private final int counts;
-	
-	private final String id;
-	
-	/**
-	 * @param counts
-	 * @param id		Id of the Actor/Sensor
-	 */
-	public PseudoActuatorSensor(String id, int counts){
-		if(counts < 1){
-			throw new IllegalArgumentException("Count ["+counts+"] must be > 0");
-		}
-		this.id = id;
-		this.counts = counts;
-		
-		init();
-	}
-	
-	
-	@Override
-	public void set() {
-		if(!hasNext()){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		count++;
-	}
-
-	@Override
-	public boolean hasNext() {
-		return (count<counts);
-	}
-
-	@Override
-	public void init() {
-		count=0;
-	}
-
-	@Override
-	public void reverse() {
-	}
-
-	@Override
-	public void reset() {
-	}
-
-	@Override
-	public Object read() {
-		return new Double(count); // Return actual count
-	}
-
-	@Override
-	public String getId() {
-		return this.id;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/guard/ChannelAccessGuard.java

@@ -1,89 +0,0 @@
-/**
- * 
- * 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.core.guard;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.util.List;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Guard;
-import ch.psi.jcae.ChannelException;
-
-/**
- * Guard checking channels to meet a certain condition
- */
-public class ChannelAccessGuard implements Guard {
-	
-	private static Logger logger = Logger.getLogger(ChannelAccessGuard.class.getName());
-	
-	/**
-	 * Flag to indicate whether a guard condition failed since the last init call
-	 * true: all conditions met, false: at least one condition failed
-	 */
-	private volatile boolean check = true;
-	
-	private final List<ChannelAccessGuardCondition<?>> conditions;
-	
-	public ChannelAccessGuard(List<ChannelAccessGuardCondition<?>> conditions){
-
-		this.conditions = conditions;
-		
-		for(final ChannelAccessGuardCondition<?> condition: conditions){
-			condition.getChannel().addPropertyChangeListener(new PropertyChangeListener() {		
-				@Override
-				public void propertyChange(PropertyChangeEvent evt) {
-					if(! evt.getNewValue().equals(condition.getValue())){
-						check=false;
-					}
-				}
-			});
-		}
-	}
-	
-	@Override
-	public void init() {
-		check = true;
-		
-		// Check one time if all conditions are met
-		for(ChannelAccessGuardCondition<?> condition: conditions){
-			try{
-				if(! (condition.getChannel().getValue(true)).equals(condition.getValue()) ){
-					check=false;
-					break;
-				}
-			}
-			catch (InterruptedException e) {
-				throw new RuntimeException("Guard interrupted ",e);
-			} catch (TimeoutException | ChannelException | ExecutionException e) {
-				logger.log(Level.WARNING, "Unable ", e);
-				check=false;
-			}
-		}
-	}
-
-	@Override
-	public boolean check() {
-		return check;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/guard/ChannelAccessGuardCondition.java

@@ -1,41 +0,0 @@
-/**
- * 
- * 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.core.guard;
-
-import ch.psi.jcae.Channel;
-
-public class ChannelAccessGuardCondition<T> {
-	
-	private final Channel<T> channel;
-	private final T value; // Value of the channel to meet condition
-
-	public ChannelAccessGuardCondition(Channel<T> channel, T value){
-		this.channel = channel;
-		this.value = value;
-	}
-	
-	public Channel<T> getChannel() {
-		return channel;
-	}
-
-	public T getValue() {
-		return value;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/ActorSensorLoop.java

@@ -1,436 +0,0 @@
-/**
- * 
- * 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.core.loops;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.logging.Logger;
-
-import com.google.common.eventbus.EventBus;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.Actor;
-import ch.psi.fda.core.ActorSetCallable;
-import ch.psi.fda.core.Guard;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.messages.DataMessage;
-import ch.psi.fda.messages.EndOfStreamMessage;
-import ch.psi.fda.messages.Metadata;
-
-/**
- * Loop of actions to accomplish a task or test.
- */
-public class ActorSensorLoop implements ActionLoop {
-	
-	private static Logger logger = Logger.getLogger(ActorSensorLoop.class.getName());
-	
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	/**
-	 * List of additional action loops that are executed at the end of each
-	 * iteration of the loop
-	 */
-	private List<ActionLoop> actionLoops;
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	/**
-	 * List of actions that are executed before the actors are set
-	 */
-	private List<Action> preActorActions;
-	
-	/**
-	 * List of actions that are executed after all actors have been set
-	 */
-	private List<Action> postActorActions;
-	
-	/**
-	 * List of actions that are executed before the sensors are read out
-	 */
-	private List<Action> preSensorActions;
-	/**
-	 * List of actions that are executed after all sensors have been read out
-	 */
-	private List<Action> postSensorActions;
-	
-	/**
-	 * List of actors of this loop
-	 */
-	private List<Actor> actors;
-	
-	/**
-	 * List of sensors of this loop
-	 */
-	private List<Sensor> sensors;
-	
-	/**
-	 * Guard used to check whether the environment was ok while reading out the sensors
-	 */
-	private Guard guard = null;
-	
-	private volatile boolean loop = false;
-	private volatile boolean abort = false;
-	
-	private final boolean zigZag;
-	
-	private List<ActorSetCallable> pactors;
-	
-	private EventBus eventBus = new EventBus();
-	
-	
-	public ActorSensorLoop(){
-		this(false);
-	}
-	
-	public ActorSensorLoop(boolean zigZag){
-		this.zigZag = zigZag;
-		this.actionLoops = new ArrayList<ActionLoop>();
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		this.preActorActions = new ArrayList<Action>();
-		this.postActorActions = new ArrayList<Action>();
-		this.preSensorActions = new ArrayList<Action>();
-		this.postSensorActions = new ArrayList<Action>();
-		
-		this.actors = new ArrayList<Actor>();
-		this.pactors = new ArrayList<ActorSetCallable>();
-		this.sensors = new ArrayList<Sensor>();
-	}
-	
-	
-	/**
-	 * Executes the actor sensor loop. The actor sensor loop is build up as follows:
-	 * preActions
-	 * loop{
-	 *  check actors - abort if there are no new steps
-	 *  pre actor actions
-	 *  set actors
-	 *  post actor actions
-	 *  pre sensor actions
-	 *  read sensors
-	 *  post sensor actions
-	 *  execute additional registered action loops
-	 * }
-	 * postActions
-	 * @throws InterruptedException 
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort = false;
-		
-		List<Metadata> metadata = new ArrayList<>();
-		
-		// Build up data message metadata based on the sensors currently registered.
-		for(Sensor s: sensors){
-			metadata.add(new Metadata(s.getId()));
-		}
-		
-		
-		/**
-		 * Thread pool for parallel execution of tasks
-		 */
-		ExecutorService executorService = Executors.newCachedThreadPool();
-		
-		loop = true;
-		
-		// Execute pre actions
-		for(Action action: preActions){
-			action.execute();
-		}
-		
-		// Initialize actors of Loop
-		for(Actor actor: actors){
-			actor.init();
-		}
-		
-		// Variable to store the last guard status
-		boolean guardOK=true;
-		
-		try{
-			
-			// Execute loop logic
-			while(loop){
-				
-				if(guardOK){
-					
-					
-					// If actors are defined for the loop check whether all of them
-					// have a next step defined if there is no actor defined only run this loop once
-					if(actors.size()>0){
-						// Check whether the actors of this loop have a next step. If not 
-						// abort the loop
-						boolean hasNext = true;
-						for(Actor actor: actors){
-							if(!actor.hasNext()){
-								hasNext=false;
-								break; // Stop actor check loop
-							}
-						}
-						
-						// If not all actors have a next step abort the loop
-						if(!hasNext){
-							break; // Stop action loop
-						}
-					}
-					else{
-						// No actors defined, only run loop once
-						loop = false;
-					}
-		
-					
-					
-					// Execute pre actor actions
-					for(Action action: preActorActions){
-						action.execute();
-					}
-					
-					if(abort){ // End loop if abort was issued
-						break;
-					}
-					
-					// Set actors
-	//				for(Actor actor: actors){
-	//					actor.set();
-	//				}
-					// Parallel set of the actors
-					try {
-						for (Future<Object> f : executorService.invokeAll(pactors)) {
-						    f.get(); //Blocks until the async set() is finished
-						}
-					} catch (ExecutionException e) {
-						throw new RuntimeException("Setting the actors failed",e);
-					}
-					
-					// Execute post actor actions
-					for(Action action: postActorActions){
-						action.execute();
-					}
-					
-					if(abort){ // End loop if abort was issued
-						break;
-					}
-				
-				}
-				
-				if(guard!=null){
-					// Initialize guard
-					guard.init();
-					guardOK=guard.check();
-					
-					// Wait until guard is ok
-					while(!guardOK){
-						logger.info("Waiting for guard condition(s) to be met");
-						// Sleep 100 milliseconds before next check
-						Thread.sleep(1000);
-						
-						// Check whether the loop is not aborted, if it is aborted
-						// break the wait loop (afterwards also the loop loop is aborted)
-						if(!loop){
-							break;
-						}
-						
-						guard.init();
-						guardOK=guard.check();
-					}
-					
-					// If loop is aborted proceed to next iteration an abort loop
-					if(!loop){
-						continue;
-					}
-				}
-				
-				// Execute pre sensor actions
-				for(Action action: preSensorActions){
-					action.execute();
-				}
-				
-				if(abort){ // End loop if abort was issued
-					break;
-				}
-				
-				// Read sensors
-				DataMessage message = new DataMessage(metadata);
-				for(Sensor sensor: sensors){
-					// Readout sensor
-					Object o = sensor.read();
-					// Add sensor data item to message
-					message.getData().add(o);
-				}
-				
-				// Execute post sensor actions
-				for(Action action: postSensorActions){
-					action.execute();
-				}
-				
-				if(abort){ // End loop if abort was issued
-					break;
-				}
-				
-				// Check guard if one is registered
-				if(guard!=null){
-					guardOK=guard.check();
-				}
-				
-				if(guardOK){
-				
-					// Post a message with the sensor data
-					eventBus.post(message);
-					
-					// Loop all configured ActionLoop objects
-					for(ActionLoop actionLoop: actionLoops){
-						actionLoop.execute();
-					}
-				}
-			}
-			
-			// Execute post actions
-			for(Action action: postActions){
-				action.execute();
-			}
-		
-		}
-		finally{
-			// Ensure that data stream is terminated ...
-			
-			// Issue end of loop control message
-			// Set iflag of the EndOfStreamMessage according to dataGroup flag of this loop
-			eventBus.post(new EndOfStreamMessage(dataGroup));
-		}
-		
-		if(zigZag){
-			// Reverse actors for the next run
-			for(Actor actor: actors){
-				actor.reverse();
-			}
-		}
-		
-		executorService.shutdownNow();
-		
-	}
-
-	@Override
-	public void abort(){
-		abort = true;
-		loop = false;
-		
-		// To abort all wait actions interrupt this thread
-		for(Action a: preSensorActions){
-			a.abort();
-		}
-		
-		// Recursively abort all registered action loops
-		for(ActionLoop actionLoop: actionLoops){
-			actionLoop.abort();
-		}
-	}
-
-	@Override
-	public void prepare() {
-		// Create callable for all actors
-		pactors.clear();
-		for(final Actor a: actors){
-			pactors.add(new ActorSetCallable(a));
-		}
-		
-		// Reset all actuators
-		for(Actor a: actors){
-			a.reset();
-		}
-		
-		// Recursively call prepare() method of all registered action loops
-		for(ActionLoop actionLoop: actionLoops){
-			actionLoop.prepare();
-		}
-	}
-
-	@Override
-	public void cleanup() {
-		// Recursively call cleanup() method of all registered action loops
-		for(ActionLoop actionLoop: actionLoops){
-			actionLoop.cleanup();
-		}
-	}
-	
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-	
-
-	@Override
-	public EventBus getEventBus(){
-		return eventBus;
-	}
-	
-	
-	public List<ActionLoop> getActionLoops() {
-		return actionLoops;
-	}
-	public List<Action> getPreActorActions() {
-		return preActorActions;
-	}
-	public List<Action> getPostActorActions() {
-		return postActorActions;
-	}
-	public List<Action> getPreSensorActions() {
-		return preSensorActions;
-	}
-	public List<Action> getPostSensorActions() {
-		return postSensorActions;
-	}
-	public List<Actor> getActors() {
-		return actors;
-	}
-	public List<Sensor> getSensors() {
-		return sensors;
-	}
-	public Guard getGuard() {
-		return guard;
-	}
-	public void setGuard(Guard guard) {
-		this.guard = guard;
-	}
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/CrlogicDeltaDataFilter.java

@@ -1,46 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-/**
- * Filter calculating the delta of two subsequent values
- */
-public class CrlogicDeltaDataFilter {
-
-	private Double lastValue = null;
-	
-	public void reset(){
-		lastValue = null;
-	}
-	
-	public Double delta(Double value){
-		
-		Double lvalue = lastValue;
-		lastValue = value;
-		
-		if(lvalue==null){
-			return Double.NaN;
-		}
-		else{
-			// Return delta
-			return(value-lvalue);
-		}
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/CrlogicLoop.java

@@ -1,809 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.Semaphore;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import com.google.common.eventbus.EventBus;
-
-import jcifs.smb.SmbFile;
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.messages.DataMessage;
-import ch.psi.fda.messages.EndOfStreamMessage;
-import ch.psi.fda.messages.Metadata;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * While using Crlogic the IOC system clock rate should/must be set to 1000 (default 60)
- * 
- * sysClkRateSet 1000
- *
- */
-public class CrlogicLoop implements ActionLoop {
-	
-	private static final Logger logger = Logger.getLogger(CrlogicLoop.class.getName());
-	
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	private boolean keepTmpFiles = false;
-	
-	private BlockingQueue<String> readQueue = new LinkedBlockingQueue<String>();
-	private volatile boolean stopReadoutThread = false;
-	private Thread readoutThread;
-	
-	/**
-	 * Default timeout (in milliseconds) for wait operations
-	 */
-	private long startStopTimeout = 8000;
-	
-	/**
-	 * Name of the NFS server to place the data of the OTF logic
-	 */
-	private final String server;
-	/**
-	 * Share on the NFS server to put the OTF data on to
-	 */
-	private final String share;
-	/**
-	 * SMB share  to access the data written by the OTF C logic
-	 */
-	private final String smbShare;
-	
-	/**
-	 * Flag whether the actor of this loop should move in zig zag mode
-	 */
-	private final boolean zigZag;
-	
-	boolean useReadback;
-	boolean useEncoder;
-	
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	/**
-	 * Prefix for the CRLOGIC channels
-	 */
-	private String prefix;
-	
-	private TemplateCrlogic template;
-	private TemplateMotor motortemplate;
-	
-	/**
-	 * Semaphore to ensure that data is read in correct sequence
-	 */
-	private Semaphore semaphore = new Semaphore(1);
-	
-	/**
-	 * List of sensors of this loop
-	 */
-	private List<CrlogicResource> sensors;
-	
-	private List<String> readoutResources;
-	private Map<Integer, CrlogicDeltaDataFilter> scalerIndices;
-	private CrlogicRangeDataFilter crlogicDataFilter;
-	
-	
-	/**
-	 * Abort status
-	 */
-	private boolean abort = false;
-	private boolean abortForce = false;
-	private Thread executionThread = null;
-	
-	private final ChannelService cservice;
-	
-	
-	private String id;
-	private String name; // name of the motor channel
-	private String readback; // name of the encoder channel
-	private double start;
-	private double end;
-	private double stepSize;
-	private double integrationTime;
-	private double additionalBacklash;
-	
-	
-	private final EventBus eventbus;
-	private List<Metadata> metadata;
-	
-	public CrlogicLoop(ChannelService cservice, String prefix, String server, String share, String smbShare, boolean zigZag){
-		eventbus = new EventBus();
-		this.cservice = cservice;
-		this.prefix = prefix;
-		this.server = server;
-		this.share = share;
-		this.smbShare = smbShare;
-		this.zigZag = zigZag;
-		
-		// Initialize lists used by the loop
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		this.sensors = new ArrayList<>();
-		this.readoutResources = new ArrayList<String>();
-		this.scalerIndices = new HashMap<Integer, CrlogicDeltaDataFilter>();
-		
-		this.crlogicDataFilter = new CrlogicRangeDataFilter();
-	}
-	
-	public void setActuator(String id, String name, String readback, double start, double end, double stepSize, double integrationTime, double additionalBacklash){
-		this.id = id;
-		this.name = name;
-		this.readback = readback;
-		this.start = start;
-		this.end = end;
-		this.stepSize = stepSize;
-		this.integrationTime = integrationTime;
-		this.additionalBacklash = additionalBacklash;
-	}
-	
-	
-	/**
-	 * Collect data from share
-	 * @param tmpFileName	Name of the temporary file
-	 * @throws InterruptedException 
-	 * @throws IOException 
-	 */
-	private void collectData(String tmpDir, String tmpFileName) throws InterruptedException, IOException {
-		semaphore.acquire();
-		if (tmpDir.startsWith("smb:")) {
-
-			SmbFile tmpFile = new SmbFile(tmpDir, tmpFileName);
-			logger.info("Collect data from " + tmpFile.getCanonicalPath());
-
-			SmbFile lockfile = new SmbFile(tmpFile.getCanonicalPath() + ".lock");
-
-			logger.info("Wait until file is written [lock file: " + lockfile.getCanonicalPath() + "]");
-			// Wait until file is created
-			while ((!tmpFile.exists()) || lockfile.exists()) {
-				try{
-					Thread.sleep(100);
-				}
-				catch(InterruptedException e){
-					abort=true;
-				}
-				 if(abort){
-					 // If abort is issued while waiting for data immediately return without
-					 // trying to read the data
-					 return;
-				 }
-			}
-
-			InputStreamReader inreader = new InputStreamReader(tmpFile.getInputStream());
-			BufferedReader in = new BufferedReader(inreader);
-			String line;
-			boolean firstline = true;
-			int linecount=0;
-			int mcounter=0;
-			
-//			boolean wasInRangeBefore = false;
-			boolean discardAnyway = false;
-			
-			while (true) {
-				line = in.readLine();
-				linecount++;
-				if (line == null) {
-					break;
-				} else {
-					// if(line.matches("^\\[.*")){
-					if (line.matches("^ *#.*")) {
-						// Skip header/comment lines
-//						logger.info("HEADER: " + line);
-					} else {
-						if (firstline) {
-							firstline = false;
-							continue;
-						}
-
-//						logger.info(line);
-
-						// Write into queue
-						DataMessage message = new DataMessage(metadata);
-						String[] tokens = line.split("\t");
-						boolean use = true;
-						
-						for(int i=0;i<tokens.length;i++){
-							String t = tokens[i];
-							Double val;
-							
-							if(i==0){
-								Double raw = new Double(t);
-								
-								if(useEncoder){
-									val = crlogicDataFilter.calculatePositionMotorUseEncoder(raw);
-								}
-								else if(useReadback){
-									val = crlogicDataFilter.calculatePositionMotorUseReadback(raw);
-								}
-								else{
-									val = crlogicDataFilter.calculatePositionMotor(raw);
-								}
-								
-								// Check whether data is within the configured range - otherwise drop data
-								use = crlogicDataFilter.filter(val);
-//								if(!use){
-//									break;
-//								}
-							}
-							else if(scalerIndices.containsKey(i)){
-								CrlogicDeltaDataFilter f = scalerIndices.get(i); 
-								val = f.delta(new Double(t));
-							}
-							else{
-								val = new Double(t);
-							}
-							
-							
-							message.getData().add(val);
-						}
-						
-						// Does not work if zigzag, ... 
-//						// Use this to filter out motor retry movements at the end of the scan
-//						wasInRangeBefore = wasInRangeBefore | use;
-//						if(!use && wasInRangeBefore){
-//							discardAnyway=true;
-//							// Optimization - terminate read loop once range is left
-//							logger.info("Terminate read loop because point is outside range");
-//							break;
-//						}
-						
-						// Filter data
-						if(use && !discardAnyway){
-							eventbus.post(message);
-							mcounter++;
-						}
-						
-						
-					}
-				}
-			}
-			in.close();
-			inreader.close();
-			
-			logger.info("Lines read: "+linecount+" Messages generated (after filtering): "+mcounter);
-			
-			// Remove temporary file
-			if(!keepTmpFiles){
-				tmpFile.delete();
-			}
-		}
-		else{
-			// TODO - File in local file system
-		}
-		
-		// Issue end of loop control message
-		eventbus.post(new EndOfStreamMessage(dataGroup));
-		semaphore.release();
-	}
-	
-	
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		try{
-		
-			// Set values for the datafilter
-			crlogicDataFilter.setStart(start);
-			crlogicDataFilter.setEnd(end);
-			
-			// Reset data filter
-			for(Integer k: scalerIndices.keySet()){
-				scalerIndices.get(k).reset();
-			}
-			
-			synchronized(this){
-				// Set abort state to false
-				abort = false;
-				abortForce = false;
-			
-			// Set execution thread to current thread
-				executionThread = Thread.currentThread();
-			}
-			
-			
-			// TODO each actuator will result in an additional sensor (at the beginning)
-			// Dependent on actuator settings (readback use encoder, ...)
-			
-			
-			// TODO filename generation?
-			final String tmpFileName = "tmp-"+System.currentTimeMillis()+".txt";
-			
-			Long timeout = 600000l; // 10 minutes move timeout
-			
-			// Check if logic is inactive, otherwise return early
-			if(!template.getStatus().getValue().equals(TemplateCrlogic.Status.INACTIVE.toString())){
-				logger.info("CRLOGIC is not inactive!");
-				// TODO Decide what to do in this situation
-				
-				if(template.getStatus().getValue().equals(TemplateCrlogic.Status.FAULT.toString())){
-					// If in fault show message and recover
-					logger.info("CRLOGIC in FAULT state");
-					logger.info("Error message: "+template.getMessage().getValue());
-					logger.info("Recover logic and set it to INACTIVE");
-					template.getStatus().setValue(TemplateCrlogic.Status.INACTIVE.toString());
-				}
-				else if(template.getStatus().getValue().equals(TemplateCrlogic.Status.ACTIVE.toString())){
-					template.getStatus().setValue(TemplateCrlogic.Status.STOP.toString());
-					template.getStatus().waitForValue(TemplateCrlogic.Status.INACTIVE.toString(), startStopTimeout);
-				}
-				else{
-					throw new RuntimeException("CRLOGIC is not inactive");
-				}
-			}
-			
-			
-			logger.info("Set parameters");
-			template.getNfsServer().setValue(server);
-			template.getNfsShare().setValue(share);
-			template.getDataFile().setValue(tmpFileName);
-			
-			int tps = template.getTicksPerSecond().getValue();
-			logger.info("Ticks per second: "+tps);
-			
-			logger.info("Set readout resources");
-			
-			template.getReadoutResources().setValue(readoutResources.toArray(new String[readoutResources.size()]));
-			
-			
-			
-			// Set ticks between interrupt to integration time
-			int ticks = (int)(tps*integrationTime);
-			template.getTicksBetweenInterrupts().setValue(ticks);
-			
-			// Prepare motor
-			double totalTimeSeconds = Math.abs((end-start)/stepSize*integrationTime);
-			int hours = (int) Math.floor(totalTimeSeconds/60/60);
-			int minutes = (int) Math.floor(totalTimeSeconds/60-hours*60);
-			int seconds = (int) Math.floor(totalTimeSeconds-hours*60*60-minutes*60);
-			
-			logger.info("Estimated time: "+hours+":"+minutes+":"+seconds);
-			
-			int direction = 1;
-			if(end-start<0){
-				direction = -1;
-			}
-			
-			double motorBaseSpeed = motortemplate.getBaseSpeed().getValue();
-			double motorHighLimit = motortemplate.getHighLimit().getValue();
-			double motorLowLimit = motortemplate.getLowLimit().getValue();
-			double motorBacklash = motortemplate.getBacklashDistance().getValue();
-			
-			boolean respectMotorMinSpeed = false; // if false set min speed to 0
-			double motorMinSpeed = 0;
-			if(respectMotorMinSpeed){
-				motorMinSpeed = motorBaseSpeed;
-			}
-			
-			// Check user parameters
-			// TODO start and end values must be between the motor high and low value - otherwise fail
-			if(start>motorHighLimit || start<motorLowLimit){
-				// Start value is outside motor high and/or low value
-				logger.info("Start value is outside motor high and/or low value");
-				throw new IllegalArgumentException("Start value is outside motor high and/or low value");
-			}
-			if(end>motorHighLimit || end<motorLowLimit){
-				// End value is outside motor high and/or low value
-				logger.info("End value is outside motor high and/or low value");
-				throw new IllegalArgumentException("End value is outside motor high and/or low value");
-			}
-			// TODO Check minimum step size
-			int minimumTicks = 10;
-			double minStepSize = motorMinSpeed*(minimumTicks/tps);
-			if(stepSize<minStepSize){
-				// Step size is too small
-				logger.info("Step size is too small");
-				throw new IllegalArgumentException("Step size is too small");
-			}
-			// TODO Check integration time
-			if(motorMinSpeed>0){
-				double maxIntegrationTime = stepSize/motorMinSpeed;
-				if(integrationTime>maxIntegrationTime){
-					logger.info("Integration time is too big");
-					// Integration time is too big
-					throw new IllegalArgumentException("Integration time is too big");
-				}
-			}
-			double motorMaxSpeed = motortemplate.getVelocity().getValue();
-			double minIntegrationTime = Math.min( (stepSize/motorMaxSpeed), ((double)minimumTicks/(double)tps) );
-			if(integrationTime<minIntegrationTime){
-				// Integration time is too small
-				logger.info("Integration time is too small [min integration time: "+minIntegrationTime+"]");
-				throw new IllegalArgumentException("Integration time is too small [min integration time: "+minIntegrationTime+"]");
-			}
-			
-			
-			// TODO Calculate and set motor speed, backlash, etc.
-			double motorSpeed = stepSize/integrationTime;
-			double backlash = (0.5*motorSpeed*motortemplate.getAccelerationTime().getValue())+motorBacklash+additionalBacklash;
-			double realEnd = end+(backlash*direction);
-			double realStart = start-(backlash*direction);
-	
-			
-			// Move to start
-			logger.info("Move motor to start ["+realStart+"]");
-			motortemplate.getSetValue().setValueAsync(realStart).get(timeout, TimeUnit.MILLISECONDS); // Will block until move is done
-			
-			
-			// Set motor paramters
-			// Backup settings
-			logger.info("Backup motor settings");
-			double backupSpeed = motortemplate.getVelocity().getValue();
-			double backupBacklash = motorBacklash;
-			double backupMinSpeed = motorBaseSpeed;
-			
-			try{
-				// Set motor settings
-				logger.info("Update motor settings");
-//				if(!respectMotorMinSpeed){
-//					motortemplate.getBaseSpeed().setValue(0d);
-//				}
-				// Set base speed as fast as possible but not faster than the original base speed.
-				double base = motorBaseSpeed;
-				if(motorSpeed<base){
-					base = motorSpeed;
-				}
-				motortemplate.getBaseSpeed().setValue(base);
-				motortemplate.getVelocity().setValue(motorSpeed);
-				motortemplate.getBacklashDistance().setValue(0d);
-				
-				
-				// Execute pre actions
-				for(Action action: preActions){
-					action.execute();
-				}
-				
-				
-				// Start crlogic logic
-				logger.info("Start CRLOGIC");
-				template.getStatus().setValue(TemplateCrlogic.Status.INITIALIZE.toString());
-				try{
-					template.getStatus().waitForValue(TemplateCrlogic.Status.ACTIVE.toString(), startStopTimeout);
-				}
-				catch(ChannelException | ExecutionException | TimeoutException e){
-					logger.info( "Failed to start CRLOGIC. Logic in status: "+template.getStatus().getValue() );
-					if(template.getStatus().getValue().equals(TemplateCrlogic.Status.FAULT.toString())){
-						logger.info("Error message: "+template.getMessage().getValue());
-					}
-					// Recover to inactive
-					template.getStatus().setValue(TemplateCrlogic.Status.INACTIVE.toString());
-					// TODO Improve error handling
-					throw new RuntimeException("Failed to start CRLOGIC. Logic in status: "+template.getStatus().getValue()+ " Error message: "+template.getMessage().getValue(), e);
-					
-				}
-
-				// Move motor(s) to end / wait until motor is stopped
-				logger.info("Move motor to end ["+realEnd+"]");
-				try{
-					motortemplate.getSetValue().setValueAsync(realEnd).get(timeout, TimeUnit.MILLISECONDS); // Will block until move is done
-				}
-				catch (InterruptedException e) {
-					if(abort & (!abortForce)){
-						// Abort motor move 
-						motortemplate.getCommand().setValue(TemplateMotor.Commands.Stop.ordinal());
-						motortemplate.getCommand().setValue(TemplateMotor.Commands.Go.ordinal());
-					}
-					else{
-						throw e;
-					}
-				}
-				logger.info("Motor reached end position");
-				
-				// Stop crlogic logic
-				logger.info("Stop CRLOGIC");
-				template.getStatus().setValue(TemplateCrlogic.Status.STOP.toString());
-				// Wait until stopped
-				logger.info("Wait until stopped");
-				try{
-					template.getStatus().waitForValue(TemplateCrlogic.Status.INACTIVE.toString(), startStopTimeout);
-				}
-				catch(ChannelException | ExecutionException | TimeoutException e){
-					logger.info( "Failed to stop CRLOGIC. Logic in status: "+template.getStatus().getValue() );
-					// TODO Improve error handling
-					throw new RuntimeException("Failed to stop CRLOGIC.  Logic in status: "+template.getStatus().getValue(), e);
-				}
-				logger.info("CRLOGIC is now stopped");
-				
-				
-				// Execute post actions
-				for(Action action: postActions){
-					action.execute();
-				}
-				
-				
-			}
-			finally{
-				logger.info("Restore motor settings");
-				motortemplate.getBaseSpeed().setValue(backupMinSpeed);
-				motortemplate.getVelocity().setValue(backupSpeed);
-				motortemplate.getBacklashDistance().setValue(backupBacklash);
-			}
-			
-			// Request read of data file
-			readQueue.put(tmpFileName);
-			
-			if(zigZag){
-				// reverse start/end
-				double aend = end;
-				end=start;
-				start=aend;
-			}
-			
-			synchronized(this){
-				executionThread = null;
-			}
-		}
-		catch(ChannelException | ExecutionException | TimeoutException e){
-			throw new RuntimeException("Unable to execute crloop", e);
-		}
-	}
-
-	@Override
-	public void abort() {
-		abort(false);
-	}
-	
-	public synchronized void abort(boolean force){
-		abort = true;
-		abortForce = force;
-		
-		// executionThread variable guarded by "this"
-		if(executionThread != null){
-			executionThread.interrupt();
-		}
-	}
-
-	@Override
-	public void prepare() {
-		
-		metadata = new ArrayList<>();
-		
-		// Build up metadata
-		metadata.add(new Metadata(this.id));
-		for(CrlogicResource s: sensors){
-			metadata.add(new Metadata(s.getId()));
-		}
-		
-		
-		stopReadoutThread = false;
-		// Start readout Thread
-		readoutThread = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				while(!stopReadoutThread){
-					String file;
-					try {
-						file = readQueue.take();
-					} catch (InterruptedException e) {
-						break;
-					}
-					// TODO Read file and 
-					try {
-						collectData(smbShare, file);
-					} catch (InterruptedException e) {
-						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-					} catch (IOException e) {
-						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-					}
-					
-				}
-				
-			}
-		});
-		readoutThread.start();
-		
-		try{
-			// Connect crlogic channels
-			template = new TemplateCrlogic();
-			logger.info("Connect channels");
-			Map<String,String> map = new HashMap<>();
-			map.put("PREFIX", prefix);
-			cservice.createAnnotatedChannels(template, map);
-			
-			// Connect motor channels
-			motortemplate = new TemplateMotor();
-			map = new HashMap<>();
-			map.put("PREFIX", this.name);
-			cservice.createAnnotatedChannels(motortemplate, map);
-			
-			useReadback = motortemplate.getUseReadback().getValue();
-			useEncoder = motortemplate.getUseEncoder().getValue();
-			
-			logger.info("Motor type: "+ TemplateMotor.Type.values()[motortemplate.getType().getValue()]);
-			logger.info("Motor use readback: "+useReadback);
-			logger.info("Motor use encoder: "+useEncoder);
-			
-			// TODO build up list of readout resources (based on sensors)
-			readoutResources.clear();
-			// first sensor is the actuator
-			
-			// Determine mode of motor
-			if((!useReadback) && (!useEncoder)){
-				// Open loop
-				if(this.readback!=null){
-					throw new IllegalArgumentException("Readback not supported if motor is configured in open loop");
-				}
-				else{
-					readoutResources.add(this.name);
-				}
-				
-			}
-			else if(useReadback && (!useEncoder)){
-				String readback;
-				// use readback link
-				if(this.readback!=null){
-					// Use specified readback
-					readback = this.readback;
-				}
-				else{
-					// Set resouce to readback link
-					readback = (motortemplate.getReadbackLink().getValue());
-					readback = readback.replaceAll(" +.*", ""); // remove NPP etc at the end
-				}
-				
-				readoutResources.add(readback);
-				
-				// Fill readback encoder settings
-				// Connect to encoder
-				TemplateEncoder encodertemplate = new TemplateEncoder();
-				map = new HashMap<>();
-				map.put("PREFIX", readback);
-				cservice.createAnnotatedChannels(encodertemplate, map);
-				
-				// Read encoder settings
-				if(encodertemplate.getDirection().getValue()==TemplateEncoder.Direction.Positive.ordinal()){
-					crlogicDataFilter.setEncoderDirection(1);
-				}
-				else{
-					crlogicDataFilter.setEncoderDirection(-1);
-				}
-				crlogicDataFilter.setEncoderOffset(encodertemplate.getOffset().getValue());
-				crlogicDataFilter.setEncoderResolution(encodertemplate.getResolution().getValue());
-				
-				// Disconnect from encoder
-				cservice.destroyAnnotatedChannels(encodertemplate);
-				
-			}
-			else if (useEncoder && (!useReadback)){
-				// use readback link
-				if(this.readback!=null){
-					throw new IllegalArgumentException("Readback not supported if motor is configured to use encoder");
-				}
-				else{
-					// Set resouce to readback link
-					readoutResources.add(this.name+"_ENC");
-				}
-			}
-			else{
-				throw new IllegalArgumentException("Motor configuration not supportet: use readback - "+useReadback+" use encoder - "+useEncoder);
-			}
-			
-			// Fill Motor specific settings
-			if(motortemplate.getDirection().getValue()==TemplateMotor.Direction.Positive.ordinal()){
-				crlogicDataFilter.setMotorDirection(1);
-			}
-			else{
-				crlogicDataFilter.setMotorDirection(-1);
-			}
-			crlogicDataFilter.setMotorEncoderResolution(motortemplate.getEncoderResolution().getValue());
-			crlogicDataFilter.setMotorOffset(motortemplate.getOffset().getValue());
-			crlogicDataFilter.setMotorReadbackResolution(motortemplate.getReadbackResolution().getValue());
-			crlogicDataFilter.setMotorResolution(motortemplate.getMotorResolution().getValue());
-			
-			// Clear all indices
-			scalerIndices.clear();
-			
-			int c = 1; // We start at 1 because the actuator right now is an implicit sensor 
-			for(CrlogicResource s: sensors){
-					readoutResources.add(s.getKey());
-					if(s.isDelta()){
-						scalerIndices.put(c, new CrlogicDeltaDataFilter());
-					}
-					c++;
-			}
-			
-			// Workaround - somehow one has to add an empty thing to the value otherwise the c logic 
-			// does not pick up the end
-			readoutResources.add("");
-		}
-		catch(Exception e){
-			throw new RuntimeException("Unable to prepare crloop: ",e);
-		}
-	}
-
-	@Override
-	public void cleanup() {
-		stopReadoutThread = true;
-		readoutThread.interrupt();
-		
-		try {
-			cservice.destroyAnnotatedChannels(template);
-			cservice.destroyAnnotatedChannels(motortemplate);
-			template = null;
-			motortemplate = null;
-			
-		} catch (Exception e) {
-			throw new RuntimeException("Unable to destroy CrlogicLoop", e);
-		}
-	}
-
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	@Override
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-	@Override
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-	
-	public List<CrlogicResource> getSensors() {
-		return sensors;
-	}
-	
-	public boolean isKeepTmpFiles() {
-		return keepTmpFiles;
-	}
-
-	public void setKeepTmpFiles(boolean keepTmpFiles) {
-		this.keepTmpFiles = keepTmpFiles;
-	}
-	
-	public EventBus getEventBus(){
-		return eventbus;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/CrlogicRangeDataFilter.java

@@ -1,274 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-/**
- * @author ebner
- *
- */
-public class CrlogicRangeDataFilter {
-
-	private double motorResolution = 1;
-	private int motorDirection = 1;
-	private double motorOffset = 0;
-	private double motorReadbackResolution = 1;
-	private double motorEncoderResolution = 1;
-	
-	private double encoderOffset = 0;
-	private double encoderResolution = 1;
-	private int encoderDirection = 1;
-	
-	private double start = 0;
-	private double end = 0;
-	private boolean positive = true;
-	
-	/**
-	 * Marker whether the value was equal
-	 */
-	private boolean wasEqualBefore = false;
-	
-	/**
-	 * @return the motorResolution
-	 */
-	public double getMotorResolution() {
-		return motorResolution;
-	}
-
-	/**
-	 * @param motorResolution the motorResolution to set
-	 */
-	public void setMotorResolution(double motorResolution) {
-		this.motorResolution = motorResolution;
-	}
-
-	/**
-	 * @return the motorDirection
-	 */
-	public int getMotorDirection() {
-		return motorDirection;
-	}
-
-	/**
-	 * @param motorDirection the motorDirection to set
-	 */
-	public void setMotorDirection(int motorDirection) {
-		this.motorDirection = motorDirection;
-	}
-
-	/**
-	 * @return the motorOffset
-	 */
-	public double getMotorOffset() {
-		return motorOffset;
-	}
-
-	/**
-	 * @param motorOffset the motorOffset to set
-	 */
-	public void setMotorOffset(double motorOffset) {
-		this.motorOffset = motorOffset;
-	}
-
-	/**
-	 * @return the motorReadbackResolution
-	 */
-	public double getMotorReadbackResolution() {
-		return motorReadbackResolution;
-	}
-
-	/**
-	 * @param motorReadbackResolution the motorReadbackResolution to set
-	 */
-	public void setMotorReadbackResolution(double motorReadbackResolution) {
-		this.motorReadbackResolution = motorReadbackResolution;
-	}
-
-	/**
-	 * @return the motorEncoderResolution
-	 */
-	public double getMotorEncoderResolution() {
-		return motorEncoderResolution;
-	}
-
-	/**
-	 * @param motorEncoderResolution the motorEncoderResolution to set
-	 */
-	public void setMotorEncoderResolution(double motorEncoderResolution) {
-		this.motorEncoderResolution = motorEncoderResolution;
-	}
-
-	/**
-	 * @return the encoderOffset
-	 */
-	public double getEncoderOffset() {
-		return encoderOffset;
-	}
-
-	/**
-	 * @param encoderOffset the encoderOffset to set
-	 */
-	public void setEncoderOffset(double encoderOffset) {
-		this.encoderOffset = encoderOffset;
-	}
-
-	/**
-	 * @return the encoderResolution
-	 */
-	public double getEncoderResolution() {
-		return encoderResolution;
-	}
-
-	/**
-	 * @param encoderResolution the encoderResolution to set
-	 */
-	public void setEncoderResolution(double encoderResolution) {
-		this.encoderResolution = encoderResolution;
-	}
-
-	/**
-	 * @return the encoderDirection
-	 */
-	public int getEncoderDirection() {
-		return encoderDirection;
-	}
-
-	/**
-	 * @param encoderDirection the encoderDirection to set
-	 */
-	public void setEncoderDirection(int encoderDirection) {
-		this.encoderDirection = encoderDirection;
-	}
-
-	
-	/**
-	 * @return the start
-	 */
-	public double getStart() {
-		return start;
-	}
-
-	/**
-	 * @param start the start to set
-	 */
-	public void setStart(double start) {
-		this.start = start;
-		if(start<=end){
-			positive=true;
-		}
-		else{
-			positive=false;
-		}
-	}
-
-	/**
-	 * @return the end
-	 */
-	public double getEnd() {
-		return end;
-	}
-
-	/**
-	 * @param end the end to set
-	 */
-	public void setEnd(double end) {
-		this.end = end;
-		if(end>=start){
-			positive=true;
-		}
-		else{
-			positive=false;
-		}
-	}
-	
-	/**
-	 * Calculate real position
-	 * @param raw
-	 * @return
-	 */
-	public double calculatePositionMotor(double raw){
-		return(((raw * motorResolution * motorReadbackResolution)/motorDirection)+motorOffset);
-	}
-	
-	/**
-	 * Calculate real motor position using the readback link
-	 * @param raw
-	 * @return
-	 */
-	public double calculatePositionMotorUseReadback(double raw){
-		return((((raw - encoderOffset) * encoderResolution * encoderDirection * motorReadbackResolution) / motorDirection) + motorOffset);
-	}
-	
-	/**
-	 * Calculate real motor position using encoder
-	 * @param raw
-	 * @return
-	 */
-	public double calculatePositionMotorUseEncoder(double raw){
-		return(raw * motorEncoderResolution * motorReadbackResolution/motorDirection + motorOffset);
-	}
-	
-	/**
-	 * Filter whether value is with the range
-	 * @param value
-	 * @return
-	 */
-	public boolean filter(Double value){
-		if(positive){
-			if(start<=value && value<=end){
-				
-				// If motor is very accurete and user backlash==null it might be that value is exactly 
-				// the end value. To prevent that unnecessary data is captured execute this check
-				if(wasEqualBefore){
-					wasEqualBefore=false; // Reset flag
-					return false;
-				}
-				
-				// Check whether was equal
-				if(value==end){
-					wasEqualBefore=true;
-				}
-				
-				return true;
-			}
-			else{
-				return false;
-			}
-		}
-		else{
-			if(end<=value && value <=start){
-				
-				if(wasEqualBefore){
-					wasEqualBefore=false; // Reset flag
-					return false;
-				}
-				
-				// Check whether was equal
-				if(value==start){
-					wasEqualBefore=true;
-				}
-				
-				return true;
-			}
-			else{
-				return false;
-			}
-		}
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/CrlogicResource.java

@@ -1,71 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-/**
- * Readout resource of crlogic
- */
-public class CrlogicResource {
-	
-	/**
-	 * Id of the data
-	 */
-	private String id;
-	/**
-	 * Id of the crlogic resource to be read out. As configured in the CRLOGIC part of the IOC startup script
-	 */
-	private String key;
-	/**
-	 * Flag whether to read back the delta of the values of this resource. (delta is done in software)
-	 */
-	private boolean delta = false;
-	
-	public CrlogicResource(){
-	}
-	
-	public CrlogicResource(String id, String key){
-		this.id = id;
-		this.key = key;
-	}
-	
-	public CrlogicResource(String id, String key, boolean delta){
-		this.id = id;
-		this.key = key;
-		this.delta = delta;
-	}
-	
-	public String getId() {
-		return id;
-	}
-	public void setId(String id) {
-		this.id = id;
-	}
-	public String getKey() {
-		return key;
-	}
-	public void setKey(String key) {
-		this.key = key;
-	}
-	public boolean isDelta() {
-		return delta;
-	}
-	public void setDelta(boolean delta) {
-		this.delta = delta;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/ParallelCrlogic.java

@@ -1,237 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.Callable;
-import java.util.concurrent.CyclicBarrier;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.TimeUnit;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import com.google.common.eventbus.EventBus;
-import com.google.common.eventbus.Subscribe;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.messages.Message;
-
-public class ParallelCrlogic implements ActionLoop {
-	
-	private static final Logger logger = Logger.getLogger(ParallelCrlogic.class.getName());
-
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	private CrlogicLoop crlogic;
-	private ScrlogicLoop scrlogic;
-	
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	private ParallelCrlogicStreamMerge merger;
-	
-	
-	private final EventBus eventbus;
-	
-	public ParallelCrlogic(CrlogicLoop crlogic, ScrlogicLoop scrlogic){
-		
-		if(crlogic==null){
-			throw new IllegalArgumentException("No Crloop specified");
-		}
-		if(scrlogic==null){
-			throw new IllegalArgumentException("No Scrloop specified");
-		}
-		
-		
-		this.eventbus = new EventBus();
-		
-		this.crlogic = crlogic;
-		// Add timestamp to sensor at the beginning of the sensor list as this is required for merging the data
-		// Timestamp will be at the second position of a message in the queue!
-		this.crlogic.getSensors().add(0, new CrlogicResource("tmp_timestamp","TIMESTAMP"));
-		this.scrlogic = scrlogic;
-		
-		// Initialize lists used by the loop
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		
-		final BlockingQueue<Message> q1 = new LinkedBlockingQueue<>();
-		final BlockingQueue<Message> q2 = new LinkedBlockingQueue<>();
-		
-		crlogic.getEventBus().register(new Object(){
-			@Subscribe
-			public void onMessage(Message m){
-				q1.add(m);
-			}
-		});
-		scrlogic.getEventBus().register(new Object(){
-			@Subscribe
-			public void onMessage(Message m){
-				q2.add(m);
-			}
-		});
-		
-		this.merger = new ParallelCrlogicStreamMerge(q1, q2, eventbus);
-	}
-	
-	@Override
-	public void prepare() {
-	}
-	
-	@Override
-	public void execute() throws InterruptedException {
-		
-		// Execute pre actions
-		for(Action action: preActions){
-			action.execute();
-		}
-		
-		
-		ExecutorService service = Executors.newFixedThreadPool(3); // 2 for the parallel data acquisition and 1 for the merger thread
-		final CyclicBarrier b = new CyclicBarrier(2);
-		
-		List<Future<Boolean>> list = new ArrayList<Future<Boolean>>();
-		
-		// Start a thread for each logic
-		logger.info("Submit logic");
-		Future<Boolean> f = service.submit(new Callable<Boolean>(){
-			@Override
-			public Boolean call() throws Exception {
-				
-				// Prepare logic
-				crlogic.prepare();
-				
-				// Ensure that really all parallel logics start in parallel
-				b.await();
-				
-				// Execute the logic of this path
-				crlogic.execute();
-	
-				// Need to stop the scrlogic logic (otherwise it would keep going to take data)
-				scrlogic.abort();
-				return true;
-			}});
-		list.add(f);
-		
-		//Start a thread for the scrlogic
-		logger.info("Submit logic");
-		f = service.submit(new Callable<Boolean>(){
-			@Override
-			public Boolean call() throws Exception {
-				
-				// Prepare logic
-				scrlogic.prepare();
-				
-				// Ensure that really all parallel logics start in parallel
-				b.await();
-				
-				// Execute the logic of this path
-				scrlogic.execute(); // This actually just starts the collection ...
-				return true;
-			}});
-		list.add(f);
-		
-		
-//		// Start data merge thread
-//		logger.info("Start data merge");
-//		f = service.submit(new Callable<Boolean>(){
-//			@Override
-//			public Boolean call() throws Exception {
-//				
-//				merger.merge();
-//				return true;
-//			}});
-//		list.add(f);
-		
-		
-		for(Future<Boolean> bf: list){
-			// Wait for completion of the thread
-			try {
-				bf.get();
-			} catch (ExecutionException e) {
-				logger.log(Level.WARNING, "Something went wrong while waiting for crthreads to finish");
-				throw new RuntimeException(e);
-			}
-		}
-		
-		merger.merge();
-		
-		// Wait until all threads have finished
-		service.shutdown();
-		service.awaitTermination(1, TimeUnit.MINUTES);
-		
-		
-		// Execute post actions
-		for(Action action: postActions){
-			action.execute();
-		}
-		
-	}
-
-	@Override
-	public void abort() {
-	}
-
-	@Override
-	public void cleanup() {
-	}
-
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	@Override
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-	@Override
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-
-	@Override
-	public EventBus getEventBus(){
-		return eventbus;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/ParallelCrlogicStreamMerge.java

@@ -1,163 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-
-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;
-
-/**
- * Class to merge two data streams into one. The secondary queues data is added to the primary queues data.
- * The resulting queue therefor will hold the same amount of elements as the primary queue does.
- * The datagroup flag set in the end of stream message will be set according to the flag set in the primary queue.
- */
-public class ParallelCrlogicStreamMerge {
-
-	
-	private BlockingQueue<Message> primaryQueue;
-	private BlockingQueue<Message> secondaryQueue;
-	
-	private final EventBus eventbus;
-	
-	private List<Metadata> metadata;
-	
-	/**
-	 * @param pqueue	Primary/master queue
-	 * @param squeue	Secondary queue
-	 */
-	public ParallelCrlogicStreamMerge(BlockingQueue<Message> pqueue, BlockingQueue<Message> squeue, EventBus ebus){
-		this.primaryQueue = pqueue;
-		this.secondaryQueue = squeue;
-	
-		this.eventbus = ebus;
-	}
-	
-	/**
-	 * Merge the streams based on the timestamp
-	 * @throws InterruptedException 
-	 */
-	public void merge() throws InterruptedException{
-		
-		metadata = new ArrayList<>();
-		
-		boolean firstPrimary = true;
-		boolean firstSecondary = true;
-		
-		// Actual data of the secondary queue
-		List<Object> currData = null;
-		
-		// Take first element of the primary queue (wait until message is available)
-		Message m = primaryQueue.take();
-		
-		while(! (m instanceof EndOfStreamMessage)){
-			
-			if(m instanceof DataMessage){
-				
-				DataMessage dm = (DataMessage) m;
-				
-				if(firstPrimary){
-					firstPrimary = false;
-					List<Metadata> pqm = dm.getMetadata();
-					metadata.add(pqm.get(0)); // add first component (this is the actuator)
-					// Skip the next component as this is the timestamp used to merge the data
-					for(int i=2;i<pqm.size();i++){
-						metadata.add(pqm.get(i));
-					}
-				}
-				
-				
-				// Get and remove merge timestamp from the data of the message 
-				Double timestamp = (Double) dm.getData().remove(1);
-				long milliseconds = (long) (timestamp*1000);
-				long nanoOffset = (long)((timestamp*1000-milliseconds)*1000000);
-				
-				while(true){
-					// Assumption: the secondary Queue holds at least the data up to the 
-					// timestamp of the primary queue
-					Message mess = secondaryQueue.peek();
-					
-					if(mess instanceof EndOfStreamMessage){
-						break;
-					}
-					
-					if(mess == null){
-						break;
-					}
-					
-					if(mess instanceof DataMessage){
-						
-						// Check whether timestamp of the next message is bigger than the timestamp of the 
-						// message from the primary queue - if the timestamp is bigger do not take message out of the queue
-						DataMessage msCheck = (DataMessage) mess;
-						
-						if(firstSecondary){
-							firstSecondary = false;
-							
-							List<Metadata> sqm = msCheck.getMetadata();
-							// Skip first two components of the message as this is the timestamp
-							for(int i=2;i<sqm.size();i++){
-								metadata.add(sqm.get(i));
-							}
-						}
-						
-						long currMilliCheck = ((Double) msCheck.getData().get(0)).longValue();
-						long currNanoCheck = ((Double) msCheck.getData().get(1)).longValue();
-	
-						if(currMilliCheck>milliseconds || (currMilliCheck==milliseconds && currNanoCheck>nanoOffset)){
-							break;
-						}
-						
-						DataMessage ms = (DataMessage) secondaryQueue.take();
-						
-						currData = ms.getData();
-						// Remove timestamps
-						currData.remove(0);
-						currData.remove(0);
-					}
-					else{
-						// No DataMessage
-						break;
-					}
-				}
-				
-				// Add data to primary data queue message and put it into the out queue
-				dm.getData().addAll(currData);
-				dm.setMetadata(metadata);
-				eventbus.post(dm);
-			}
-			
-			
-			m = primaryQueue.take();
-		}
-		
-		// Add the end of stream message of the primary queue
-		eventbus.post(m);
-		
-		// Clear all remaining messages in secondary queue  
-		secondaryQueue.clear();
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/ScrlogicLoop.java

@@ -1,305 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.CountDownLatch;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Logger;
-
-import com.google.common.eventbus.EventBus;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.messages.DataMessage;
-import ch.psi.fda.messages.EndOfStreamMessage;
-import ch.psi.fda.messages.Metadata;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.impl.type.DoubleTimestamp;
-
-/**
- *         Assumptions: - The delay between the monitor writing the value to the
- *         monitor queue and the readout of all the queues is sufficient to
- *         prevent the situation that some monitors of events close to each
- *         other on different IOC's have not arrived yet. - The sequence of
- *         monitors fired for one channel is according to the sequence of the
- *         causes. No monitor package is overtaking an other package on the
- *         network.
- * 
- *         - No monitor events are lost on the network (while using monitors you
- *         cannot guarantee this)
- * 
- *         The data queue returned by this logic includes two items for the
- *         timestamp and nanoseconds offset. These two items are the first two
- *         items of a message The id's are: crTimestampMilliseconds
- *         crTimestampOffsetNanoseconds
- */
-public class ScrlogicLoop implements ActionLoop {
-
-	private static String ID_TIMESTAMP_MILLISECONDS = "crTimestampMilliseconds";
-	private static String ID_TIMESTAMP_OFFSET_NANOSECONDS = "crTimestampOffsetNanoseconds";
-
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(ScrlogicLoop.class.getName());
-
-
-	/**
-	 * Data queue sensor data is posted to. A message consists of a list of data
-	 * objects that are read out of the sensors of this loop.
-	 */
-//	private final BlockingQueue<Message> dataQueue = new LinkedBlockingQueue<Message>();
-
-	private boolean dataGroup = false;
-	private final List<Action> preActions = new ArrayList<Action>();
-	private final List<Action> postActions = new ArrayList<Action>();
-
-	private List<String> sensorIds;
-	private List<Channel<DoubleTimestamp>> sensors;
-
-	/**
-	 * List of monitors that were attached to the sensor channels (i.e
-	 * workaround)
-	 */
-	private final List<PropertyChangeListener> monitors = new ArrayList<>();
-
-	/**
-	 * List of blocking queues that hold the data for one sensor (channel)
-	 */
-	private final List<BlockingQueue<TimestampedValue>> queues = new ArrayList<BlockingQueue<TimestampedValue>>();
-
-	private CountDownLatch latch;
-
-	private final EventBus eventbus;
-	private List<Metadata> metadata;
-	
-	public ScrlogicLoop(List<String> sensorIds, List<Channel<DoubleTimestamp>> sensors) {
-		this.eventbus = new EventBus();
-		this.sensorIds = sensorIds;
-		this.sensors = sensors;
-	}
-
-	@Override
-	public void execute() throws InterruptedException {
-
-		// Clear all queues
-		queues.clear();
-		latch = new CountDownLatch(1);
-
-			// Attach monitors to the channels (this is actually a workaround)
-			for (Channel<DoubleTimestamp> sensor : sensors) {
-				final BlockingQueue<TimestampedValue> q = new LinkedBlockingQueue<TimestampedValue>();
-				queues.add(q);
-				PropertyChangeListener listener = new PropertyChangeListener() {
-					
-					@Override
-					public void propertyChange(PropertyChangeEvent evt) {
-						if(evt.getPropertyName().equals("value")){
-							DoubleTimestamp v = (DoubleTimestamp) evt.getNewValue();
-							q.add(new TimestampedValue(v.getValue(), v.getTimestamp().getTime(), v.getNanosecondOffset()));
-						}
-					}
-				};
-				sensor.addPropertyChangeListener(listener);
-				monitors.add(listener);
-				
-			}
-
-		logger.info("Start data acquisition");
-
-		latch.await();
-
-		// Remove monitors
-		
-		for (int i = 0; i < sensors.size(); i++) {
-			Channel<DoubleTimestamp> sensor = sensors.get(i);
-			sensor.removePropertyChangeListener(monitors.get(i));
-		}
-
-		// Merge data
-		merge();
-
-		// Clear data queues
-		for (BlockingQueue<TimestampedValue> q : queues) {
-			q.clear();
-		}
-		queues.clear();
-		
-
-		// Put end of stream to the queue
-		eventbus.post(new EndOfStreamMessage(dataGroup));
-		
-	}
-
-	@Override
-	public void abort() {
-		latch.countDown();
-	}
-
-	@Override
-	public void prepare() {
-		
-		metadata = new ArrayList<>();
-
-		// Build up data message metadata based on the channels registered.
-		metadata.add(new Metadata(ID_TIMESTAMP_MILLISECONDS));
-		metadata.add(new Metadata(ID_TIMESTAMP_OFFSET_NANOSECONDS));
-		for (String id : sensorIds) {
-			metadata.add(new Metadata(id));
-		}
-	}
-
-	@Override
-	public void cleanup() {
-	}
-
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	@Override
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-	@Override
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-
-	private boolean hasNext(){
-		for (BlockingQueue<TimestampedValue> q: queues) {
-			if(!q.isEmpty()){
-				return true;
-			}
-		}
-		return false;
-	}
-	
-	/**
-	 * Merge data collected by different monitor
-	 * 
-	 * @throws InterruptedException
-	 */
-	private void merge() throws InterruptedException {
-		// Array to hold temporary channel values
-		TimestampedValue[] cvalues = new TimestampedValue[queues.size()];
-		TimestampedValueComparator comparator = new TimestampedValueComparator();
-
-		// Oldest value written
-		TimestampedValue globalOldest = null;
-		List<Integer> indexes = new ArrayList<Integer>();
-
-		while (hasNext()) {
-			Thread.sleep(10); // Ensure that close by monitors have time to
-								// catch up / also ensure context switch
-
-			// Oldest value of this run
-			TimestampedValue oldest = null;
-			// Queue index of the oldest value of this run
-			indexes.clear();
-
-			// Find oldest element in any of the queues
-			for (int i = 0; i < queues.size(); i++) {
-
-				BlockingQueue<TimestampedValue> q = queues.get(i);
-				TimestampedValue ttcheck = q.peek();
-
-				if (ttcheck != null) {
-					if (oldest == null) {
-						// Update the oldest variable with current element
-						oldest = ttcheck;
-						indexes.clear();
-						indexes.add(i);
-					} else if (comparator.compare(ttcheck, oldest) < 0) { 
-						// Check whether timestamp is less (older) than the current oldest timestamp.
-						oldest = ttcheck;
-						indexes.clear();
-						indexes.add(i);
-					} else if (comparator.compare(ttcheck, oldest) == 0) {
-						// SAME TIMESTAMP
-						indexes.add(i);
-					} else {
-					}
-				}
-			}
-
-			// logger.info("Index: "+index+" Permits: "+semaphore.availablePermits());
-			// System.out.println("indexes: "+indexes.size());
-
-			if (indexes.size() > 0) {
-				long timestamp = 0l;
-				long nanoOffset = 0l;
-
-				for (Integer index : indexes) {
-					// Get next older value
-					cvalues[index] = queues.get(index).poll();
-
-					if (globalOldest != null) {
-						if (comparator.compare(cvalues[index], globalOldest) >= 0) {
-							// Update the global oldest variable
-							globalOldest = cvalues[index];
-							timestamp = cvalues[index].getTimestamp();
-							nanoOffset = cvalues[index].getNanosecondsOffset();
-						} else {
-							// Monitors did not fire in sequence (an newer
-							// monitor overtook an older (from an other IOC))
-							logger.warning("Timestamped value out of sequence - discard value !!!!");
-							// Continue with next value ...
-							continue;
-						}
-					} else {
-						globalOldest = cvalues[index];
-					}
-				}
-
-				// Assemble data message ...
-				DataMessage message = new DataMessage(metadata);
-
-				message.getData().add(new Double(timestamp));
-				message.getData().add(new Double(nanoOffset));
-
-				for (int y = 0; y < cvalues.length; y++) {
-					if (cvalues[y] != null) {
-						message.getData().add(new Double(cvalues[y].getValue()));
-					} else {
-						message.getData().add(Double.NaN);
-					}
-				}
-//				System.out.println(message);
-				eventbus.post(message);
-			}
-
-		}
-	}
-	
-	public EventBus getEventBus(){
-		return eventbus;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/TemplateCrlogic.java

@@ -1,114 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.annotation.CaChannel;
-
-public class TemplateCrlogic {
-
-	/**
-	 * Ticks per second - IOC setting
-	 * ATTENTION - This field must only be set bu the IOC - ATTENTION
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}:TPS")
-	private Channel<Integer> ticksPerSecond;
-
-	/**
-	 * Status of the OTFSCAN IOC logic
-	 */
-	public enum Status { SETUP, INACTIVE, INITIALIZE, ACTIVE, STOP, FAULT, ERROR };
-	@CaChannel(type=String.class, name ="${PREFIX}:STATUS")
-	private Channel<String> status;
-	
-	/**
-	 * Message from the OTFSCAN IOC logic
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:MSG")
-	private Channel<String> message;
-
-	/**
-	 * IOC ticks between data acquisition interrupts
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}:TBINT")
-	private Channel<Integer> ticksBetweenInterrupts;
-
-	/**
-	 * Name or ip address of the NFS server to save the data to
-	 * (depending on the IOC setup)
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:NFSSE")
-	private Channel<String> nfsServer;
-	
-	/**
-	 * Name of the NFS share on the NFS server
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:NFSSH")
-	private Channel<String> nfsShare;
-
-	/**
-	 * Name of the data file
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:DFNAM")
-	private Channel<String> dataFile;
-	
-	/**
-	 * Flag to identify whether the data file should be appended
-	 */
-	@CaChannel(type=Boolean.class, name ="${PREFIX}:FAPPE")
-	private Channel<Boolean> appendFile;
-
-	/**
-	 * Readout resources
-	 */
-	@CaChannel(type=String[].class, name ="${PREFIX}:RRES")
-	private Channel<String[]> readoutResources;
-	
-	
-	
-	public Channel<Integer> getTicksPerSecond() {
-		return ticksPerSecond;
-	}
-	public Channel<String> getStatus() {
-		return status;
-	}
-	public Channel<String> getMessage() {
-		return message;
-	}
-	public Channel<Integer> getTicksBetweenInterrupts() {
-		return ticksBetweenInterrupts;
-	}
-	public Channel<String> getNfsServer() {
-		return nfsServer;
-	}
-	public Channel<String> getNfsShare() {
-		return nfsShare;
-	}
-	public Channel<String> getDataFile() {
-		return dataFile;
-	}
-	public Channel<Boolean> getAppendFile() {
-		return appendFile;
-	}
-	public Channel<String[]> getReadoutResources() {
-		return readoutResources;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/TemplateEncoder.java

@@ -1,59 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.annotation.CaChannel;
-
-public class TemplateEncoder {
-	
-	/**
-	 * Resolution	- $(P)$(E)_SCL
-	 */
-	@CaChannel(type=Double.class, name="${PREFIX}_SCL")
-	private Channel<Double> resolution;
-
-	/**
-	 * Offset	- $(P)$(E)_OFF
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}_OFF")
-	private Channel<Double> offset;
-
-	/**
-	 * Direction	- $(P)$(E)_DIR
-	 */
-	public enum Direction {Negative, Positive};
-	@CaChannel(type=Integer.class, name ="${PREFIX}_DIR")
-	private Channel<Integer> direction;
-
-	
-	
-	public Channel<Double> getResolution() {
-		return resolution;
-	}
-	public Channel<Double> getOffset() {
-		return offset;
-	}
-	public Channel<Integer> getDirection() {
-		return direction;
-	}
-	
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/TemplateMotor.java

@@ -1,471 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.annotation.CaChannel;
-
-public class TemplateMotor {
-
-	public enum Type {SOFT_CHANNEL, MOTOR_SIMULATION, OMS_VME58, OMS_MAXv};
-	
-	/**
-	 * ## Drive section ##
-	 * # User coordinates #
-	 */
-	
-	/**
-	 * .HLM	High limit	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.HLM")
-	private Channel<Double> highLimit;
-	
-	/**
-	 * .LLM	Low limit	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.LLM")
-	private Channel<Double> lowLimit;
-	
-	/**
-	 * .RBV	Readback value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.RBV", monitor=true)
-	private Channel<Double> readbackValue;
-	
-	/**
-	 * .VAL	Set value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.VAL", monitor=true)
-	private Channel<Double> setValue;
-
-	/**
-	 * .RLV	Relative move value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.RLV")
-	private Channel<Double> relativeMoveValue;
-	
-	/**
-	 * .TWV	Teak value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.TWV")
-	private Channel<Double> tweakValue;
-	
-	/**
-	 * .TWR	Tweak reverse - move left	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.TWR")
-	private Channel<Integer> tweakReverse;
-	
-	/**
-	 * .TWF	Tweak forward - move right	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.TWF")
-	private Channel<Integer> tweakForward;
-	
-	/**
-	 * .JOGR	Jog reverse	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.JOGR")
-	private Channel<Integer> jogReverse;
-	
-	/**
-	 * .JOGF	Jog forward	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.JOGF")
-	private Channel<Integer> jogForward;
-	
-	/**
-	 * .HOMR	Home reverse	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.HOMR")
-	private Channel<Integer> homeReverse;
-	
-	/**
-	 * .HOMF	Home forward	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.HOMF")
-	private Channel<Integer> homeForward;
-
-	/**
-	 * .EGU	Engineering unit	- String
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}.EGU")
-	private Channel<String> engineeringUnit;
-
-	/**
-	 * .DTYP	Type	- String (e.g. "OMS MAXv") see enum Type
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.DTYP")
-	private Channel<Integer> type;
-	
-	/**
-	 * .DESC	Description	- String
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}.DESC")
-	private Channel<String> description;
-
-	
-	/**
-	 * # Dial coordinates #
-	 */
-	
-	/**
-	 * .DHLM	Dial high limit	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DHLM")
-	private Channel<Double> dialHighLimit;
-	
-	/**
-	 * .DLLM	Dial low limit	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DLLM")
-	private Channel<Double> dialLowLimit;
-	
-	/**
-	 * .DRBV	Dial readback value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DRBV", monitor=true)
-	private Channel<Double> dialReadbackValue;
-	
-	/**
-	 * .DVAL	Dial set value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DVAL", monitor=true)
-	private Channel<Double> dialSetValue;
-
-	/**
-	 * .RVAL	Raw value	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.RVAL", monitor=true)
-	private Channel<Integer> rawValue;
-	
-	/**
-	 * .RRBV	Raw readback value	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.RRBV", monitor=true)
-	private Channel<Integer> rawReadbackValue;
-
-	/**
-	 * .SPMG	Stop/Pause/Move/Go	- (0:"Stop", 1:"Pause", 2:"Move", 3:"Go")	- 3
-	 */
-	public enum Commands { Stop, Pause, Move, Go };
-	@CaChannel(type=Integer.class, name ="${PREFIX}.SPMG")
-	private Channel<Integer> command;
-	
-
-	/**
-	 * ## Calibration section ##
-	 */
-	
-	/**
-	 * .SET	Set/Use Switch	- (0:"Use", 1:"Set")	- 0
-	 */
-	public enum Calibration {Use, Set};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.SET")
-	private Channel<Integer> calibration;
-	
-	/**
-	 * .OFF	User offset (EGU)	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.OFF")
-	private Channel<Double> offset;
-	
-	/**
-	 * .FOFF	Offset-Freeze Switch	- (0:"Variable", 1:"Frozen") - 1
-	 */
-	public enum OffsetMode {Variable, Frozen};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.FOFF")
-	private Channel<Integer> offsetMode;
-	
-	/**
-	 * .DIR	User direction	- (0:"Pos", 1:"Neg")
-	 */
-	public enum Direction {Positive, Negative};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.DIR")
-	private Channel<Integer> direction;
-
-	
-	/**
-	 * ## Dynamics ##
-	 */
-	
-	/**
-	 * .VELO	Velocity (EGU/s)	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.VELO")
-	private Channel<Double> velocity;
-	
-	/**
-	 * .BVEL	Backlash velocity (EGU/s) - double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.BVEL")
-	private Channel<Double> backlashVelocity;
-	
-	/**
-	 * .VBAS	Base speed (EGU/s) - double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.VBAS")
-	private Channel<Double> baseSpeed;
-	
-	/**
-	 * .ACCL	Acceleration time / seconds to velocity	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.ACCL")
-	private Channel<Double> accelerationTime;
-	
-	/**
-	 * .BACC	Backlash acceleration time / seconds to velocity	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.BACC")
-	private Channel<Double> backlashAccelerationTime;
-	
-	/**
-	 * .BDST	Backlash distance (EGU)	- double 
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.BDST")
-	private Channel<Double> backlashDistance;
-	
-	/**
-	 * .FRAC	Move fraction	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.FRAC")
-	private Channel<Double> moveFracion;
-	
-
-	/**
-	 * ## Resolution ##
-	 */
-	
-	/**
-	 * .MRES	Motor resolution	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.MRES")
-	private Channel<Double> motorResolution;
-	
-	/**
-	 * .ERES	Encoder resolution	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.ERES")
-	private Channel<Double> encoderResolution;
-	
-	/**
-	 * .RRES	Readback resolution	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.RRES")
-	private Channel<Double> readbackResolution;
-	
-	/**
-	 * .RDBD	Retry deadband (EGU)	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.RDBD")
-	private Channel<Double> retryDeadband;
-	
-	/**
-	 * .RTRY	Max retry count	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.RTRY")
-	private Channel<Integer> maxRetryCount;
-	
-	/**
-	 * .RCNT	Retry count	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.RCNT", monitor=true)
-	private Channel<Integer> retryCount;
-	
-	/**
-	 * .UEIP	Use encoder (if present) - (0:"No", 1:"Yes")
-	 */
-	@CaChannel(type=Boolean.class, name ="${PREFIX}.UEIP")
-	private Channel<Boolean> useEncoder;
-	
-	/**
-	 * .URIP	Use readback link (if present)	- (0:"No", 1:"Yes")
-	 */
-	@CaChannel(type=Boolean.class, name ="${PREFIX}.URIP")
-	private Channel<Boolean> useReadback;
-	
-	/**
-	 * .DLY	Readback delay (s)	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DLY")
-	private Channel<Double> readbackDelay;
-	
-	/**
-	 * .RDBL	Readback link	- String
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}.RDBL")
-	private Channel<String> readbackLink;
-	
-	/**
-	 * .OMSL	Output mode select	- (0:"supervisory", 1:"closed_loop")
-	 */
-	public enum OutputMode {Supervisory, Closed_Loop};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.OMSL")
-	private Channel<Integer> outputMode;
-	
-	/**
-	 * ## Status ## 
-	 */
-	
-	/**
-	 * .DMOV	Done move	- int
-	 */
-	@CaChannel(type=Boolean.class, name ="${PREFIX}.DMOV", monitor=true)
-	private Channel<Boolean> moveDone;
-
-	
-	
-	public Channel<Double> getHighLimit() {
-		return highLimit;
-	}
-	public Channel<Double> getLowLimit() {
-		return lowLimit;
-	}
-	public Channel<Double> getReadbackValue() {
-		return readbackValue;
-	}
-	public Channel<Double> getSetValue() {
-		return setValue;
-	}
-	public Channel<Double> getRelativeMoveValue() {
-		return relativeMoveValue;
-	}
-	public Channel<Double> getTweakValue() {
-		return tweakValue;
-	}
-	public Channel<Integer> getTweakReverse() {
-		return tweakReverse;
-	}
-	public Channel<Integer> getTweakForward() {
-		return tweakForward;
-	}
-	public Channel<Integer> getJogReverse() {
-		return jogReverse;
-	}
-	public Channel<Integer> getJogForward() {
-		return jogForward;
-	}
-	public Channel<Integer> getHomeReverse() {
-		return homeReverse;
-	}
-	public Channel<Integer> getHomeForward() {
-		return homeForward;
-	}
-	public Channel<String> getEngineeringUnit() {
-		return engineeringUnit;
-	}
-	public Channel<Integer> getType() {
-		return type;
-	}
-	public Channel<String> getDescription() {
-		return description;
-	}
-	public Channel<Double> getDialHighLimit() {
-		return dialHighLimit;
-	}
-	public Channel<Double> getDialLowLimit() {
-		return dialLowLimit;
-	}
-	public Channel<Double> getDialReadbackValue() {
-		return dialReadbackValue;
-	}
-	public Channel<Double> getDialSetValue() {
-		return dialSetValue;
-	}
-	public Channel<Integer> getRawValue() {
-		return rawValue;
-	}
-	public Channel<Integer> getRawReadbackValue() {
-		return rawReadbackValue;
-	}
-	public Channel<Integer> getCommand() {
-		return command;
-	}
-	public Channel<Integer> getCalibration() {
-		return calibration;
-	}
-	public Channel<Double> getOffset() {
-		return offset;
-	}
-	public Channel<Integer> getOffsetMode() {
-		return offsetMode;
-	}
-	public Channel<Integer> getDirection() {
-		return direction;
-	}
-	public Channel<Double> getVelocity() {
-		return velocity;
-	}
-	public Channel<Double> getBacklashVelocity() {
-		return backlashVelocity;
-	}
-	public Channel<Double> getBaseSpeed() {
-		return baseSpeed;
-	}
-	public Channel<Double> getAccelerationTime() {
-		return accelerationTime;
-	}
-	public Channel<Double> getBacklashAccelerationTime() {
-		return backlashAccelerationTime;
-	}
-	public Channel<Double> getBacklashDistance() {
-		return backlashDistance;
-	}
-	public Channel<Double> getMoveFracion() {
-		return moveFracion;
-	}
-	public Channel<Double> getMotorResolution() {
-		return motorResolution;
-	}
-	public Channel<Double> getEncoderResolution() {
-		return encoderResolution;
-	}
-	public Channel<Double> getReadbackResolution() {
-		return readbackResolution;
-	}
-	public Channel<Double> getRetryDeadband() {
-		return retryDeadband;
-	}
-	public Channel<Integer> getMaxRetryCount() {
-		return maxRetryCount;
-	}
-	public Channel<Integer> getRetryCount() {
-		return retryCount;
-	}
-	public Channel<Boolean> getUseEncoder() {
-		return useEncoder;
-	}
-	public Channel<Boolean> getUseReadback() {
-		return useReadback;
-	}
-	public Channel<Double> getReadbackDelay() {
-		return readbackDelay;
-	}
-	public Channel<String> getReadbackLink() {
-		return readbackLink;
-	}
-	public Channel<Integer> getOutputMode() {
-		return outputMode;
-	}
-	public Channel<Boolean> getMoveDone() {
-		return moveDone;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/TemplateVSC16Scaler.java

@@ -1,80 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import java.util.List;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.annotation.CaChannel;
-
-public class TemplateVSC16Scaler {
-
-	/**
-	 * Command
-	 */
-	public enum Command {Done, Count};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.CNT")
-	private Channel<Integer> command;
-	
-	
-	public enum Mode {OneShot, AutoCount};
-	/**
-	 * Count mode
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.CONT")
-	private Channel<Integer> mode;
-	
-	/**
-	 * Channel description
-	 */
-	@CaChannel(type=Boolean.class, name={"${PREFIX}.NM1", "${PREFIX}.NM2", "${PREFIX}.NM3", "${PREFIX}.NM4", "${PREFIX}.NM5", "${PREFIX}.NM6", "${PREFIX}.NM7", "${PREFIX}.NM8", "${PREFIX}.NM9", "${PREFIX}.NM10", "${PREFIX}.NM11", "${PREFIX}.NM12", "${PREFIX}.NM13", "${PREFIX}.NM14", "${PREFIX}.NM15", "${PREFIX}.NM16"})
-	private List<Channel<Boolean>> channelDescription;
-	
-	/**
-	 * Channel gate
-	 */
-	@CaChannel(type=Boolean.class, name={"${PREFIX}.G1", "${PREFIX}.G2", "${PREFIX}.G3", "${PREFIX}.G4", "${PREFIX}.G5", "${PREFIX}.G6", "${PREFIX}.G7", "${PREFIX}.G8", "${PREFIX}.G9", "${PREFIX}.G10", "${PREFIX}.G11", "${PREFIX}.G12", "${PREFIX}.G13", "${PREFIX}.G14", "${PREFIX}.G15", "${PREFIX}.G16"})
-	private List<Channel<Boolean>> channelGate;
-	
-	/**
-	 * Channel preset count
-	 * If gate is on scaler will only count until this value
-	 */
-	@CaChannel(type=Integer.class, name={"${PREFIX}.PR1", "${PREFIX}.PR2", "${PREFIX}.PR3", "${PREFIX}.PR4", "${PREFIX}.PR5", "${PREFIX}.PR6", "${PREFIX}.PR7", "${PREFIX}.PR8", "${PREFIX}.PR9", "${PREFIX}.PR10", "${PREFIX}.PR11", "${PREFIX}.PR12", "${PREFIX}.PR13", "${PREFIX}.PR14", "${PREFIX}.PR15", "${PREFIX}.PR16"})
-	private List<Channel<Integer>> channelPresetCount;
-
-	
-	
-	public Channel<Integer> getCommand() {
-		return command;
-	}
-	public Channel<Integer> getMode() {
-		return mode;
-	}
-	public List<Channel<Boolean>> getChannelDescription() {
-		return channelDescription;
-	}
-	public List<Channel<Boolean>> getChannelGate() {
-		return channelGate;
-	}
-	public List<Channel<Integer>> getChannelPresetCount() {
-		return channelPresetCount;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/TimestampedValue.java

@@ -1,43 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-public class TimestampedValue {
-
-	private final Double value;
-	private final long timestamp;
-	private final long nanosecondsOffset;
-	
-	public TimestampedValue(Double value, long timestamp, long nanosecondsOffset){
-		this.value = value;
-		this.timestamp = timestamp;
-		this.nanosecondsOffset = nanosecondsOffset;
-	}
-
-	public Double getValue() {
-		return value;
-	}
-	public long getTimestamp() {
-		return timestamp;
-	}
-	public long getNanosecondsOffset() {
-		return nanosecondsOffset;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/TimestampedValueComparator.java

@@ -1,44 +0,0 @@
-/**
- * 
- * 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.core.loops.cr;
-
-import java.util.Comparator;
-
-/**
- * Comparator for comparint 2 timestamped values
- */
-public class TimestampedValueComparator implements Comparator<TimestampedValue> {
-
-	@Override
-	public int compare(TimestampedValue o1, TimestampedValue o2) {
-		if (o1.getTimestamp() < o2.getTimestamp()) {
-			return -1;
-		} else if (o1.getTimestamp() > o2.getTimestamp()) {
-			return 1;
-		} else if (o1.getTimestamp() == o2.getTimestamp()) {
-			if (o1.getNanosecondsOffset() < o2.getNanosecondsOffset()) {
-				return -1;
-			} else if (o1.getNanosecondsOffset() > o2.getNanosecondsOffset()) {
-				return 1;
-			}
-		}
-		return 0;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/otf/DistributedFile.java

@@ -1,158 +0,0 @@
-/**
- * 
- * Copyright 2012 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.core.loops.otf;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-
-import jcifs.smb.SmbFile;
-
-public class DistributedFile {
-
-	private SmbFile smbfile = null;
-	private File file = null;
-	
-	public DistributedFile(SmbFile file){
-		this.smbfile = file;
-	}
-	
-	public DistributedFile(File file){
-		this.file = file;
-	}
-	
-	public DistributedFile(String url) throws MalformedURLException{
-		if(url.startsWith("smb://")){
-			smbfile = new SmbFile(url);
-		}
-		else {
-			file = new File(url);
-		}
-	}
-
-	
-	public String getCanonicalPath() throws IOException{
-		if(smbfile!=null){
-			return(smbfile.getCanonicalPath());
-		}
-		else{
-			return file.getCanonicalPath();
-		}
-	}
-
-
-	/**
-	 * @return
-	 * @throws IOException 
-	 */
-	public boolean exists() throws IOException {
-		if(smbfile!=null){
-			return(smbfile.exists());
-		}
-		else{
-			return file.exists();
-		}
-	}
-
-
-	/**
-	 * @return
-	 */
-	public boolean isDirectory() throws IOException {
-		if(smbfile!=null){
-			return(smbfile.isDirectory());
-		}
-		else{
-			return file.isDirectory();
-		}
-	}
-
-
-	/**
-	 * @return
-	 */
-	public DistributedFile[] listFiles() throws IOException {
-		if(smbfile!=null){
-			SmbFile[] files = smbfile.listFiles();
-			DistributedFile[] dfiles = new DistributedFile[files.length];
-			for(int i=0;i<files.length;i++){
-				dfiles[i] = new DistributedFile(files[i]);
-			}
-			return(dfiles);
-		}
-		else{
-			File[] files = file.listFiles();
-			DistributedFile[] dfiles = new DistributedFile[files.length];
-			for(int i=0;i<files.length;i++){
-				dfiles[i] = new DistributedFile(files[i]);
-			}
-			return(dfiles);
-		}
-	}
-
-	/**
-	 * @return
-	 */
-	public String getName() {
-		if(smbfile!=null){
-			return(smbfile.getName());
-		}
-		else{
-			return file.getName();
-		}
-	}
-
-	/**
-	 * @return
-	 */
-	public boolean isFile() throws IOException {
-		if(smbfile!=null){
-			return(smbfile.isFile());
-		}
-		else{
-			return file.isFile();
-		}
-	}
-
-	/**
-	 * 
-	 */
-	public void delete() throws IOException {
-		if(smbfile!=null){
-			smbfile.delete();
-		}
-		else{
-			file.delete();
-		}
-	}
-
-	/**
-	 * @return
-	 */
-	public InputStreamReader getInputStream() throws IOException {
-		if(smbfile!=null){
-			return(new InputStreamReader(smbfile.getInputStream()));
-		}
-		else{
-			return new FileReader(file);
-		}
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/otf/OTFLoop.java

@@ -1,439 +0,0 @@
-/**
- * 
- * 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.core.loops.otf;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-
-import com.google.common.eventbus.EventBus;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.sensors.TimestampSensor;
-import ch.psi.fda.messages.DataMessage;
-import ch.psi.fda.messages.EndOfStreamMessage;
-import ch.psi.fda.messages.Metadata;
-
-/**
- * ActionLoop that is implementing the OTF Scan logic.
- * While executing the loop a full OTF scan procedure is executed.
- */
-public class OTFLoop implements ActionLoop {
-	
-	private static Logger logger = Logger.getLogger(OTFLoop.class.getName());
-	
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	/**
-	 * Maximum number of monitored channels
-	 */
-	private static final int numberOfMonitoredChannels = 8;
-	/**
-	 * Maximum number of Scaler channels
-	 */
-	private static final int numberOfScalerChannels = 16;
-	
-	/**
-	 * Default timeout (in milliseconds) for wait operations
-	 */
-	private long timeout = 8000;
-	
-	/**
-	 * Name of the NFS server to place the data of the OTF logic
-	 */
-	private final String server;
-	/**
-	 * Share on the NFS server to put the OTF data on to
-	 */
-	private final String share;
-	/**
-	 * SMB share  to access the data written by the OTF C logic
-	 */
-	private final String smbShare;
-	
-	/**
-	 * Flag whether the actor of this loop should move in zig zag mode
-	 */
-	private final boolean zigZag;
-	
-	/**
-	 * Bean holding all OTF channels and functionality.
-	 */
-	private TemplateOTF obean;
-
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	/**
-	 * List of sensors of this loop
-	 */
-	private List<Sensor> sensors;
-	
-	
-	private List<Integer> dataIndexes;
-	
-	/**
-	 * Execution count of this loop. This count is used to determine the 
-	 * file name of the OTF file.
-	 */
-	private int executionCount;
-	
-	/**
-	 * Flag that indicates that the loop was requested to abort.
-	 */
-	private volatile boolean abort = false;
-	
-	
-	private String id;
-	private String name; // name of the motor channel
-	private String readback; // name of the encoder channel
-	private double start;
-	private double end;
-	private double stepSize;
-	private double integrationTime;
-	private double additionalBacklash;
-	
-	private final EventBus eventbus;
-	private List<Metadata> metadata;
-	
-	/**
-	 * @param channelPrefix	Prefix of the OTF related records, e.g. MTEST-HW3-OTF
-	 * @param server		NFS server the OTF C Logic should put its data to
-	 * @param share			Share on NFS server to put the OTF C Logic data
-	 * @param smbShare		SMB share to get the data written by the OTF C Logic
-	 * @param zigZag		Operate loop in zig zag mode
-	 */
-	public OTFLoop(TemplateOTF obean, String server, String share, String smbShare, boolean zigZag){
-		
-		this.eventbus = new EventBus();
-		
-		this.obean = obean;
-		
-		// Store loop configuration
-		this.server = server;
-		this.share = share;
-		this.smbShare = smbShare;
-		this.zigZag = zigZag;
-		
-		// Initialize lists used by the loop
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		this.sensors = new ArrayList<Sensor>();
-	}
-	
-	public void setActuator(String id, String name, String readback, double start, double end, double stepSize, double integrationTime, double additionalBacklash){
-		this.id = id;
-		this.name = name;
-		this.readback = readback;
-		this.start = start;
-		this.end = end;
-		this.stepSize = stepSize;
-		this.integrationTime = integrationTime;
-		this.additionalBacklash = additionalBacklash;
-	}
-	
-	
-	@Override
-	public void execute() throws InterruptedException {
-		
-		// Execute pre actions
-		for(Action action: preActions){
-			action.execute();
-		}
-		
-		// Start scan
-		obean.start();
-		
-		// Wait for end of scan
-		obean.waitUntilStopped();
-		
-		// Read data from file
-		collectData();
-
-		// Execute post actions
-		for(Action action: postActions){
-			action.execute();
-		}
-		
-		
-		// Issue end of loop control message
-		eventbus.post(new EndOfStreamMessage(dataGroup));
-		
-		// Increase execution count
-		executionCount++;
-	}
-
-	@Override
-	public void abort() {
-		// Abort otf scan logic
-		obean.abort();
-		
-		abort=true;
-	}
-	
-	@Override
-	public void prepare() {
-		executionCount = 0;
-		
-		// Set abort flag to false
-		abort=false;
-		
-		// list with all monitored channels
-		List<String> monitoredChannels = new ArrayList<String>();
-		dataIndexes = new ArrayList<Integer>();
-		dataIndexes.add(1); // The first one is always the readback of the motor
-		int channelCount =0;
-		for(Sensor s: sensors){
-			if(s instanceof OTFNamedChannelSensor){
-				// Monitored channel
-				OTFNamedChannelSensor so = (OTFNamedChannelSensor) s;
-				if(channelCount>=numberOfMonitoredChannels){
-					throw new IllegalArgumentException("Only up to "+numberOfMonitoredChannels+" channels can be monitored by OTF");
-				}
-				
-				monitoredChannels.add(so.getName());
-				dataIndexes.add(2+numberOfScalerChannels+channelCount);
-				
-				
-				channelCount++;
-			}
-			else if (s instanceof OTFScalerChannelSensor){
-				OTFScalerChannelSensor so = (OTFScalerChannelSensor) s;
-				if(so.getIndex()>=numberOfScalerChannels){
-					throw new IllegalArgumentException("Scaler index must be between 0<=index<"+numberOfScalerChannels);
-				}
-				dataIndexes.add(2+so.getIndex()); // scalers follow directly after the readback
-			}
-			else if (s instanceof TimestampSensor){
-				dataIndexes.add(2+numberOfScalerChannels+numberOfMonitoredChannels);
-			}
-//			else if (s instanceof OTFReadbackSensor){
-//				dataIndexes.add(1);
-//			}
-			else{
-				throw new IllegalArgumentException("Sensor type "+s.getClass()+" is not supported by this loop");
-			}
-		}
-		
-		// Set OTF parameters
-		try{
-			obean.resetToDefaults();
-			
-			// Set actor properties
-			obean.setMotor(this.name);
-			obean.waitUntilMotorOk(timeout);
-	
-			obean.setBegin(this.start);
-			obean.setEnd(this.end);
-			obean.setStepSize(this.stepSize);
-			obean.setIntegrationTime(this.integrationTime);
-			
-			// Override encoder if specified
-			if(this.readback!=null){
-				obean.setUseEncoder(true);
-				obean.setEncoder(this.readback);
-				obean.waitUntilEncoderOk(timeout);
-			}
-			
-			// Set user backlash
-			obean.setUserBacklash(this.additionalBacklash);
-			
-			
-			// NFS settings
-			obean.setNfsServer(server);
-			obean.setNfsShare(share);
-			
-			obean.setFileNameGeneration(true);
-			obean.setAppendFile(false);
-			obean.setZigZag(zigZag); // Set ZigZag because there might be iterations
-			obean.setFileNameFormat("%06d"); // Force an update of the filename/counter by setting file format twice with different values
-			obean.setFileNameFormat("%06d.txt");
-	    	
-			
-			
-			// Set monitored channels
-			obean.setMonitoredChannels(monitoredChannels.toArray(new String[monitoredChannels.size()]));
-		}
-		catch(Exception e){
-			throw new RuntimeException("Unable to set OTF configuration parameters",e);
-		}
-		
-		
-		// Cleanup temporary directory
-		try{
-			DistributedFile tmpDir = new DistributedFile(smbShare);
-			if( !tmpDir.exists() || !tmpDir.isDirectory() ){
-				throw new RuntimeException("Cannot access OTF temporary directory "+tmpDir.getCanonicalPath());
-			}
-			DistributedFile[] files = tmpDir.listFiles();
-	
-			for(int i=0;i<files.length;i++){
-				// Only delete item if it is not a directory and if it matches the given pattern.
-				if(files[i].isFile() && files[i].getName().matches("[0-9]+.txt")){
-					files[i].delete();
-					logger.fine("Delete file: "+files[i].getName());
-				}
-			}
-		}
-		catch(MalformedURLException e){
-			throw new RuntimeException(e);
-		} catch (IOException e) {
-			throw new RuntimeException("Unable to access share (temporary files)",e);
-		}
-		
-		metadata = new ArrayList<>();
-		metadata.add(new Metadata(id)); // Id of the readback of the motor
-		
-		// Build up data message metadata based on the sensors currently registered.
-		for(Sensor s: sensors){
-			metadata.add(new Metadata(s.getId()));
-		}
-	}
-
-	@Override
-	public void cleanup() {
-	}
-	
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	/**
-	 * Collect data written by the OTFScan logic
-	 * @param dataSet
-	 * @param tmpFile
-	 */
-	private void collectData() {
-		try{
-			final int timestampIndex = 2+numberOfScalerChannels+numberOfMonitoredChannels;
-			
-			DistributedFile tmpFile = new DistributedFile(smbShare +"/"+ String.format("%06d.txt", executionCount));
-			logger.fine("Collect data from "+tmpFile.getCanonicalPath());
-
-			DistributedFile lockfile = new DistributedFile(tmpFile.getCanonicalPath() + ".lock");
-			
-			logger.fine("Wait until file is written [lock file: "+lockfile.getCanonicalPath()+"]");
-			// Wait until file is created
-			while ((!tmpFile.exists()) || lockfile.exists()) {
-				Thread.sleep(500);
-				if(abort){
-					// If abort is issued while waiting for data immediately return without
-					// trying to read the data
-					return;
-				}
-			}
-				
-			logger.fine("Read file " + tmpFile.getCanonicalPath());
-			InputStreamReader inreader = tmpFile.getInputStream();
-			BufferedReader in = new BufferedReader(inreader);
-			String line;
-			boolean firstline = true;
-			while (true) {
-				line = in.readLine();
-					if (line == null) {
-						break;
-				} else {
-					if(line.matches("^\\[.*")){
-						// Skip header lines
-					}
-					else{
-						if(firstline){
-							firstline=false;
-							continue;
-						}
-						
-						DataMessage message = new DataMessage(metadata);
-						// Add data to dataset
-						String[] tokens = line.split("\t");
-
-						for(Integer i: dataIndexes){
-							try{
-								if(i == timestampIndex) {
-									// Calculate time in milliseconds
-									Double seconds = new Double(tokens[i]);
-									Double nanoseconds = new Double(tokens[i+1]);
-									
-									Double v = seconds*1000+Math.floor(nanoseconds*0.000001);
-									message.getData().add(v);
-								}
-								else {
-									
-									message.getData().add(new Double(tokens[i]));
-								}
-							}
-							catch(NumberFormatException e){
-									logger.warning("Cannot parse component ["+tokens[i]+"] from source file - will add 0 for this component");
-									message.getData().add(new Double(0));
-							}
-						}
-						eventbus.post(message);
-					}
-				}
-			}
-			in.close();
-			inreader.close();
-		} catch(InterruptedException e){
-			throw new RuntimeException("An interrupt occured while waiting for the file to show up",e);
-		} catch (IOException e) {
-			throw new RuntimeException("An IO Exception occured while reading the OTF data file",e);
-		}
-	}
-	
-	
-	public List<Sensor> getSensors() {
-		return sensors;
-	}
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getEventBus()
-	 */
-	@Override
-	public EventBus getEventBus() {
-		return eventbus;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/otf/OTFNamedChannelSensor.java

@@ -1,69 +0,0 @@
-/**
- * 
- * 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.core.loops.otf;
-
-import ch.psi.fda.core.Sensor;
-
-/**
- * Sensor to read out a named (Epics) channel. This sensor can only be used within the 
- * OTFLoop. If it is used in other loops, the read value will always be 0.
- * @author ebner
- *
- */
-public class OTFNamedChannelSensor implements Sensor {
-
-	/**
-	 * Name of the channel
-	 */
-	private final String name;
-	
-	/**
-	 * Global id of the sensor
-	 */
-	private final String id;
-	
-	/**
-	 * Constructor
-	 * @param id		Global id of the sensor
-	 * @param name		Name of the (Epics) channel
-	 */
-	public OTFNamedChannelSensor(String id, String name){
-		this.id = id;
-		this.name = name;
-	}
-	
-	@Override
-	public Object read() {
-		// Always return 0 if read() method is called.
-		return 0d;
-	}
-
-	/**
-	 * @return the name of the channel
-	 */
-	public String getName() {
-		return name;
-	}
-
-	@Override
-	public String getId() {
-		return id;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/otf/OTFScalerChannelSensor.java

@@ -1,67 +0,0 @@
-/**
- * 
- * 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.core.loops.otf;
-
-import ch.psi.fda.core.Sensor;
-
-/**
- * Sensor to read out a scaler channel. This sensor can only be used within the 
- * OTFLoop. If it is used in other loops, the read value will always be 0.
- *
- */
-public class OTFScalerChannelSensor implements Sensor {
-
-	/**
-	 * Index of the scaler channel. The index starts at 0;
-	 */
-	private final int index;
-	
-	/**
-	 * Global id of the sensor
-	 */
-	private final String id;
-	
-	/**
-	 * Constructor
-	 * @param id		Global id of the sensor
-	 * @param index		Index of the scaler channel. Index starts at 0.
-	 */
-	public OTFScalerChannelSensor(String id, int index){
-		this.id = id;
-		this.index = index;
-	}
-	
-	@Override
-	public Object read() {
-		return 0d;
-	}
-
-	/**
-	 * @return the index of the scaler channel
-	 */
-	public int getIndex() {
-		return index;
-	}
-
-	@Override
-	public String getId() {
-		return id;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/otf/TemplateOTF.java

@@ -1,964 +0,0 @@
-/**
- * 
- * 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.core.loops.otf;
-
-import java.util.List;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-
-import ch.psi.jcae.annotation.CaChannel;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-
-/**
- * Bean holding all OTF channels and functionality
- * @author ebner
- *
- */
-public class TemplateOTF {
-
-	public enum Status { SETUP, INACTIVE, INITIALIZE, ACTIVE, STOP, FAULT, ERROR };
-	public enum Command { NONE, START, STOP };
-	
-	private long timeoutMotorOk = 8000;
-	private long commandTimeout = 20000; // Maximum time until a command should take effect
-
-	@CaChannel(type=String.class, name ="${PREFIX}:UMOT")
-	private Channel<String> motor;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:MENC")
-	private Channel<String> encoder;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UBEG")
-	private Channel<Double> begin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UBEG.DRVL")
-	private Channel<Double> beginMin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UBEG.DRVH")
-	private Channel<Double> beginMax;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UEND")
-	private Channel<Double> end;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UEND.DRVL")
-	private Channel<Double> endMin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UEND.DRVH")
-	private Channel<Double> endMax;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:USSIZ")
-	private Channel<Double> stepSize;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:USSIZ.DRVL")
-	private Channel<Double> stepSizeMin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UITIM")
-	private Channel<Double> integrationTime;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UITIM.DRVL")
-	private Channel<Double> integrationTimeMin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UITIM.DRVH")
-	private Channel<Double> integrationTimeMax;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UBCL")
-	private Channel<Double> userBacklash;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:NFSSE")
-	private Channel<String> nfsServer;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:NFSSH")
-	private Channel<String> nfsShare;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:DFNAM")
-	private Channel<String> fileName;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:FFORM")
-	private Channel<String> fileNameFormat;
-	
-	@CaChannel(type=Integer.class, name="${PREFIX}:FCNT")
-	private Channel<Integer> fileCount;
-	
-	@CaChannel(type=Integer.class, name="${PREFIX}:FCNT.B")
-	private Channel<Integer> resetFileCounter;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:FAPPE")
-	private Channel<Boolean> appendFile;
-
-	@CaChannel(type=Boolean.class, name="${PREFIX}:FUSE")
-	private Channel<Boolean> fileNameGeneration;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:UZIGZ")
-	private Channel<Boolean> zigZag;
-	
-	@CaChannel(type=Integer.class, name="${PREFIX}:UCOM")
-	private Channel<Integer> command;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:SCRU", monitor=true)
-	private Channel<Boolean> scanRunning;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:MUENC")
-	private Channel<Boolean> useEncoder;
-	
-	@CaChannel(type=String.class, name={"${PREFIX}:CTM0","${PREFIX}:CTM1","${PREFIX}:CTM2","${PREFIX}:CTM3","${PREFIX}:CTM4","${PREFIX}:CTM5","${PREFIX}:CTM6","${PREFIX}:CTM7"})
-	private List<Channel<String>> monitoredChannels;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:OTF", monitor=true)
-	private Channel<Boolean> running;
-	
-	@CaChannel(type=Integer.class, name="${PREFIX}:USTAT", monitor=true)
-	private Channel<Integer> status;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:MOK", monitor=true)
-	private Channel<Boolean> motorOk;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:EOK", monitor=true)
-	private Channel<Boolean> encoderOk;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:MSG")
-	private Channel<String> message;
-
-	/**
-	 * Get the trigger name that can be used by the sscan record to trigger an OTFScan
-	 * @return	Name of the trigger that can be used by sscan record
-	 */
-	public String getSScanTriggerName(){
-		return(running.getName());
-	}
-
-	/**
-	 * Start OTF scan
-	 */
-	public void start() {
-		try{
-		if(getStatus().equals(Status.INACTIVE)){
-			
-			// Send START command
-			this.command.setValue(Command.START.ordinal());
-			
-			// Wait until OtF logic is active
-			this.scanRunning.waitForValue(true, commandTimeout);
-		}
-		else{
-			throw new RuntimeException("Cannot start scan, status is not INACTIVE.\nThe current status is: "+getStatus()+" . The OTF logic need to be recovered manually [Message: "+getMessage()+"]");
-		}
-		}
-		catch(Exception e){
-			throw new RuntimeException("Unable to start OTF scan.",e);
-		}
-	}
-	
-	/**
-	 * Abort scan
-	 */
-	public void abort() {
-		try{
-			// Send STOP command
-			this.command.setValue(Command.STOP.ordinal());
-	
-			// Do not wait for put to return
-			this.running.setValueNoWait(false);
-		}
-		catch(Exception e){
-			throw new RuntimeException("Unable to abort OTF logic" ,e);
-		}
-	}
-	
-	/**
-	 * Stop OTF scan
-	 * @throws Exception
-	 */
-	public void stop() throws Exception{
-		if(!getStatus().equals(Status.INACTIVE) || !getStatus().equals(Status.FAULT)){
-			
-			// Send STOP command
-			this.command.setValue(Command.STOP.ordinal());
-
-			// Wait until logic is stopped
-			status.waitForValue(Status.INACTIVE.ordinal(), commandTimeout);
-		}
-		
-	}
-
-	/**
-	 * Wait until scan has stopped
-	 * @throws InterruptedException 
-	 */
-	public void waitUntilStopped() throws InterruptedException {
-		try {
-			scanRunning.waitForValue(false); // Use of default wait timeout
-			
-			// Check whether the status is INACTIVE otherwise get messge from OTF and throw an exception
-			if(status.getValue() != Status.INACTIVE.ordinal()){
-				throw new RuntimeException("OTFSCAN failed with message: "+message.getValue());
-			}
-			
-		} catch (ExecutionException | ChannelException | TimeoutException e) {
-			throw new RuntimeException("An error occurred while waiting for the OTF logic to finish.", e);
-		}
-	}
-	
-	/**
-	 * Wait until scan has stopped
-	 * @param waitTimeout
-	 * @throws InterruptedException 
-	 */
-	public void waitUntilStopped(Long waitTimeout) throws InterruptedException {
-		try {
-			scanRunning.waitForValue(false, waitTimeout);
-			
-			// Check whether the status is INACTIVE otherwise get messge from OTF and throw an exception
-			if(status.getValue() != Status.INACTIVE.ordinal()){
-				throw new RuntimeException("OTFSCAN failed with message: "+message.getValue());
-			}
-			
-		} catch (ExecutionException | ChannelException | TimeoutException e) {
-			throw new RuntimeException("An error occurred while waiting for the OTF logic to finish.", e);
-		}
-		
-		
-		
-	}
-	
-	/**
-	 * Reset OTFScan records to defaults
-	 * @throws CAException
-	 * @throws InterruptedException 
-	 */
-	public void resetToDefaults() throws InterruptedException{
-		try{
-		setMonitoredChannels(new String[]{});
-		setMotor("");
-		begin.setValue(0d);
-		end.setValue(0d);
-		stepSize.setValue(0d);
-		integrationTime.setValue(0d);
-		zigZag.setValue(false);
-		setAppendFile(false);
-		setFileNameGeneration(true);
-		setFileName("");
-		setFileNameFormat("%06d.txt");
-		resetFileCounter();
-		
-		setUserBacklash(0d);
-		
-//		setNfsServer("");
-//		setNfsShare("");
-		
-		waitUntilMotorNotOk(timeoutMotorOk);
-		}
-		catch(ExecutionException | ChannelException e){
-			throw new RuntimeException(e);
-		}
-	}
-
-	/**
-	 * Get motor of the OTFScan axis
-	 * @return	Name of the OTF motor
-	 * @throws CAException
-	 */
-	public String getMotor() throws InterruptedException {
-		try {
-			return(this.motor.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set motor of the OTFScan axis
-	 * @param motor
-	 * @throws CAException
-	 */
-	public void setMotor(String motor) throws InterruptedException {
-		try{
-			this.motor.setValue(motor);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get encoder of the OTFScan axis
-	 * @return	Name of the used encoder
-	 * @throws CAException
-	 */
-	public String getEncoder() throws InterruptedException {
-		try{
-			return(this.encoder.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set encoder to use of the OTFScan axis
-	 * @param encoder
-	 * @throws CAException
-	 */
-	public void setEncoder(String encoder) throws InterruptedException {
-		try{
-			this.encoder.setValue(encoder);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get begin position of the scan
-	 * @return Begin position scan
-	 * @throws CAException
-	 */
-	public Double getBegin() throws InterruptedException {
-		try{
-			return(this.begin.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set begin position of scan
-	 * @param begin
-	 * @throws Exception
-	 */
-	public void setBegin(Double begin) throws InterruptedException {
-		try{
-			if(begin==null){
-				throw new IllegalArgumentException("Begin position must not be null");
-			}
-			
-			if(begin < beginMin.getValue() || begin > beginMax.getValue()){
-				throw new IllegalArgumentException("Cannot set begin value to "+begin+ ". Value is outside range [min: "+beginMin.getValue()+" max: "+beginMax.getValue()+"]");
-			}
-			
-			this.begin.setValue(begin);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get minimum value of the begin position
-	 * @return	Min value for begin
-	 * @throws CAException
-	 */
-	public Double getMinBegin() throws InterruptedException {
-		try{
-			return(this.beginMin.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get maximum value of the begin position
-	 * @return	Max value for begin
-	 * @throws CAException
-	 */
-	public Double getMaxBegin() throws InterruptedException {
-		try{
-			return(this.beginMax.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get end position of the scan
-	 * @return End position scan
-	 * @throws CAException
-	 */
-	public Double getEnd() throws InterruptedException {
-		try{
-			return(this.end.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set end positon of scan
-	 * @param end
-	 * @throws CAException
-	 */
-	public void setEnd(Double end) throws InterruptedException {
-		try{
-			if(end==null){
-				throw new IllegalArgumentException("End position must not be null");
-			}
-			
-			if(end < endMin.getValue() || end > endMax.getValue()){
-				throw new IllegalArgumentException("Cannot set end value to "+end+ ". Value is outside range [min: "+endMin.getValue()+" max: "+endMax.getValue()+"]");
-			}
-			
-			this.end.setValue(end);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get minimum value of end position
-	 * @return	Min value for end
-	 * @throws CAException
-	 */
-	public Double getMinEnd() throws InterruptedException {
-		try{
-			return(this.endMin.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	/**
-	 * Get maximum value of end position
-	 * @return 	Max value for end
-	 * @throws CAException
-	 */
-	public Double getMaxEnd() throws InterruptedException {
-		try{
-			return(this.endMax.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get scan step size
-	 * @return Step size
-	 * @throws CAException
-	 */
-	public Double getStepSize() throws InterruptedException {
-		try{
-			return(this.stepSize.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set step size of scan
-	 * @param stepSize
-	 * @throws CAException
-	 */
-	public void setStepSize(Double stepSize) throws InterruptedException {
-		try{
-			if(integrationTime==null){
-				throw new IllegalArgumentException("Step size must not be null");
-			}
-			
-			// Check if step size is greater than min step size
-			if(stepSizeMin.getValue() != 0 && stepSize < stepSizeMin.getValue()){
-				throw new IllegalArgumentException("Step size value ["+stepSize+"] is less than minimum step size ["+stepSizeMin.getValue()+"]!");
-			}
-			
-			this.stepSize.setValue(stepSize);
-	
-			// TODO WORKAROUND - Wait to "ensure" that step size related fields are updated (i.e. min/max integration time)
-			Thread.sleep(1);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get minimum integration time
-	 * @return	Min value for step size
-	 * @throws CAException
-	 */
-	public double getMinStepSize() throws InterruptedException {
-		try{
-			return(this.stepSizeMin.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get scan integration time (time that is spend in one step)
-	 * @return	Integration time
-	 * @throws CAException
-	 */
-	public Double getIntegrationTime() throws InterruptedException {
-		try{
-			return(this.integrationTime.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-	/**
-	 * Set integration time of scan
-	 * @param integrationTime
-	 * @throws CAException
-	 */
-	public void setIntegrationTime(Double integrationTime) throws InterruptedException {
-		try{
-		if(integrationTime==null){
-			throw new IllegalArgumentException("Integration time must not be null");
-		}
-		
-		// Check range (if limit is set to 0 then limit is not set)
-		double min = integrationTimeMin.getValue();
-		double max = integrationTimeMax.getValue();
-		if(min!= 0 && max!= 0){
-			if(integrationTime < min || integrationTime > max){
-				throw new IllegalArgumentException("Integration time ["+integrationTime+"] is outside range [min: "+min+" max: "+max+"]");
-			}
-		}
-		else {
-			if(min!= 0 && integrationTime<min){
-				throw new IllegalArgumentException("Integration time ["+integrationTime+"] is outside range [min: "+min+" max: - ]");
-			}
-			else if(max!= 0 && integrationTime>max){
-				throw new IllegalArgumentException("Integration time ["+integrationTime+"] is outside range [min: -  max: "+max+"]");
-			}
-		}
-		
-		this.integrationTime.setValue(integrationTime);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get minimum integration time
-	 * @return	Min value for integration time
-	 * @throws CAException
-	 */
-	public Double getMinIntegrationTime() throws InterruptedException {
-		try{
-		return(this.integrationTimeMin.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	/**
-	 * Get maximum integration time
-	 * @return	Max value for integration time
-	 * @throws CAException
-	 */
-	public Double getMaxIntegrationTime() throws InterruptedException {
-		try{
-		return(this.integrationTimeMax.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get additional user defined backlash
-	 * @return	User backlash
-	 * @throws CAException 
-	 */
-	public Double getUserBacklash() throws InterruptedException {
-		try{
-		return(this.userBacklash.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-	/**
-	 * Set additional user defined backlash
-	 * @param userBacklash
-	 * @throws CAException
-	 */
-	public void setUserBacklash(Double userBacklash) throws InterruptedException {
-		try{
-			if(userBacklash==null){
-				throw new IllegalArgumentException("User backlash must not be null");
-			}
-			
-			this.userBacklash.setValue(userBacklash);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get the current NFS server the data is written to
-	 * @return	Name of NFS server
-	 * @throws CAException
-	 */
-	public String getNfsServer() throws InterruptedException {
-		try{
-		return(this.nfsServer.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set name of the NFS server the data is written to
-	 * @param nfsServer
-	 * @throws CAException
-	 */
-	public void setNfsServer(String nfsServer) throws InterruptedException {
-		try{
-		this.nfsServer.setValue(nfsServer);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get the NFS share the data is written to
-	 * @return	Name of NFS share
-	 * @throws CAException
-	 */
-	public String getNfsShare() throws InterruptedException {
-		try{
-			return(this.nfsShare.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set name of the NFS share the data is written to
-	 * @param nfsShare
-	 * @throws CAException
-	 */
-	public void setNfsShare(String nfsShare) throws InterruptedException {
-		try{
-			this.nfsShare.setValue(nfsShare);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get the name of the data file
-	 * @return	Name of data file name
-	 * @throws CAException
-	 */
-	public String getFileName() throws InterruptedException {
-		try{
-		return(this.fileName.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-	/**
-	 * Set name of the data file
-	 * @param filename
-	 * @throws CAException
-	 */
-	public void setFileName(String filename) throws InterruptedException {
-		try{
-			this.fileName.setValue(filename);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get File name formate
-	 * @return	Get format for file name
-	 * @throws CAException
-	 */
-	public String getFileNameFormat() throws InterruptedException {
-		try{
-			return(this.fileNameFormat.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set file name formate of the data file
-	 * @param fileNameFormat
-	 * @throws Exception
-	 */
-	public void setFileNameFormat(String fileNameFormat) throws InterruptedException {
-		try{
-			this.fileNameFormat.setValue(fileNameFormat);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get value of the IOC based file name counter
-	 * @return	File counter
-	 * @throws CAException
-	 */
-	public int getFileCounter() throws InterruptedException {
-		try{
-		return(this.fileCount.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Reset the IOC based file counter
-	 * @throws CAException
-	 */
-	public void resetFileCounter() throws InterruptedException {
-		try{
-		this.resetFileCounter.setValue(1);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get if append file option is activated
-	 * @return	Append file flag
-	 * @throws CAException
-	 */
-	public boolean isAppendFile() throws InterruptedException {
-		try{
-		return(this.appendFile.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set whether to append the specified file if the file exists
-	 * @param append
-	 * @throws CAException
-	 */
-	public void setAppendFile(boolean append) throws InterruptedException {
-		try{
-		this.appendFile.setValue(append);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get if file name generation is on or off
-	 * @return	File name generation flag
-	 * @throws CAException
-	 */
-	public boolean isFileNameGeneration() throws InterruptedException {
-		try{
-		return(this.fileNameGeneration.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set Whether the file name should be generated out of the file name format and the file counter
-	 * @param generation
-	 * @throws CAException
-	 */
-	public void setFileNameGeneration(boolean generation) throws InterruptedException {
-		try{
-			this.fileNameGeneration.setValue(generation);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get if ZigZag scan option is on or off
-	 * @return	ZigZag flag
-	 * @throws CAException
-	 */
-	public boolean isZigZag() throws InterruptedException {
-		try{
-			return(this.zigZag.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set ZigZag scan mode on/off
-	 * @param zigZag	ZigZag mode on = true, ZigZag mode off = false
-	 * @throws CAException
-	 */
-	public void setZigZag(boolean zigZag) throws InterruptedException {
-		try{
-			this.zigZag.setValue(zigZag);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get whether encoder is used
-	 */
-	public boolean isUseEncoder() throws InterruptedException {
-		try{
-			return(this.useEncoder.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set flag to use encoder
-	 * @throws CAException
-	 */
-	public void setUseEncoder(boolean flag) throws InterruptedException {
-		try{
-		this.useEncoder.setValue(flag);
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get the channels that are currently monitored by the OTFScan logic
-	 * @return	Names of the monitored channels
-	 * @throws CAException
-	 */
-	public String[] getMonitoredChannels() throws InterruptedException {
-		try{
-			String[] values = new String[this.monitoredChannels.size()];
-			
-			for(int i=0; i<this.monitoredChannels.size();i++){
-				values[i] = monitoredChannels.get(i).getValue();
-			}
-			
-			return(values);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Set the channels that need to be monitored.
-	 * Note: As OTF only supports 8 channels to be monitored, only the first 8 
-	 * values of the passed channelNames are considered.
-	 * @param values	Array of channel names to be monitored
-	 * @throws CAException
-	 */
-	public void setMonitoredChannels(String[] values) throws InterruptedException {
-		
-		try{
-			if(values.length>monitoredChannels.size()){
-				throw new IllegalArgumentException("Only up to "+monitoredChannels.size()+" monitored channels are supported by OTF");
-			}
-			
-			for(int i=0; i<this.monitoredChannels.size(); i++){
-				if(values != null && i<values.length){
-					this.monitoredChannels.get(i).setValue(values[i]);
-				}
-				else{
-					this.monitoredChannels.get(i).setValue("");
-				}
-			}
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Returns whether an scan is running
-	 * @return	Running flag
-	 * @throws CAException 
-	 */
-	public boolean isRunning() throws InterruptedException {
-		try{
-			return(running.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get status of the scan
-	 * @return Status of the scan
-	 * @throws CAException 
-	 */
-	public Status getStatus() throws InterruptedException {
-		try{
-			return(Status.values()[this.status.getValue()]);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Get the (error) message from the OTF records
-	 * @return	Message from OTF C logic
-	 * @throws CAException
-	 */
-	public String getMessage() throws InterruptedException {
-		try{
-			return(message.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Check whether the specified motor is recognized as ok (i.e. it is registered as OTFScan motor)
-	 * @return	Flag whether motor is ok
-	 * @throws CAException 
-	 */
-	public boolean isMotorOk() throws InterruptedException {
-		try{
-			return(motorOk.getValue());
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Wait until the motor flag goes to ok
-	 * @param timeout	Timout in milliseconds
-	 * 
-	 * @throws CAException	If motor ok flag does not switch to ok within the specified timeout
-	 */
-	public void waitUntilMotorOk(long timeout) throws InterruptedException {
-		try{
-		motorOk.waitForValue(true, timeout);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Wait until the motor flag goes to not ok
-	 * @param timeout	Timout in milliseconds
-	 * 
-	 * @throws CAException	If motor ok flag does not switch to ok within the specified timeout
-	 */
-	public void waitUntilMotorNotOk(long timeout) throws InterruptedException {
-		try{
-		motorOk.waitForValue(false, timeout);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	
-	public void waitUntilEncoderOk(long timeout) throws InterruptedException {
-		try{
-		if(!useEncoder.getValue()){
-			return;
-		}
-		encoderOk.waitForValue(true, timeout);
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/manipulator/JythonManipulation.java

@@ -1,283 +0,0 @@
-/**
- * 
- * 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.core.manipulator;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.script.ScriptEngine;
-import javax.script.ScriptEngineManager;
-import javax.script.ScriptException;
-
-import ch.psi.fda.core.Manipulation;
-import ch.psi.fda.core.scripting.JythonParameterMapping;
-import ch.psi.fda.core.scripting.JythonParameterMappingChannel;
-import ch.psi.fda.core.scripting.JythonParameterMappingGlobalVariable;
-import ch.psi.fda.core.scripting.JythonParameterMappingID;
-import ch.psi.fda.messages.DataMessage;
-import ch.psi.fda.messages.Metadata;
-
-public class JythonManipulation implements Manipulation{
-
-	private static Logger logger = Logger.getLogger(JythonManipulation.class.getName());
-	
-	/**
-	 * Pattern of the entry function of the jython script
-	 */
-	private static final String entryFunction = "process";
-	private static final String entryFunctionPattern = "def "+entryFunction+"\\((.*)\\):";
-	
-	/**
-	 * Code of the manipulation. The script need to implement a function of the type:
-	 * <code>
-	 * def process():
-	 *     # ... your code
-	 *     return value
-	 * </code>
-	 * 
-	 * The number of parameters of the script are not limited. So <code>process(a)</code> is valid
-	 * as well as <code>process(a,b,c,d,e,f)</code>.
-	 * However for each parameter there need to be a mapping inside the mapping list! If there is no
-	 * mapping inside the Manipulator evaluating this Manipulation will throw an Exception.
-	 */
-	private final String script;
-	
-	/**
-	 * Id of the resulting component
-	 */
-	private final String id;
-	
-	/**
-	 * Mapping of components to manipulation code variables
-	 */
-	private final List<JythonParameterMapping> mapping;
-
-	private final boolean returnArray;
-	
-	/**
-	 * Script engine of the manipulator
-	 */
-	private ScriptEngine engine;
-	/**
-	 * Component index of the script parameter. The sequence of the indexes in this array correspond to the script
-	 * parameter position, i.e. the first index corresponds to the first parameter.
-	 */
-//	private Integer[] parameterIndex;
-	private List<String> parameterIds = new ArrayList<>();
-	/**
-	 * Parameter array of the entry function
-	 */
-	private String[] parameter;
-	
-	/**
-	 * Jython entry call
-	 */
-	private String jythonCall;
-	
-	
-	private Map<String,Object> gvariables = new HashMap<String,Object>();
-	
-	
-	public JythonManipulation(String id, String script, List<JythonParameterMapping> mapping){
-		this(id, script, mapping, false);
-	}
-	
-	/**
-	 * Constructor
-	 * @param id
-	 * @param script
-	 * @param mapping
-	 */
-	public JythonManipulation(String id, String script, List<JythonParameterMapping> mapping, boolean returnArray){
-		this.id = id;
-		this.script = script;
-		this.mapping = mapping;
-		this.returnArray = returnArray;
-	}
-	
-	/**
-	 * @return the script
-	 */
-	public String getScript() {
-		return script;
-	}
-
-	/**
-	 * @return the mapping
-	 */
-	public List<JythonParameterMapping> getMapping() {
-		return mapping;
-	}
-
-
-	@Override
-	public String getId() {
-		return id;
-	}
-	
-
-	@Override
-	public void initialize(List<Metadata> metadata){
-		
-		// Workaround for Jython memory leak 
-		// http://blog.hillbrecht.de/2009/07/11/jython-memory-leakout-of-memory-problem/
-		System.setProperty("python.options.internalTablesImpl","weak");
-		
-		// Create new script engine
-		this.engine = new ScriptEngineManager().getEngineByName("python");
-		
-		// Determine script entry function and the function parameters
-		Pattern pattern = Pattern.compile(entryFunctionPattern);
-		Matcher matcher = pattern.matcher(this.script);
-		if(matcher.find() && matcher.groupCount()==1){
-			if(!matcher.group(1).trim().equals("")){
-				logger.finest("Entry function '"+entryFunctionPattern+"' found - Identified parameters: "+matcher.group(1));
-				parameter = matcher.group(1).split(" *, *");
-			}
-			else{
-				parameter = new String[0];
-			}
-		}
-		else{
-			throw new IllegalArgumentException("Cannot determine entry function: "+entryFunctionPattern);
-		}
-		
-		// Load manipulation script
-		try {
-			engine.eval(this.script);
-		} catch (ScriptException e) {
-			throw new RuntimeException("Unable to load manipulation script", e);
-		}
-		
-		// Determine component index of the needed parameters
-		// If the component index of the parameter cannot be determined an IllegalArgumentException is thrown
-//		parameterIndex = new Integer[parameter.length];
-		parameterIds = new ArrayList<>();
-		for(int i=0;i<parameter.length; i++){
-			String p = parameter[i];
-			p = p.trim();
-			boolean found = false;
-			
-			for(JythonParameterMapping jpm: this.mapping){
-				if(jpm.getVariable().equals(p)){
-					if(jpm instanceof JythonParameterMappingID){
-						JythonParameterMappingID pm = (JythonParameterMappingID)jpm;
-						// Mapping for parameter found, determine index of the corresponding component
-//						parameterIndex[i] = metadata.getIndex(pm.getRefid());
-						parameterIds.add(pm.getRefid());
-					}
-					else if (jpm instanceof JythonParameterMappingChannel){
-						JythonParameterMappingChannel<?> pm = (JythonParameterMappingChannel<?>) jpm;
-//						parameterIndex[i] = null;
-						parameterIds.add(null);
-						engine.put(pm.getVariable(), pm.getChannel());
-					}
-					else if (jpm instanceof JythonParameterMappingGlobalVariable){
-						JythonParameterMappingGlobalVariable pm = (JythonParameterMappingGlobalVariable)jpm;
-						parameterIds.add(null);
-//						parameterIndex[i] = null;
-						
-						engine.put(pm.getVariable(), pm.getGlobalVariable());
-					}
-					found=true;
-					break;
-				}
-			}
-			// If there is no mapping nothing can be found
-			// If there are mappings everything need to be found
-			if(!found){
-				throw new IllegalArgumentException("No mapping compontent found for parameter "+p);
-			}
-		}
-		
-		StringBuffer buffer = new StringBuffer();
-		buffer.append(entryFunction);
-		buffer.append("(");
-		
-		for(String p: parameter){
-			buffer.append(p);
-			buffer.append(",");
-		}
-		
-		buffer.setCharAt(buffer.length()-1, ')');
-		
-		jythonCall = buffer.toString();
-	}
-	
-	@Override
-	public Object execute(DataMessage message){
-		
-		// Set global variables - WORKAROUND gvariables
-		// This block is not in initialization as we want to assure that all invocations
-		// of this manipulation will get the same value (i.e. to prevent inconsistent behaviour
-		// if variable was changed during an execution of the manipulation)
-		for(String k: gvariables.keySet()){
-			engine.put(k, gvariables.get(k));
-		}
-		
-		// Manipulate data
-		for(int i=0;i<parameterIds.size();i++){
-			if(parameterIds.get(i) != null){
-				engine.put(parameter[i], message.getData(parameterIds.get(i)));
-			}
-		}
-		
-		try {
-			if(returnArray){
-				return((double[]) engine.eval(jythonCall));
-			}
-			else{
-				// Due to the typeless nature of Python an Integer of Float/Double might be returned from the 
-				// Python code (e.g. depending on the factors in a calculation)
-				// Always return the return value to a double. If this cannot be done return NaN
-				Object r = engine.eval(jythonCall);
-				if(r instanceof Double){
-					return((Double) r);
-				}
-				else if( r instanceof Integer){
-					return(((Integer)r).doubleValue());
-				}
-				else{
-//					return Double.NaN;
-					return r;
-				}
-			}
-		} catch (ScriptException e) {
-//			throw new RuntimeException("Data manipulaton [id: "+id+"] failed while executing the manipulation script",e);
-			logger.log(Level.WARNING, "Data manipulaton [id: "+id+"] failed while executing the manipulation script");
-			return Double.NaN;
-		}
-	}
-	
-	/**
-	 * Workaround to put variables into the jython engine.
-	 * @param name
-	 * @param value
-	 */
-	public void setVariable(String name, Object value){
-		gvariables.put(name, value);
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/scripting/JythonGlobalVariable.java

@@ -1,55 +0,0 @@
-/**
- * 
- * 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.core.scripting;
-
-/**
- * @author ebner
- *
- */
-public class JythonGlobalVariable {
-	private String name;
-	private double value;
-	
-	/**
-	 * @return the name
-	 */
-	public String getName() {
-		return name;
-	}
-	/**
-	 * @param name the name to set
-	 */
-	public void setName(String name) {
-		this.name = name;
-	}
-	/**
-	 * @return the value
-	 */
-	public double getValue() {
-		return value;
-	}
-	/**
-	 * @param value the value to set
-	 */
-	public void setValue(double value) {
-		this.value = value;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/scripting/JythonParameterMapping.java

@@ -1,55 +0,0 @@
-/**
- * 
- * 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.core.scripting;
-
-/**
- * Mapping of a parameter to something
- * @author ebner
- *
- */
-public abstract class JythonParameterMapping {
-
-	/**
-	 * Variable name inside the script
-	 */
-	private String variable;
-	
-	/**
-	 * Constructor
-	 * @param variable
-	 */
-	public JythonParameterMapping(String variable){
-		this.variable = variable;
-	}
-	
-	/**
-	 * @return the variable
-	 */
-	public String getVariable() {
-		return variable;
-	}
-	/**
-	 * @param variable the variable to set
-	 */
-	public void setVariable(String variable) {
-		this.variable = variable;
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/scripting/JythonParameterMappingChannel.java

@@ -1,42 +0,0 @@
-/**
- * 
- * 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.core.scripting;
-
-import ch.psi.jcae.Channel;
-
-
-/**
- * Mapping of a script parameter to a channel bean.
- * @author ebner
- *
- */
-public class JythonParameterMappingChannel<T> extends JythonParameterMapping {
-	
-	private Channel<T> channel;
-	
-	public JythonParameterMappingChannel(String variable, Channel<T> channel){
-		super(variable);
-		this.channel = channel;
-	}
-	
-	public Channel<T> getChannel() {
-		return channel;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/scripting/JythonParameterMappingGlobalVariable.java

@@ -1,56 +0,0 @@
-/**
- * 
- * 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.core.scripting;
-
-
-/**
- * Mapping of a script parameter to a component via the Id.
- * @author ebner
- *
- */
-public class JythonParameterMappingGlobalVariable extends JythonParameterMapping {
-	
-	private JythonGlobalVariable globalVariable;
-		
-	/**
-	 * Constuctor
-	 * @param variable
-	 * @param globalVariable
-	 */
-	public JythonParameterMappingGlobalVariable(String variable, JythonGlobalVariable globalVariable){
-		super(variable);
-		this.globalVariable = globalVariable;
-	}
-
-	/**
-	 * @return the globalVariable
-	 */
-	public JythonGlobalVariable getGlobalVariable() {
-		return globalVariable;
-	}
-
-	/**
-	 * @param globalVariable the globalVariable to set
-	 */
-	public void setGlobalVariable(JythonGlobalVariable globalVariable) {
-		this.globalVariable = globalVariable;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/scripting/JythonParameterMappingID.java

@@ -1,58 +0,0 @@
-/**
- * 
- * 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.core.scripting;
-
-
-/**
- * Mapping of a script parameter to a component via the Id.
- * @author ebner
- *
- */
-public class JythonParameterMappingID extends JythonParameterMapping {
-	
-	/**
-	 * Id of the component to map to this variable
-	 */
-	private String refid;
-		
-	/**
-	 * Constructor accepting varible/id pair
-	 * @param variable
-	 * @param refid
-	 */
-	public JythonParameterMappingID(String variable, String refid){
-		super(variable);
-		this.refid = refid;
-	}
-	
-	/**
-	 * @return the refid
-	 */
-	public String getRefid() {
-		return refid;
-	}
-	/**
-	 * @param refid the refid to set
-	 */
-	public void setRefid(String refid) {
-		this.refid = refid;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/sensors/ChannelAccessSensor.java

@@ -1,72 +0,0 @@
-/**
- * 
- * 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.core.sensors;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Sensor;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-
-/**
- * Channel Access sensor capable of reading a channel access channel
- */
-public class ChannelAccessSensor<T> implements Sensor {
-
-	private static Logger logger = Logger.getLogger(ChannelAccessSensor.class.getName());
-	
-	private Channel<T> channel;
-	private final String id;
-	private boolean failOnSensorError = true;
-	
-	public ChannelAccessSensor(String id, Channel<T> channel){
-		this.id = id;
-		this.channel = channel;
-	}
-	
-	public ChannelAccessSensor(String id, Channel<T> channel, boolean failOnSensorError){
-		this.id = id;
-		this.channel = channel;
-		this.failOnSensorError = failOnSensorError;
-	}
-	
-	@Override
-	public Object read() throws InterruptedException {
-		logger.finest("Read sensor "+channel.getName());
-		
-		T v;
-		try {
-			v = channel.getValue();
-		} catch (TimeoutException | ChannelException | ExecutionException e) {
-			if(failOnSensorError){
-				throw new RuntimeException("Unable to get value from channel [name:"+channel.getName()+"]",e);
-			}
-			v = null;
-		}
-		return(v);
-	}
-
-	@Override
-	public String getId() {
-		return id;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/sensors/ComplexSensor.java

@@ -1,56 +0,0 @@
-package ch.psi.fda.core.sensors;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.Sensor;
-/**
- * Complex sensor that complements an other sensor with pre and post actions.
- * Before reading out the complemented sensor the pre actions are executed. After the
- * readout the post actions.
- */
-public class ComplexSensor implements Sensor {
-
-	private static Logger logger = Logger.getLogger(ComplexSensor.class.getName());
-	
-	private String id;
-	private final Sensor sensor;
-	private final List<Action> preActions;
-	private final List<Action> postActions;
-
-	public ComplexSensor(String id, Sensor sensor){
-		this.id = id;
-		this.sensor = sensor;
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-	}
-
-	@Override
-	public Object read() throws InterruptedException {
-		logger.finest("Execute pre actions");
-		for(Action action: preActions){
-			action.execute();
-		}
-		
-		Object value = sensor.read();
-		
-		logger.finest("Execute post actions");
-		for(Action action: postActions){
-			action.execute();
-		}
-		
-		return value;
-	}
-
-	@Override
-	public String getId() {
-		return id;
-	}
-
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/sensors/TimestampSensor.java

@@ -1,46 +0,0 @@
-/**
- * 
- * 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.core.sensors;
-
-import ch.psi.fda.core.Sensor;
-
-/**
- * Sensor to read the current time in milliseconds
- */
-public class TimestampSensor implements Sensor {
-
-	private final String id; // Global id of the sensor
-	
-	public TimestampSensor(String id){
-		this.id = id;
-	}
-	
-	@Override
-	public Object read() {
-		// Return current time in milliseconds
-		return new Double(System.currentTimeMillis());
-	}
-
-	@Override
-	public String getId() {
-		return id;
-	}
-
-}

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

@@ -453,11 +453,6 @@ public class DataDeserializerMDA implements DataDeserializer {
 	}
 }
 
-/**
- * Helper class
- * @author ebner
- *
- */
 class RecursiveReturnContainer{
 	private List<Message> message = new ArrayList<Message>();
 	private List<Metadata> metadata = new ArrayList<>();

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

@@ -48,10 +48,6 @@ public class DataDeserializerTXT implements DataDeserializer {
 	private List<Integer> dindex;
 	private List<Integer> iindex;
 	
-	/**
-	 * Default Constructor
-	 * @param file
-	 */
 	public DataDeserializerTXT(EventBus b, File file){
 		this.bus = b;
 		this.file = file;

ch.psi.fda/src/main/java/ch/psi/fda/model/ModelManager.java

@@ -1,100 +0,0 @@
-/**
- * 
- * 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.model;
-
-import java.io.File;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.UnmarshalException;
-import javax.xml.bind.Unmarshaller;
-import javax.xml.namespace.QName;
-import javax.xml.transform.Source;
-import javax.xml.transform.stream.StreamSource;
-import javax.xml.validation.Schema;
-import javax.xml.validation.SchemaFactory;
-
-import org.xml.sax.SAXException;
-import org.xml.sax.SAXParseException;
-
-import ch.psi.fda.model.v1.Configuration;
-
-/**
- * Manage the serialization and deserialization of the FDA data model
- */
-public class ModelManager {
-
-	/**
-	 * De-serialize an instance of the FDA data model
-	 * 
-	 * @param file	File to deserialize
-	 * @throws JAXBException	Something went wrong while unmarshalling
-	 * @throws SAXException		Cannot read model schema file
-	 */
-	public static Configuration unmarshall(File file) throws JAXBException, SAXException {
-
-		JAXBContext context = JAXBContext.newInstance(Configuration.class);
-		Unmarshaller u = context.createUnmarshaller();
-
-		// Validation
-		SchemaFactory sf = SchemaFactory.newInstance(javax.xml.XMLConstants.W3C_XML_SCHEMA_NS_URI);
-		Source s = new StreamSource(Configuration.class.getResourceAsStream("/model-v1.xsd"));
-		Schema schema = sf.newSchema(new Source[]{s}); // Use schema reference provided in XML
-		u.setSchema(schema);
-		
-		try{
-			Configuration model = (Configuration) u.unmarshal(new StreamSource(file), Configuration.class).getValue();
-			return (model);
-		}
-		catch(UnmarshalException e){
-			// Check 
-			if(e.getLinkedException() instanceof SAXParseException){
-				throw new RuntimeException("Configuration file does not comply to required model specification\nCause: "+e.getLinkedException().getMessage(), e);
-			}
-			throw e;
-		}
-	}
-	
-	/**
-	 * Serialize an instance of the FDA data model
-	 * 
-	 * @param model				Model datastructure
-	 * @param file				File to write the model data into
-	 * @throws JAXBException	Something went wrong while marshalling model
-	 * @throws SAXException		Cannot read model schema files
-	 */
-	public static void marshall(Configuration model, File file) throws JAXBException, SAXException{
-		QName qname = new QName("http://www.psi.ch/~ebner/models/scan/1.0", "configuration");
-		
-		JAXBContext context = JAXBContext.newInstance(Configuration.class);
-		Marshaller m = context.createMarshaller();
-		m.setProperty("jaxb.formatted.output", true);
-		
-		// Validation
-		SchemaFactory sf = SchemaFactory.newInstance(javax.xml.XMLConstants.W3C_XML_SCHEMA_NS_URI);
-		Source s = new StreamSource(Configuration.class.getResourceAsStream("/model-v1.xsd"));
-		Schema schema = sf.newSchema(new Source[]{s}); // Use schema reference provided in XML
-		m.setSchema(schema);
-		
-		m.marshal( new JAXBElement<Configuration>(qname, Configuration.class, model ), file);
-	}
-}

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

@@ -1,80 +0,0 @@
-/**
- * 
- * 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.logging.Logger;
-
-import ch.psi.fda.aq.Acquisition;
-import ch.psi.fda.aq.AcquisitionConfiguration;
-import ch.psi.fda.model.v1.Configuration;
-import ch.psi.jcae.ChannelService;
-
-import com.google.common.eventbus.EventBus;
-
-public class AcquisitionJob implements Runnable {
-
-	private static final Logger logger = Logger.getLogger(AcquisitionJob.class.getName());
-
-	private final AcquisitionConfiguration config;
-	private final ChannelService cService;
-	private final ZMQDataService zmqService;
-
-	private final String trackingId;
-	private final Configuration configuration;
-
-	public AcquisitionJob(ChannelService cService, ZMQDataService zmqService, AcquisitionConfiguration config, String trackingId, Configuration configuration) {
-		this.zmqService = zmqService;
-		this.cService = cService;
-		this.config = config;
-
-		this.trackingId = trackingId;
-		this.configuration = configuration;
-	}
-
-	@Override
-	public void run() {
-
-		Acquisition acquisition = null;
-		try {
-
-			logger.info("Execute - " + trackingId);
-
-			EventBus ebus = new EventBus();
-			zmqService.setTrackingId(trackingId);
-			ebus.register(zmqService);
-
-			// Post visualization configuration
-			ebus.post(configuration.getVisualization());
-			
-			acquisition = new Acquisition(cService, config);
-			acquisition.initalize(ebus, configuration);
-			acquisition.execute();
-			logger.info("" + trackingId + " done");
-
-			// Cleanup
-			ebus.unregister(zmqService);
-		} catch (InterruptedException e) {
-			logger.info("Execution of "+trackingId+ " was interrupted");
-		} finally {
-			if(acquisition!=null){
-				acquisition.destroy();
-			}
-		}
-	}
-}

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

@@ -1,99 +0,0 @@
-/**
- * 
- * 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.io.File;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
-import javax.inject.Inject;
-
-import ch.psi.fda.cdump.Cdump;
-import ch.psi.fda.cdump.CdumpConfiguration;
-import ch.psi.fda.rest.model.CdumpRequest;
-import ch.psi.fda.serializer.SerializerTXT;
-import ch.psi.jcae.ChannelService;
-
-import com.google.common.eventbus.AsyncEventBus;
-import com.google.common.eventbus.EventBus;
-
-public class CdumpEngine {
-
-	private Cdump cdump;
-	private EventBus bus;
-	
-	private ZMQDataService zmqService;
-	private ChannelService cservice;
-	private CdumpConfiguration configuration;
-	
-	private boolean stream = false;
-	
-	private ExecutorService eservice;
-	
-	
-	@Inject
-	public CdumpEngine(ChannelService cservice, ZMQDataService zmqService, CdumpConfiguration configuration){
-		this.cservice = cservice;
-		this.zmqService = zmqService;
-		this.configuration = configuration;
-		
-		eservice = Executors.newSingleThreadExecutor();
-	}
-	
-	
-	public void acquire(String trackingId, final CdumpRequest request){
-		if(cdump!=null){
-			throw new IllegalStateException("Cdump is already running");
-		}
-		
-		bus = new AsyncEventBus(Executors.newSingleThreadExecutor());
-		cdump = new Cdump(cservice,bus,configuration);
-
-		SerializerTXT serializer = new SerializerTXT(new File(request.getFilename()));
-		serializer.setShowDimensionHeader(false);
-		bus.register(serializer);
-		
-		stream = (request.getStream()!=null && request.getStream().getIds().length>0) ;
-		if(stream){
-			// Stream data via ZMQ
-			zmqService.setTrackingId(trackingId);
-			// TODO set id filter !!!
-			bus.register(zmqService);
-		}
-		
-		eservice.execute(new Runnable() {
-			@Override
-			public void run() {
-				cdump.acquire(request.getSamplingRate());
-			}
-		});
-	}
-	
-	
-	public void stop(){
-		cdump.stop();
-		cdump = null;
-		bus.unregister(zmqService);
-	}
-	
-	
-	public boolean isActive(){
-		return cdump!=null;
-	}
-}

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

@@ -19,7 +19,9 @@
 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;
@@ -27,105 +29,124 @@ 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.aq.AcquisitionConfiguration;
-import ch.psi.fda.model.v1.Configuration;
+import ch.psi.fda.edescriptor.EDescriptor;
 import ch.psi.jcae.ChannelService;
 
 /**
  * Main engine for data acquisition.
  */
-public class AcquisitionEngine {
+public class ExecutionEngine {
+	
+	private static final Logger logger = Logger.getLogger(ExecutionEngine.class.getName());
 	
-	private final AcquisitionConfiguration config;
 	private final ChannelService cService;
 	private final ZMQDataService zmqService;
 	
 	private final ExecutorService eservice = Executors.newSingleThreadExecutor();
-	private final Map<String, Future<?>> erequests = new HashMap<>();
+	private final Map<String, JobEntry> erequests = new HashMap<>();
 	
 	@Inject
-	public AcquisitionEngine(ChannelService cService, ZMQDataService zmqService, AcquisitionConfiguration config) {
+	public ExecutionEngine(ChannelService cService, ZMQDataService zmqService) {
 		this.zmqService = zmqService;
 		this.cService = cService;
-		this.config = config;
 	}
 	
 	/**
 	 * Submit a scan to be executed. This will generate an execution request which is
 	 * enqueued in the execution queue.
 	 * 
-	 * @param configuration
-	 * @return
+	 * @param trackingId Tracking id
+	 * @param edescriptor	Edescriptor
 	 */
-	public void submit(String trackingId, Configuration configuration){
+	public void submit(String trackingId, EDescriptor edescriptor){
 
-		if(erequests.keySet().contains(trackingId) && !erequests.get(trackingId).isDone()){ // Allow finished tracking ids to be reused for new scans
+		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");
 		}
 		
-		AcquisitionJob job = new AcquisitionJob(cService, zmqService, config, trackingId, configuration);
+		ExecutionJob job = new ExecutionJob(cService, zmqService, trackingId, edescriptor);
 		Future<?> future = eservice.submit(job);
-		erequests.put(trackingId, future);
+		erequests.put(trackingId, new JobEntry(future, job));
 	}
 	
 	
 	public void terminateAll() {
-		for(Future<?> f: erequests.values()){
-			f.cancel(true);
-		}
-		
-		for(Future<?> f: erequests.values()){
+		logger.info("Terminate all jobs");
+		Set<String> keys = new HashSet<String>();
+		keys.addAll(erequests.keySet());
+		for(String trackingId: keys){
 			try{
-				f.get(10, TimeUnit.SECONDS);
+				terminate(trackingId);
 			}
-			catch(CancellationException | InterruptedException | ExecutionException | TimeoutException e){
-				// Nothing to be done here
+			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
+	 * is still in the execution queue it gets removed there.
+	 * 
+	 * @param trackingId	Tracking ID
 	 */
 	public void terminate(String trackingId){
+		logger.info("Terminate TrackingId: "+trackingId);
 		
-		final Future<?> f = erequests.get(trackingId);
-		if(f==null){
-			throw new IllegalArgumentException("There is no request running/pending with tracking id "+trackingId);
+		if(!erequests.containsKey(trackingId)){
+			throw new WebApplicationException("There is no request for tracking id "+trackingId, 404);
 		}
-		f.cancel(true);
+		
+		final JobEntry f = erequests.get(trackingId);
+		f.getFuture().cancel(true);
+		f.getJob().stop();
+		
+		
 		try{
-			f.get(10, TimeUnit.SECONDS);
+			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) {
-		Future<?> f = erequests.get(trackingId);
-		if(f==null){
+		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
-	 * @throws ExecutionException 
-	 * @throws InterruptedException 
+	 * @param trackingId Tracking ID
+	 * @throws ExecutionException -
+	 * @throws InterruptedException -
 	 */
 	public void wait(String trackingId) throws InterruptedException, ExecutionException{
-		Future<?> f = erequests.get(trackingId);
+		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");
 	}
 }

ch.psi.fda/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();
+		}
+	}
+}

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

@@ -1,43 +0,0 @@
-/**
- * 
- * 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 ch.psi.fda.model.v1.Configuration;
-
-/**
- * @author ebner
- *
- */
-public class ExecutionRequest {
-	
-	private final String trackingId;
-	private final Configuration configuration;
-	
-	public ExecutionRequest(String trackingId, Configuration configuration){
-		this.trackingId = trackingId;
-		this.configuration = configuration;
-	}
-
-	public String getTrackingId() {
-		return trackingId;
-	}
-	public Configuration getConfiguration() {
-		return configuration;
-	}
-}

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

@@ -17,8 +17,9 @@ 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.install.ApplicationConfigurator;
+import ch.psi.fda.ui.ApplicationConfigurator;
 import sun.misc.Signal;
 import sun.misc.SignalHandler;
 
@@ -66,20 +67,18 @@ public class FdaServer {
 		
 		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));
+		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 ...");
 
@@ -103,6 +102,11 @@ public class FdaServer {
 		
 		server.shutdownNow();
 		logger.info("Server terminated");
-		System.exit(0); // TODO need to shutdown ChannelService correctly !!!!
+		
+		// Destroy global resources
+		binder.destroy();
+		
+		// Using System.exit() to ensure that JVM is going down
+		System.exit(0);
 	}
 }

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

@@ -1,90 +0,0 @@
-/**
- * 
- * 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.io.File;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
-import javax.inject.Inject;
-
-import ch.psi.fda.fdaq.FdaqConfiguration;
-import ch.psi.fda.fdaq.FdaqService;
-import ch.psi.fda.rest.model.FdaqRequest;
-import ch.psi.fda.serializer.SerializerTXT;
-
-import com.google.common.eventbus.AsyncEventBus;
-import com.google.common.eventbus.EventBus;
-
-/**
- * 
- */
-public class FdaqEngine {
-
-	private FdaqService fdaq;
-	private EventBus bus;
-	private ZMQDataService zmqService;
-	private boolean stream = false;
-	
-	private ExecutorService eservice;
-	
-	@Inject
-	public FdaqEngine(ZMQDataService zmqService){
-		this.zmqService = zmqService;
-		
-		eservice = Executors.newSingleThreadExecutor();
-	}
-	
-	public void acquire(String trackingId, FdaqRequest request){
-		
-		if(fdaq!=null && fdaq.isRunning()){
-			throw new IllegalStateException("FDAQ is already running");
-		}
-		
-		bus = new AsyncEventBus(Executors.newSingleThreadExecutor());
-		fdaq = new FdaqService(bus, new FdaqConfiguration());
-
-		SerializerTXT serializer = new SerializerTXT(new File(request.getFilename()));
-		serializer.setShowDimensionHeader(false);
-		bus.register(serializer);
-		
-		stream = (request.getStream()!=null && request.getStream().getIds().length>0) ;
-		if(stream){
-			// Stream data via ZMQ
-			zmqService.setTrackingId(trackingId);
-			// TODO Set id filter !!!!
-			bus.register(zmqService);
-		}
-		
-		
-		eservice.execute(new Runnable() {
-			@Override
-			public void run() {
-				fdaq.acquire();
-			}
-		});
-	}
-	
-	public void stop(){
-		fdaq.stop();
-		bus.unregister(zmqService);
-
-		// TODO check whether serializer also needs to be unregistered ...
-	}
-}

ch.psi.fda/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);
+	}
+	
+	
+
+}

ch.psi.fda/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;
+	}
+}

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

@@ -6,25 +6,29 @@ import javax.inject.Singleton;
 
 import org.glassfish.hk2.utilities.binding.AbstractBinder;
 
-import ch.psi.fda.aq.AcquisitionConfiguration;
-import ch.psi.fda.cdump.CdumpConfiguration;
 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(DefaultChannelService.class).to(ChannelService.class).in(Singleton.class);
-    	bind(AcquisitionConfiguration.class).to(AcquisitionConfiguration.class).in(Singleton.class);
-    	
-    	bind(AcquisitionEngine.class).to(AcquisitionEngine.class).in(Singleton.class);
-    	bind(FdaqEngine.class).to(FdaqEngine.class).in(Singleton.class);
-   
-    	// ZMQ data service singleton
-    	bind(new ZMQDataService(10000)).to(ZMQDataService.class);
-    	
-    	bind(CdumpEngine.class).to(CdumpEngine.class).in(Singleton.class);
-    	bind(CdumpConfiguration.class).to(CdumpConfiguration.class).in(Singleton.class);
+    	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();
     }
 }

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

@@ -21,20 +21,17 @@ package ch.psi.fda.rest;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.ObjectOutputStream;
-import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
 import org.jeromq.ZMQ;
 
 import ch.psi.fda.messages.Message;
-import ch.psi.fda.model.v1.Visualization;
 
 import com.google.common.eventbus.Subscribe;
 
 /**
- * @author ebner
- *
+ * Service to stream out messages via ZMQ
  */
 public class ZMQDataService {
 	
@@ -69,7 +66,7 @@ public class ZMQDataService {
 	
 	@Subscribe
 	public void onMessage(Message m) {
-		logger.fine(m.toString());
+//		logger.fine(m.toString());
 		socket.sendMore("{\"htype\": [\"fda-2.1\"], \"trackingId\":\"" + trackingId + "\"}");
 		try (
 				ByteArrayOutputStream b = new ByteArrayOutputStream(); 
@@ -82,20 +79,21 @@ public class ZMQDataService {
 		}
 	}
 	
-	@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);
-		}
-	}
+	// 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;

ch.psi.fda/src/main/java/ch/psi/fda/rest/model/CdumpRequest.java

@@ -1,48 +0,0 @@
-/**
- * 
- * 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.model;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-@XmlRootElement
-public class CdumpRequest {
-	private String filename;
-	private Stream stream;
-	
-	private String samplingRate;
-
-	public String getFilename() {
-		return filename;
-	}
-	public void setFilename(String filename) {
-		this.filename = filename;
-	}
-	public Stream getStream() {
-		return stream;
-	}
-	public void setStream(Stream stream) {
-		this.stream = stream;
-	}
-	public String getSamplingRate() {
-		return samplingRate;
-	}
-	public void setSamplingRate(String samplingRate) {
-		this.samplingRate = samplingRate;
-	}
-}