new version

-- however still lots of bugs in there !

.gitignore

@@ -0,0 +1,8 @@
+/bin
+/target
+/build
+.gradle
+.settings
+.project
+.classpath
+/schema/

Readme.md

@@ -0,0 +1,165 @@
+# Overview
+This package holds the core functionality of FDA.
+
+# Usage
+use -Djava.util.logging.config.file=logging.properties` to configure logging
+
+## Server
+
+The FDA server is started as follows:
+
+```
+./bin/server -h
+usage: fda
+ -h         Help
+ -p <arg>   Server port (default: 8080)
+ -s <arg>   Server address (default: localhost)
+```
+
+Start new scan:
+
+```
+curl -X PUT -d @scan1d.xml -H 'Content-Type:application/xml' http://localhost:8080/fda/scan
+```
+
+## Viewer
+
+```
+./bin/viewer -h
+usage: viewer
+ -h         Help
+ -p <arg>   Server port (default: 10000)
+ -s <arg>   Server address (default: localhost)
+ ```
+
+
+# Development
+When checking out the project from the repository there is the `target/generated-sources/xjc` folder missing.
+After checking out the project execute `mvn compile` to create the folder and the required classes.
+
+To build project use `mvn clean install`.
+
+To upload the latest version to the central artifact repository use `mvn clean deploy`.
+Create Zip file via `mvn clean compile assembly:assembly`
+
+To use the FDA libary in an other project (like the GUI project) use:
+
+```
+<dependency>
+    <groupId>ch.psi</groupId>
+    <artifactId>fda</artifactId>
+    <version>x.x.x</version>
+</dependency>
+```
+
+## REST
+FDA offers a rest service to execute scans. There are 3 distinct service for fda scan, fdaq and cdump.
+
+### FDA Service
+
+Submit scan
+
+```
+PUT fda/{trackingId}
+Content-Type: application/xml
+<configuration>
+...
+</configuration>
+
+204 - Success
+
+```
+
+Stop/cancel scan
+
+```
+DELETE fda/{trackingId}
+
+204 - Success
+```
+
+Stop all scans
+
+```
+DELETE fda
+
+204 - Success
+```
+
+Check if scan is running
+
+```
+GET fda/{trackingId}/running
+
+200 - true/false
+```
+
+Wait for scan done (blocks until scan is done)
+
+```
+GET fda/{trackingId}/done
+
+204 - Success
+```
+
+# Notes
+## Upgrade FDA 1.x to 2.x
+In existing fda.properties file the following property need to be added: `ch.psi.fda.aq.data.dir=../data`
+
+## Upgrade FDA 2.6.1
+There are 2 new properties for crlogic:
+
+```
+ch.psi.fda.aq.crlogic.ioc=X05LA-VME-ES2
+ch.psi.fda.aq.crlogic.prefix=X05LA-ES2-CRL
+```
+
+
+# FDAQ
+## Overview
+This software is used to readout the FDAQ box developed at X10SA.
+On The FDAQ box there are 2 socket servers, one for retrieving the data and one for resetting the socket
+server for data retrieval.
+
+The fdaq code provides exactly 2 functionalities. It can query on the data socket for data (need to specifying how many data point to read),
+and it can send a reset request on the reset channel.
+
+## Usage
+
+To acquire data into a file use:
+
+```
+java -jar ch.psi.fda.fdaq-<version>.jar <file>
+```
+
+You can terminate the acquisition with *CTRL+C*. If you submit 2 consequtive *CTRL+C* the program will terminate immediately (and data might be lost);
+
+
+
+This will take the default connections settings:
+
+  * Hostname: mchip015.psi.ch
+  * Port: 2233
+  * Kill Port: 2234
+  * Number Of Elements: Integer.MAX_VALUE/2
+
+If you need to specify different settings create a property files with following content:
+
+```
+ch.psi.fda.fdaq.hostname=myhost
+ch.psi.fda.fdaq.port=1234
+ch.psi.fda.fdaq.killPort=4321
+```
+
+Use `-Dch.psi.fda.fdaq.config.file=<file>` to use this property file as base configuration.
+
+
+
+## Development
+A standalone jar can be build via `mvn clean compile assembly:single`.
+
+To upload the latest version to the artifact repository use ` mvn clean compile deploy`.
+
+
+## Notes
+Trigger port is `Trigger In 1`. For testing apply a 1kHz signal.

build.gradle

@@ -0,0 +1,92 @@
+apply plugin: 'java'
+apply plugin: 'eclipse'
+
+sourceCompatibility = 1.7
+
+version = '3.0.0'
+
+buildscript {
+  repositories {
+    maven {
+      url "https://plugins.gradle.org/m2/"
+    }
+  }
+  dependencies {
+    classpath "com.github.jacobono:gradle-jaxb-plugin:1.3.5"
+  }
+}
+
+apply plugin: "com.github.jacobono.jaxb"
+
+repositories {
+    mavenCentral()
+    maven { url "http://artifacts.psi.ch/artifactory/libs-releases" }
+    maven { url "http://artifacts.psi.ch/artifactory/libs-snapshots" }
+}
+
+dependencies {
+	compile 'ch.psi:jcae:2.4.1'
+	compile 'com.google.inject:guice:3.0'
+	compile 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:2.5.1'
+	compile 'org.glassfish.jersey.media:jersey-media-sse:2.5.1'
+	compile 'org.glassfish.jersey.media:jersey-media-json-jackson:2.5.1'
+	compile 'org.zeromq:jeromq:0.3.4'
+	compile 'org.apache.commons:cli:1.2'
+	// For reading/writing Matlab files
+	compile 'com.jmatio:jmatio:0.2u2psi1'
+	// Library for reading/writing XDR Format (MDA)
+	compile 'org.freehep:freehep-xdr:2.0.4'
+	compile 'ch.psi:plot:2.1-SNAPSHOT'
+	
+	compile 'com.google.guava:guava:>15.0'
+	
+	compile 'com.sun.mail:javax.mail:1.5.0'
+	compile 'javax.inject:javax.inject:1'
+	compile 'org.python:jython:2.5.3'
+	compile 'com.fasterxml.jackson.core:jackson-databind:2.5.2'
+	
+	
+	jaxb 'com.sun.xml.bind:jaxb-xjc:2.2.7-b41'
+    jaxb 'com.sun.xml.bind:jaxb-impl:2.2.7-b41'
+    jaxb 'javax.xml.bind:jaxb-api:2.2.7'
+	
+    testCompile 'junit:junit:4.+'
+}
+
+task sourcesJar(type: Jar, dependsOn: classes) {
+    classifier = 'sources'
+    from sourceSets.main.allSource
+}
+
+/*
+task javadocJar(type: Jar, dependsOn: javadoc) {
+    classifier = 'javadoc'
+    from javadoc.destinationDir
+}
+*/
+
+artifacts {
+    archives sourcesJar
+    //archives javadocJar
+}
+
+jaxb{
+	xsdDir = "src/main/resources"
+	xjc {
+	     generatePackage = "ch.psi.fda.model.v1" 
+	}
+}
+
+apply plugin: 'maven'
+
+uploadArchives {
+    repositories {
+        mavenDeployer {
+            repository(url: "http://artifacts.psi.ch/artifactory/libs-snapshots-local"){
+            	authentication(userName: "upload", password: "{DESede}eWKHxAtQ2Dc=")
+            }
+            pom.groupId = 'ch.psi'
+            pom.artifactId = 'fda'
+        }
+    }
+}

ch.psi.fda/.classpath

@@ -1,37 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<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"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>

ch.psi.fda/.gitignore

@@ -1 +0,0 @@
-/target

ch.psi.fda/.project

@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>ch.psi.fda</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.m2e.core.maven2Builder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.m2e.core.maven2Nature</nature>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-	</natures>
-</projectDescription>

ch.psi.fda/.settings/org.eclipse.core.resources.prefs

@@ -1,3 +0,0 @@
-eclipse.preferences.version=1
-encoding//src/main/java=UTF-8
-encoding//src/test/java=UTF-8

ch.psi.fda/.settings/org.eclipse.jdt.core.prefs

@@ -1,5 +0,0 @@
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
-org.eclipse.jdt.core.compiler.compliance=1.7
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.7

ch.psi.fda/.settings/org.eclipse.m2e.core.prefs

@@ -1,5 +0,0 @@
-#Tue Oct 18 15:52:42 CEST 2011
-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1

ch.psi.fda/pom.xml

@@ -1,255 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<groupId>ch.psi</groupId>
-	<artifactId>fda</artifactId>
-	<version>1.1.41</version>
-
-	<dependencies>
-	
-		<dependency>
-			<groupId>org.glassfish.jersey.containers</groupId>
-			<artifactId>jersey-container-grizzly2-http</artifactId>
-			<version>2.3.1</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.glassfish.jersey.media</groupId>
-			<artifactId>jersey-media-sse</artifactId>
-			<version>2.3.1</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.glassfish.jersey.media</groupId>
-			<artifactId>jersey-media-json-jackson</artifactId>
-			<version>2.3.1</version>
-		</dependency>
-	
-	
-		<dependency>
-			<groupId>org.jeromq</groupId>
-			<artifactId>jeromq</artifactId>
-			<version>0.2.0</version>
-		</dependency>
-	
-	
-		<dependency>
-			<groupId>com.google.guava</groupId>
-			<artifactId>guava</artifactId>
-			<version>15.0</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>
-			<version>4.8.2</version>
-			<scope>test</scope>
-		</dependency>
-	</dependencies>
-
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<configuration>
-					<encoding>UTF-8</encoding>
-					<source>1.7</source>
-					<target>1.7</target>
-				</configuration>
-			</plugin>
-			<!-- Generate Javadoc Jar -->
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-javadoc-plugin</artifactId>
-				<version>2.8</version>
-				<executions>
-					<execution>
-						<id>attach-javadocs</id>
-						<goals>
-							<goal>jar</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-			<!-- Generate Source Jar -->
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-source-plugin</artifactId>
-				<version>2.1.2</version>
-				<executions>
-					<execution>
-						<id>attach-sources</id>
-						<goals>
-							<goal>jar</goal>
-						</goals>
-					</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$</pattern>
-									<replacement>.html</replacement>
-								</fileMapper>
-							</fileMappers>
-						</transformationSet>
-					</transformationSets>
-				</configuration>
-			</plugin>
-		</plugins>
-		<pluginManagement>
-			<plugins>
-				<!--This plugin's configuration is used to store Eclipse m2e settings 
-					only. It has no influence on the Maven build itself. -->
-				<plugin>
-					<groupId>org.eclipse.m2e</groupId>
-					<artifactId>lifecycle-mapping</artifactId>
-					<version>1.0.0</version>
-					<configuration>
-						<lifecycleMappingMetadata>
-							<pluginExecutions>
-								<pluginExecution>
-									<pluginExecutionFilter>
-										<groupId>
-											org.jvnet.jaxb2.maven2
-										</groupId>
-										<artifactId>
-											maven-jaxb2-plugin
-										</artifactId>
-										<versionRange>
-											[0.8.0,)
-										</versionRange>
-										<goals>
-											<goal>generate</goal>
-										</goals>
-									</pluginExecutionFilter>
-									<action>
-										<ignore></ignore>
-									</action>
-								</pluginExecution>
-							</pluginExecutions>
-						</lifecycleMappingMetadata>
-					</configuration>
-				</plugin>
-				
-				<plugin>
-				<artifactId>maven-assembly-plugin</artifactId>
-				<configuration>
-					<finalName>${project.name}-${project.version}</finalName>
-					<appendAssemblyId>false</appendAssemblyId>
-					<archive>
-						<!-- <manifest>
-							<mainClass>ch.psi.fda.AcquisitionMain</mainClass>
-						</manifest> -->
-					</archive>
-					<descriptorRefs>
-						<descriptorRef>jar-with-dependencies</descriptorRef>
-					</descriptorRefs>
-				</configuration>
-			</plugin>
-				
-			</plugins>
-		</pluginManagement>
-	</build>
-
-	<distributionManagement>
-		<snapshotRepository>
-			<id>i.snapshots</id>
-			<name>Artifactory Snapshots</name>
-			<url>http://yoke/artifactory/libs-snapshots-local</url>
-		</snapshotRepository>
-		<repository>
-			<id>i.releases</id>
-			<name>Atrifactory Releases</name>
-			<url>http://yoke/artifactory/libs-releases-local</url>
-		</repository>
-	</distributionManagement>
-</project>

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.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.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.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.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/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.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.sensors.TimestampSensor;
-
-/**
- * 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/rest/AcquisitionEngine.java

@@ -1,170 +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 java.util.UUID;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Logger;
-
-import javax.inject.Inject;
-
-import com.google.common.eventbus.EventBus;
-
-import ch.psi.fda.aq.Acquisition;
-import ch.psi.fda.aq.AcquisitionConfiguration;
-import ch.psi.fda.model.v1.Configuration;
-import ch.psi.jcae.ChannelService;
-
-/**
- * Main engine for data acquisition.
- */
-public class AcquisitionEngine {
-	
-	private static final Logger logger = Logger.getLogger(AcquisitionEngine.class.getName());
-
-	private AcquisitionConfiguration config;
-	private ChannelService cservice;
-	private final ZMQDataService dservice;
-	
-	/**
-	 * Variable holding the current acquisition
-	 */
-	private volatile Acquisition acquisition;
-	private volatile ExecutionRequest currentRequest;
-	
-	private ExecutorService eservice;
-	
-	
-	private BlockingQueue<ExecutionRequest> requests = new LinkedBlockingQueue<>();
-	
-	@Inject
-	public AcquisitionEngine(ChannelService cservice, ZMQDataService dservice, AcquisitionConfiguration config) {
-		this.dservice = dservice;
-		this.cservice = cservice;
-		this.config = config;
-
-		// Start main execution loop 
-		eservice = Executors.newSingleThreadExecutor();
-		eservice.execute(new Runnable() {
-			@Override
-			public void run() {
-				try {
-					while (!Thread.currentThread().isInterrupted()) {
-						try {
-							ExecutionRequest r = requests.take();
-
-							logger.info("Execute - " + r.getTrackingId());
-
-							EventBus ebus = new EventBus();
-							// Provide tracking id to data service and register the service to the event bus
-							AcquisitionEngine.this.dservice.setTrackingId(r.getTrackingId()); 
-							ebus.register(AcquisitionEngine.this.dservice);
-
-							synchronized (AcquisitionEngine.this) { // synchronize access to acquisition object via the AcquisitionEngine object
-								acquisition = new Acquisition(AcquisitionEngine.this.cservice, AcquisitionEngine.this.config);
-								currentRequest = r;
-							}
-							acquisition.initalize(ebus, r.getConfiguration());
-							acquisition.execute();
-							logger.info("" + r.getTrackingId() + " done");
-							
-							// Cleanup
-							ebus.unregister(AcquisitionEngine.this.dservice);
-						} finally {
-							acquisition.destroy();
-							
-							synchronized (AcquisitionEngine.this) {
-								acquisition = null;
-								currentRequest = null;
-							}
-						}
-					}
-				} catch (InterruptedException e) {
-				}
-			}
-		});
-	}
-	
-	/**
-	 * Submit a scan to be executed. This will generate an execution request which is
-	 * enqueued in the execution queue.
-	 * 
-	 * @param configuration
-	 * @return
-	 */
-	public String submit(Configuration configuration){
-		ExecutionRequest r = new ExecutionRequest(UUID.randomUUID().toString(), configuration);
-		try{
-			requests.put(r);
-		} catch (InterruptedException e) {
-		}
-		return r.getTrackingId();
-	}
-	
-	
-	/**
-	 * Terminate the currently executed request
-	 */
-	public void terminate(){
-		synchronized(this){
-			if(acquisition==null){
-				return;
-			}
-			
-			logger.info("Stop current acquisition");
-			acquisition.abort();
-		}
-	}
-	
-	/**
-	 * 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
-	 */
-	public void terminate(String trackingId){
-		
-		// If request is currently executed terminate it
-		if(currentRequest.getTrackingId().equals(trackingId)){
-			terminate();
-			return;
-		}
-		
-		// Remove request from request queue
-		ExecutionRequest rremove = null;
-		for(ExecutionRequest r:requests){
-			if(r.getTrackingId().equals(trackingId)){
-				rremove = r; // We have to split the filtering and termination as we otherwise get a concurrent access exception.
-				break;
-			}
-		}
-		if(rremove!=null){
-			boolean b = requests.remove(rremove);
-			// There is a chance that between the upper loop and here the request
-			// already got dequeued. This check ensures that the requests got removed
-			// if not it got dequeued and therefore we have to terminate the current
-			// execution.
-			if(!b){ 
-				terminate();
-			}
-		}
-	}
-}

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

@@ -1,22 +0,0 @@
-package ch.psi.fda.rest;
-
-
-import javax.inject.Singleton;
-
-import org.glassfish.hk2.utilities.binding.AbstractBinder;
-
-import ch.psi.fda.aq.AcquisitionConfiguration;
-import ch.psi.jcae.ChannelService;
-import ch.psi.jcae.impl.DefaultChannelService;
-
-public class ResourceBinder extends AbstractBinder {
-
-    @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(ZMQDataService.class).to(ZMQDataService.class).in(Singleton.class);
-    }
-
-}

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

@@ -1,49 +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.services;
-
-import javax.inject.Inject;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.core.MediaType;
-
-import ch.psi.fda.model.v1.Configuration;
-import ch.psi.fda.rest.AcquisitionEngine;
-
-@Path("fda")
-public class ScanService {
-
-	@Inject
-	private AcquisitionEngine aengine;
-	
-	@POST
-	@Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
-//	@Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
-	public String execute(Configuration configuration) throws InterruptedException{
-		return aengine.submit(configuration);
-	}
-	
-	@DELETE
-	public void stop(){
-		aengine.terminate();
-	}
-}

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

@@ -1,23 +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.serializer;
-
-public interface DataSerializer {
-}

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

@@ -1,197 +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.serializer;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.logging.Logger;
-
-import com.google.common.eventbus.Subscribe;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-
-/**
- * Serialize data received by a DataQueue
- */
-public class DataSerializerTXT implements DataSerializer{
-	
-	private static final Logger logger = Logger.getLogger(DataSerializerTXT.class.getName());
-	
-	private File file;
-	
-	private boolean appendSuffix = true;
-
-	
-	private boolean first = true;
-	private File outfile;
-	
-	private int icount;
-	private String basename;
-	private String extension;
-	private boolean newfile;
-	private boolean dataInBetween;
-	private BufferedWriter writer;
-	private StringBuffer b;
-	private StringBuffer b1;
-	
-	
-	/**
-	 * @param metadata
-	 * @param file
-	 * @param appendSuffix	Flag whether to append a _0000 suffix after the original file name
-	 */
-	public DataSerializerTXT(File file, boolean appendSuffix){
-		this.file = file;
-		this.appendSuffix = appendSuffix;
-	}
-
-	@Subscribe
-	public void onMessage(Message message){
-		try{
-		if(first){
-			first=false;
-			// Write header
-						
-						
-						
-						icount = 0;
-						newfile = true;
-						dataInBetween = false;
-						writer = null;
-						
-						// Get basename of the file
-						basename = this.file.getAbsolutePath(); // Determine file name
-						extension = basename.replaceAll("^.*\\.", ""); // Determine extension
-						basename = basename.replaceAll("\\."+extension+"$", "");
-		}
-		
-		if(message instanceof DataMessage){
-			dataInBetween = true;
-			if(newfile){
-				
-				b = new StringBuffer();
-				b1 = new StringBuffer();
-				b.append("#");
-				b1.append("#");
-				for(Metadata c: ((DataMessage) message).getMetadata()){
-
-					b.append(c.getId());
-					b.append("\t");
-					
-					b1.append(c.getDimension());
-					b1.append("\t");
-				}
-				b.setCharAt(b.length()-1, '\n');
-				b1.setCharAt(b1.length()-1, '\n');
-				
-				// Open new file and write header
-				// Construct file name
-				if(appendSuffix){
-					outfile = new File(String.format("%s_%04d.%s", basename, icount, extension));
-				}
-				else{
-					outfile = new File(String.format("%s.%s", basename, extension));
-				}
-				
-				// Open file
-				logger.fine("Open new data file: "+outfile.getAbsolutePath());
-				writer = new BufferedWriter(new FileWriter(outfile));
-				
-				// Write header
-				writer.write(b.toString());
-				writer.write(b1.toString());
-				
-				newfile=false;
-			}
-			
-			// Write message to file - each message will result in one line
-			DataMessage m = (DataMessage) message;
-			StringBuffer buffer = new StringBuffer();
-			for(Object o: m.getData()){
-				if(o.getClass().isArray()){
-					// If the array object is of type double[] display its content
-					if(o instanceof double[]){
-						double[] oa = (double[]) o;
-						for(double o1 : oa){
-							buffer.append(o1);
-							buffer.append(" "); // Use space instead of tab
-						}
-						buffer.replace(buffer.length()-1,buffer.length()-1 , "\t"); // Replace last space with tab
-					}
-					else if(o instanceof Object[]){
-						// TODO need to be recursive ...
-						Object[] oa = (Object[])o;
-						for(Object o1 : oa){
-							buffer.append(o1);
-							buffer.append(" "); // Use space instead of tab
-						}
-						buffer.replace(buffer.length()-1,buffer.length()-1 , "\t"); // Replace last space with tab
-					}
-					else{
-						buffer.append("-"); // Not supported
-					}
-				}
-				else{
-					buffer.append(o);
-					buffer.append("\t");
-				}
-			}
-			
-			if(buffer.length()>0){
-				buffer.deleteCharAt(buffer.length()-1); // Remove last character (i.e. \t)
-				buffer.append("\n"); // Append newline
-			}
-			writer.write(buffer.toString());
-		}
-		else if(message instanceof StreamDelimiterMessage){
-			StreamDelimiterMessage m = (StreamDelimiterMessage) message;
-			logger.info("Delimiter - number: "+m.getNumber()+" iflag: "+m.isIflag());
-			if(m.isIflag() && appendSuffix){
-				// Only increase iflag counter if there was data in between
-				// subsequent StreamDelimiterMessages.
-				if(dataInBetween){
-					icount++;
-				}
-				dataInBetween = false;
-				
-				// Set flag to open new file
-				newfile = true;
-				
-				// Close file
-				writer.close();
-			}
-		}
-		else if (message instanceof EndOfStreamMessage){
-			if(writer!=null){
-				// Close file
-				writer.close(); //If the stream was closed previously this has no effect
-			}
-		}
-		} catch (IOException e) {
-			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
-		}
-	}
-}

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

@@ -1,281 +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.visualizer;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import javax.swing.JPanel;
-import javax.swing.SwingUtilities;
-
-import com.google.common.eventbus.Subscribe;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.plot.Plot;
-import ch.psi.plot.xy.LinePlot;
-import ch.psi.plot.xy.XYSeriesCollectionP;
-import ch.psi.plot.xy.XYSeriesP;
-import ch.psi.plot.xyz.MatrixPlot;
-import ch.psi.plot.xyz.MatrixPlotData;
-
-/**
- * Visualizer for visualizing data
- */
-public class Visualizer {
-	
-	private static Logger logger = Logger.getLogger(Visualizer.class.getName());
-	
-	private boolean updateAtStreamElement = true;
-	private boolean updateAtStreamDelimiter = true;
-	private boolean updateAtEndOfStream = false;
-	
-	private int ecount;
-	private boolean clearPlot;
-	private List<SeriesDataFilter> filters;
-	
-	private boolean first = true;
-	
-	public Visualizer(List<SeriesDataFilter> filters){
-		this.filters = filters;
-	}
-	
-	
-	@Subscribe
-	public void onDataMessage(final DataMessage message){
-		
-			if(first){
-				first=false;
-//				filters = VisMapper.mapVisualizations(visualizations);
-				// TODO somehow handle dimension / clear
-			}
-		
-			// Clear is here as the plot should not be cleared after the last point is plotted
-			// but just before the first point of the next plot (cycle)
-			if (clearPlot) {
-				for (SeriesDataFilter f: filters) {
-					Plot plot = f.getPlot();
-					if(plot instanceof MatrixPlot){
-						((MatrixPlotData) ((MatrixPlot)plot).getData()).clear();
-					}
-				}
-				clearPlot = false;
-			}
-
-			for(SeriesDataFilter filter: filters){
-				if(filter instanceof XYSeriesDataFilter){
-					XYSeriesDataFilter xyfilter = (XYSeriesDataFilter) filter;
-					
-					if(xyfilter.getActualSeries()==null || xyfilter.isNewseries()){
-						// First series that is filled by this filter!
-						XYSeriesP s = new XYSeriesP(xyfilter.getSeriesName() + " " + ecount + "-" + xyfilter.getCount());
-						((LinePlot)xyfilter.getPlot()).getData().addSeries(s);
-						xyfilter.setActualSeries(s);
-						xyfilter.setNewseries(false);
-					}
-					
-					XYSeriesP series = xyfilter.getActualSeries(); // TODO Does not work with multiple series filter per plot !!!!
-					
-					// There might be other values than double in the data, therefore we have to check for it
-					Object dX = message.getData(xyfilter.getIdX());
-					Object dY = message.getData(xyfilter.getIdY());
-					Double dataX = Double.NaN;
-					Double dataY = Double.NaN;
-					if(dX instanceof Double){
-						dataX = (Double) dX;
-					}
-					if(dY instanceof Double){
-						dataY = (Double) dY;
-					}
-					
-					// Add Data to the series
-					series.add(dataX , dataY, updateAtStreamElement);
-				}
-				if(filter instanceof XYSeriesArrayDataFilter){
-					final XYSeriesArrayDataFilter xyfilter = (XYSeriesArrayDataFilter) filter;
-					
-					// Ensure that there is no concurrent modification exception or synchronization problems with the
-					// Swing update task
-					SwingUtilities.invokeLater(new Runnable(){
-
-						@Override
-						public void run() {
-							XYSeriesP series = new XYSeriesP(xyfilter.getSeriesName() + "-" + xyfilter.getCount()); // Series name must be unique
-							xyfilter.incrementCount();
-
-//								((LinePlot)xyfilter.getPlot()).getData().removeAllSeries(); // Remove all series from the data
-							// If we can agree only to display one series at a time also a clear() on the actual series is better
-							XYSeriesCollectionP sc = ((LinePlot)xyfilter.getPlot()).getData();
-							sc.addSeries(series);
-							
-							// Remove outdated series
-							if(sc.getSeriesCount()>xyfilter.getMaxSeries()){
-								// Remove oldest series
-								sc.removeSeries(0);
-							}
-							
-							double[] data = message.getData(xyfilter.getIdY());
-							// Copy data starting from offset to size
-							int size = data.length;
-							int offset = xyfilter.getOffset();
-							if(xyfilter.getSize()>0 && offset+xyfilter.getSize()<data.length){
-								size = offset + xyfilter.getSize();
-							}
-							for(int i=offset;i<size;i++){
-								series.add(i,data[i], false); // Do not fire change event - this would degrade performance drastically
-							}
-							series.fireSeriesChanged();
-						}
-						
-					});
-				}
-				else if(filter instanceof XYZSeriesDataFilter){
-					XYZSeriesDataFilter xyzfilter = (XYZSeriesDataFilter) filter;
-					try{
-						((MatrixPlot)xyzfilter.getPlot()).getData().addData((Double) message.getData(xyzfilter.getIdX()),(Double) message.getData(xyzfilter.getIdY()), (Double) message.getData(xyzfilter.getIdZ()));
-					}
-					catch (Exception e) {
-						// Ignore if something goes wrong while adding a datapoint
-						logger.log(Level.WARNING, "Unable to plot datapoint in matrix plot", e);
-					}
-				}
-				else if(filter instanceof XYZSeriesArrayDataFilter){
-					XYZSeriesArrayDataFilter xyzfilter = (XYZSeriesArrayDataFilter) filter;
-					try{
-						double[] data = (double[]) message.getData(xyzfilter.getIdZ());
-						double y = (Double) message.getData(xyzfilter.getIdY());
-						int offset = xyzfilter.getOffset();
-						int size = xyzfilter.getSize();
-						for(int i=offset;i<offset+size; i++){
-							((MatrixPlot)xyzfilter.getPlot()).getData().addData(i, y, data[i]);
-						}
-						// Update data if update by point is enabled
-						if(updateAtStreamElement){
-							xyzfilter.getPlot().update();
-						}
-					}
-					catch (Exception e) {
-						// Ignore if something goes wrong while adding a datapoint
-						logger.log(Level.WARNING, "Unable to plot datapoint in matrix plot", e);
-					}
-				}
-			}
-	}
-	
-	
-	@Subscribe
-	public void onStreamDelimiterMessage(StreamDelimiterMessage message){
-			for(SeriesDataFilter filter: filters){
-				if(filter instanceof XYSeriesDataFilter){
-					// Create new series
-					XYSeriesDataFilter xyfilter = (XYSeriesDataFilter) filter;
-//					if (message.getNumber() == xyfilter.getDimensionX()) {
-						if (message.getNumber() == 0) { // TODO need to check this - here we assume that always at the lowest level we create a new series 
-						// Indicate to create new series at the next message
-						xyfilter.setCount(xyfilter.getCount()+1); // Increment count of the filter
-						xyfilter.setNewseries(true);
-					}
-				}
-			}
-
-			// Update matrix plot at the end of each line
-			if(updateAtStreamDelimiter){
-				for(SeriesDataFilter f: filters){
-					Plot plot = f.getPlot();
-//				for (Plot plot: plots) {
-					if(plot instanceof MatrixPlot){
-						((MatrixPlot)plot).update();
-					}
-					else if(plot instanceof LinePlot){
-						((LinePlot) plot).update();
-					}
-				}
-			}
-
-			// Clear matrix plot if iflag is encountered
-			// TODO: One need to check whether the iflag belongs to a delimiter
-			// of a higher dimension than the highest dimension (axis) that
-			// is involved in the plot
-			if (message.isIflag()) {
-				clearPlot = true;
-			}
-	}
-	
-	@Subscribe
-	public void onEndOfStreamMessage(EndOfStreamMessage message){
-		ecount++;
-		
-		// Update plots if updateAtEndOfStream flag is set
-		if(updateAtEndOfStream){
-			// Update matrix plots
-			for(SeriesDataFilter f: filters){
-				Plot plot = f.getPlot();
-				if(plot instanceof MatrixPlot){
-					((MatrixPlot)plot).update();
-					((MatrixPlot)plot).adaptColorMapScale(); // Update color scale at the end
-				}
-				else if(plot instanceof LinePlot){
-					((LinePlot) plot).update();
-				}
-			}
-		}
-	}
-	
-	public void configure(){
-		ecount = 0;
-		clearPlot = false;
-	}
-	
-	/**
-	 * Get the plot panels for the visualizations
-	 * @return	List of configured JPanels
-	 */
-	public List<JPanel> getPlotPanels(){
-		List<JPanel> panels = new ArrayList<JPanel>();
-		for(SeriesDataFilter f: filters){
-			panels.add(f.getPlot().getChartPanel());
-		}
-		
-		return panels;
-	}
-
-	public boolean isUpdateAtStreamElement() {
-		return updateAtStreamElement;
-	}
-	public void setUpdateAtStreamElement(boolean updateAtStreamElement) {
-		this.updateAtStreamElement = updateAtStreamElement;
-	}
-	public boolean isUpdateAtStreamDelimiter() {
-		return updateAtStreamDelimiter;
-	}
-	public void setUpdateAtStreamDelimiter(boolean updateAtStreamDelimiter) {
-		this.updateAtStreamDelimiter = updateAtStreamDelimiter;
-	}
-	public boolean isUpdateAtEndOfStream() {
-		return updateAtEndOfStream;
-	}
-	public void setUpdateAtEndOfStream(boolean updateAtEndOfStream) {
-		this.updateAtEndOfStream = updateAtEndOfStream;
-	}
-	
-}

ch.psi.fda/src/test/ioc/X/MTEST-PC-FDA/App/config/scripts/medm.sh

@@ -1,21 +0,0 @@
-#!/bin/bash
-
-BASEDIR=$(cd $(dirname $0);pwd)
-
-EPICS_DISPLAY_PATH=/work/sls/config/medm:$EPICS_DISPLAY_PATH
-export EPICS_DISPLAY_PATH
-
-# OTFSCAN MEDM
-medm -x -macro "P=MTEST-HW3-OTFX" G_OTFSCAN_user.adl &
-
-# Motor MEDM
-medm -x -macro "P=MTEST-HW3:, M=MOT1" motorx_more.adl &
-#medm -x -macro "ENC=MTEST-HW3:EC1" G_ECM_514A_encoder.adl &
-
-medm -x -macro "P=MTEST-HW3:, M=MOT2" motorx_more.adl &
-#medm -x -macro "ENC=MTEST-HW3:EC2" G_ECM_514A_encoder.adl &
-
-medm -x -macro "P=MTEST-PC-MOTOR:, M=MOT1" motorx_more.adl &
-
-# Scaler MEDM
-medm -x -macro "P=MTEST-HW3:, S=JS" scaler16.adl &

ch.psi.fda/src/test/ioc/X/MTEST-PC-FDA/MTEST-PC-FDA_startup.script

@@ -1,2 +0,0 @@
-# Load test template
-dbLoadTemplate("MTEST-PC-FDA_test.subs")

ch.psi.fda/src/test/ioc/X/MTEST-PC-FDA/MTEST-PC-FDA_test.subs

@@ -1,5 +0,0 @@
-file test.template {
-    {
-        P = MTEST-PC-FDA:
-    }
-}

ch.psi.fda/src/test/ioc/X/MTEST-PC-FDA/Makefile

@@ -1,17 +0,0 @@
-MODULE = MTEST-PC-FDA
-export MODULE
-
-build:
-
-clean:
-
-install: build
-	swit -V -ioc MTEST-PC-FDA
-
-help:
-	@echo "The following targets are available with this Makefile:-"
-	@echo "make (calls default target)"
-	@echo "make build (default)"
-	@echo "make install"
-	@echo "make clean"
-	@echo "make help"

ch.psi.fda/src/test/ioc/X/MTEST-PC-FDA/test.template

@@ -1,42 +0,0 @@
-# Binary Output
-record(bo, "$(P)BO") {
-  field(DESC, "Binary Output")
-}
-
-# Binary Output
-record(bo, "$(P)BO2") {
-  field(DESC, "Binary Output 2")
-  field(VAL, "0")
-}
-
-# Analog Output
-record(ao, "$(P)AO") {
-  field(PREC, "6")
-  field(DESC, "Analog Output")
-}
-
-# String Output
-record(stringout, "$(P)SOUT") {
-}
-
-# Double Waveform (100 Elements)
-record(waveform, "$(P)DWAVE") {
-  field(DESC, "Double Waveform")
-  field(PREC, "6")
-  field(NELM, "100")
-  field(FTVL, "DOUBLE")
-}
-
-# Integer Waveform (100 Elements)
-record(waveform, "$(P)LWAVE") {
-  field(DESC, "Long Waveform")
-  field(NELM, "100")
-  field(FTVL, "LONG")
-}
-
-# Character Waveform (100 Elements)
-record(waveform, "$(P)CWAVE") {
-  field(DESC, "Character Waveform")
-  field(NELM, "100")
-  field(FTVL, "CHAR")
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/loops/DistributedFileTest.java

@@ -1,146 +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;
-
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.logging.Logger;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.TestConfiguration;
-import ch.psi.fda.core.loops.otf.DistributedFile;
-
-/**
- * @author ebner
- *
- */
-public class DistributedFileTest {
-
-	
-	private static final Logger logger = Logger.getLogger(DistributedFileTest.class.getName());
-	
-	DistributedFile file;
-	DistributedFile smbfile;
-	
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-		file  = new DistributedFile("src/test/resources");
-		smbfile = new DistributedFile(TestConfiguration.getInstance().getSmbShare());
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.DistributedFile#getCanonicalPath()}.
-	 * @throws IOException 
-	 */
-	@Test
-	public void testGetCanonicalPath() throws IOException {
-		logger.info(file.getCanonicalPath());
-		logger.info(smbfile.getCanonicalPath());
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.DistributedFile#exists()}.
-	 * @throws IOException 
-	 */
-	@Test
-	public void testExists() throws IOException {
-		if(!file.exists()){
-			fail("Indicating wrong file status (file actually exists)");
-		}
-		if(!smbfile.exists()){
-			fail("Indicating wrong file status (file actually exists)");
-		}
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.DistributedFile#isDirectory()}.
-	 * @throws IOException 
-	 */
-	@Test
-	public void testIsDirectory() throws IOException {
-		if(!file.isDirectory()){
-			fail("Indicating wrong file type (file is directory)");
-		}
-		if(!smbfile.isDirectory()){
-			fail("Indicating wrong file type (file is directory)");
-		}
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.DistributedFile#listFiles()}.
-	 */
-	@Test
-	public void testListFiles() {
-//		fail("Not yet implemented");
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.DistributedFile#getName()}.
-	 */
-	@Test
-	public void testGetName() {
-		logger.info(file.getName());
-		logger.info(smbfile.getName());
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.DistributedFile#isFile()}.
-	 * @throws IOException 
-	 */
-	@Test
-	public void testIsFile() throws IOException {
-		if(file.isFile()){
-			fail("Indicating wrong file type (file is directory)");
-		}
-		if(smbfile.isFile()){
-			fail("Indicating wrong file type (file is directory)");
-		}
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.DistributedFile#delete()}.
-	 */
-	@Test
-	public void testDelete() {
-//		fail("Not yet implemented");
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.DistributedFile#getInputStream()}.
-	 */
-	@Test
-	public void testGetInputStream() {
-//		fail("Not yet implemented");
-	}
-
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/loops/OTFLoopTest.java

@@ -1,229 +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 static org.junit.Assert.*;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import com.google.common.eventbus.Subscribe;
-
-import ch.psi.fda.TestConfiguration;
-import ch.psi.fda.core.loops.otf.OTFLoop;
-import ch.psi.fda.core.loops.otf.OTFNamedChannelSensor;
-import ch.psi.fda.core.loops.otf.OTFScalerChannelSensor;
-import ch.psi.fda.core.loops.otf.TemplateOTF;
-import ch.psi.fda.core.messages.ControlMessage;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.TimestampSensor;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-import ch.psi.jcae.impl.DefaultChannelService;
-
-public class OTFLoopTest {
-
-	private static Logger logger = Logger.getLogger(OTFLoopTest.class.getName());
-	
-	private ChannelService cservice;
-	
-	
-	
-	private static final TestConfiguration configuration = TestConfiguration.getInstance();
-	
-	
-	private OTFLoop loopZigZag;
-	private OTFLoop loop;
-	private Channel<Integer> statusChannel;
-	
-	@Before
-	public void setUp() throws Exception {
-		cservice = new DefaultChannelService();
-		statusChannel = cservice.createChannel(new ChannelDescriptor<>(Integer.class, configuration.getOtfPrefix()+":USTAT"));
-		
-		OTFScalerChannelSensor s2 = new OTFScalerChannelSensor("id1", 0);
-		OTFScalerChannelSensor s3 = new OTFScalerChannelSensor("id2", 1);
-		TimestampSensor s4 = new TimestampSensor("id3");
-		OTFNamedChannelSensor s5 = new OTFNamedChannelSensor("id4", configuration.getAnalogIn1());
-		
-		Map<String, String> macros = new HashMap<>();
-		macros.put("PREFIX", configuration.getOtfPrefix());
-		TemplateOTF template = new TemplateOTF();
-		cservice.createAnnotatedChannels(template, macros);
-		
-		
-		// ZigZag loop
-		loopZigZag = new OTFLoop(template, configuration.getServer(), configuration.getShare(), configuration.getSmbShare(), true);
-		loopZigZag.setActuator("id0", configuration.getMotor1(), null, 0, 8, 0.5, 0.5, 0);
-		loopZigZag.getSensors().add(s2);
-		loopZigZag.getSensors().add(s3);
-		loopZigZag.getSensors().add(s4);
-		loopZigZag.getSensors().add(s5);
-		
-		
-		// Normal loop
-		loop = new OTFLoop(template, configuration.getServer(), configuration.getShare(), configuration.getSmbShare(), false);
-		loop.setActuator("id0", configuration.getMotor1(), null, 0, 8, 0.5, 0.5, 0);		
-		loop.getSensors().add(s2);
-		loop.getSensors().add(s3);
-		loop.getSensors().add(s4);
-		loop.getSensors().add(s5);
-	}
-
-	@After
-	public void tearDown() throws Exception {
-		cservice.destroy();
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.OTFLoop#execute()}.
-	 * Test ordinary 1D OTF scan
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws CAException 
-	 */
-	@Test
-	public void testExecute() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		
-		Object l = new Object(){
-			boolean first = true;
-			@Subscribe
-			public void onMessage(DataMessage m) {
-				if(first){
-					first = false;
-					
-					int numberOfSensors = 5;
-					if(m.getMetadata().size() != numberOfSensors){
-						fail("Loop returned wrong number of components inside the data message metadata");
-					}
-					
-					boolean fail = false;
-					for(int x=0;x<numberOfSensors; x++){
-						if(! m.getMetadata().get(x).getId().equals("id"+x)){
-							fail = true;
-						}
-					}
-					
-					if(fail){
-						fail("Ids of the component metadata elements inside the data message metadata is not correct");
-					}
-				}
-				logger.info(m.toString());
-			}
-		};
-		
-		loop.getEventBus().register(l);
-		
-		loop.prepare();
-		loop.execute();
-		loop.cleanup();
-		
-		if(statusChannel.getValue()!=1){
-			fail("OTF C Logic status is not on INACTIVE");
-		}
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.OTFLoop#execute()}.
-	 * Test OTF ZigZag mode
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws CAException 
-	 */
-	@Test
-	public void testExecuteZigZag() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		
-		loopZigZag.getEventBus().register(new TestCollector());
-		
-		loopZigZag.prepare();
-		
-		loopZigZag.execute();
-		loopZigZag.execute();
-		
-		loopZigZag.cleanup();
-		
-		if(statusChannel.getValue()!=1){
-			fail("OTF C Logic status is not on INACTIVE");
-		}
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.otf.OTFLoop#execute()}.
-	 * Test abort functionality while executing an OTF scan
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws CAException 
-	 */
-	@Test
-	public void testExecuteAbort() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		
-		loop.getEventBus().register(new TestCollector());
-		
-		// Thread to simulate asynchronous abort operation
-		Thread t1 = new Thread(new Runnable() {
-			@Override
-			public void run() {
-				try {
-					Thread.sleep(6000); // Wait some seconds before aborting the loop
-					loop.abort();
-				} catch (InterruptedException e) {
-					logger.log(Level.SEVERE, "An Exception occured while testing the abort functionality", e);
-				}
-			}
-		});
-		t1.start();
-		
-		loop.prepare();
-		
-		loop.execute();
-		
-		loop.cleanup();
-		
-		if(statusChannel.getValue()!=1){
-			fail("OTF C Logic status is not on INACTIVE");
-		}
-	}
-	
-	class TestCollector {
-		@Subscribe
-		public void onMessage(Message m) {
-			if (m instanceof DataMessage) {
-				DataMessage x = (DataMessage) m;
-				logger.info(x.toString());
-			} else if (m instanceof ControlMessage) {
-				logger.info("---- " + m.toString() + " ----");
-			}
-		}
-	}
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/loops/cr/ParallelCrlogicStreamMergeTest.java

@@ -1,121 +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.LinkedBlockingQueue;
-import java.util.logging.Logger;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import com.google.common.eventbus.EventBus;
-import com.google.common.eventbus.Subscribe;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
-
-public class ParallelCrlogicStreamMergeTest {
-	
-	private static final Logger logger = Logger.getLogger(ParallelCrlogicStreamMergeTest.class.getName());
-	
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testMerge() throws InterruptedException {
-	
-		List<Metadata> dmm = new ArrayList<>();
-		dmm.add(new Metadata("cractuator"));
-		dmm.add(new Metadata("tstamp"));
-		
-		BlockingQueue<Message> dataQueue = new LinkedBlockingQueue<Message>();
-		DataMessage dm = new DataMessage(dmm);
-		dm.getData().add(0.0035d);
-		dm.getData().add(10.000000123);
-		dataQueue.add(dm);
-		
-		dm = new DataMessage(dmm);
-		dm.getData().add(0.015);
-		dm.getData().add(10.000000143);
-		dataQueue.add(dm);
-		
-		dm = new DataMessage(dmm);
-		dm.getData().add(0.026);
-		dm.getData().add(10.000000163);
-		dataQueue.add(dm);
-		
-		dataQueue.add(new EndOfStreamMessage());
-
-		
-		List<Metadata> dmm2 = new ArrayList<>();
-		dmm2.add(new Metadata("milli"));
-		dmm2.add(new Metadata("nano"));
-		dmm2.add(new Metadata("sensor1"));
-		
-		BlockingQueue<Message> dataQueue2 = new LinkedBlockingQueue<Message>();
-		DataMessage dm2 = new DataMessage(dmm2);
-		dm2.getData().add(9000d);
-		dm2.getData().add(122d);
-		dm2.getData().add(0.1d);
-		dataQueue2.add(dm2);
-		
-		dm2 = new DataMessage(dmm2);
-		dm2.getData().add(10000d);
-		dm2.getData().add(122d);
-		dm2.getData().add(1d);
-		dataQueue2.add(dm2);
-		
-		dm2 = new DataMessage(dmm2);
-		dm2.getData().add(10000d);
-		dm2.getData().add(153d);
-		dm2.getData().add(2d);
-		dataQueue2.add(dm2);
-		
-		dm2 = new DataMessage(dmm2);
-		dm2.getData().add(10000d);
-		dm2.getData().add(162d);
-		dm2.getData().add(3d);
-		dataQueue2.add(dm2);
-		
-		dataQueue2.add(new EndOfStreamMessage());
-
-		EventBus b = new EventBus();
-		b.register(new Object(){
-			@Subscribe
-			public void onMessage(Message m){
-				logger.info(m.toString());
-			}
-		});
-		ParallelCrlogicStreamMerge streamMerge = new ParallelCrlogicStreamMerge(dataQueue, dataQueue2, b);
-		streamMerge.merge();
-	}
-
-}

ch.psi.fda/src/test/resources/home/config/logging.properties

@@ -1,32 +0,0 @@
-# Specify the handlers to create in the root logger
-##handlers = java.util.logging.ConsoleHandler, java.util.logging.FileHandler
-handlers = java.util.logging.ConsoleHandler
-
-# Set the default logging level for the root logger
-.level=ALL
-
-# Set the default logging level for new ConsoleHandler instances
-java.util.logging.ConsoleHandler.level=ALL
-
-# Set the default formatter for new ConsoleHandler instances
-java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
-
-# Set the default logging level for new FileHandler instances
-##java.util.logging.FileHandler.level=ALL
-
-# Set the default formatter for new ConsoleHandler instances
-##java.util.logging.FileHandler.formatter=java.util.logging.SimpleFormatter
-
-# Naming of the output file:
-##java.util.logging.FileHandler.pattern=/Users/ebner/Workspace/Eclipse/workspace-xasec/ch.psi.x10/resources/logs/fda-%u.%g.log
-
-# Limiting size of output file in bytes (10000kb):
-##java.util.logging.FileHandler.limit=10000000
-
-# Number of output files to cycle through, by appending an
-# integer to the base file name:
-##java.util.logging.FileHandler.count=10
-
-# Set the default logging level for the logger named com.mycompany
-ch.psi.fda.level=ALL
-com.cosylab.epics.level=ALL

ch.psi.fda/src/test/resources/jcae.properties

@@ -1,4 +0,0 @@
-# Test properties file
-ch.psi.jcae.ContextFactory.addressList=129.129.130.255 129.129.130.37 129.129.145.26 129.129.130.88 129.129.130.142
-
-ch.psi.jcae.ChannelBeanFactory.retries=4

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,6 @@
+#Thu Mar 17 08:20:35 CET 2016
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.2.1-bin.zip

gradlew

@@ -0,0 +1,164 @@
+#!/usr/bin/env bash
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn ( ) {
+    echo "$*"
+}
+
+die ( ) {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+esac
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched.
+if $cygwin ; then
+    [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+fi
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >&-
+APP_HOME="`pwd -P`"
+cd "$SAVED" >&-
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
+function splitJvmOpts() {
+    JVM_OPTS=("$@")
+}
+eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
+JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+
+exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"

gradlew.bat

@@ -0,0 +1,90 @@
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windowz variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+if "%@eval[2+2]" == "4" goto 4NT_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+goto execute
+
+:4NT_args
+@rem Get arguments from the 4NT Shell from JP Software
+set CMD_LINE_ARGS=%$
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

src/main/assembly/assembly.xml

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

src/main/assembly/bin/convert

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

src/main/assembly/bin/scan

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

src/main/assembly/bin/scan_local

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

src/main/assembly/bin/server

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

src/main/assembly/bin/viewer

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

src/main/assembly/bin/visualize

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

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

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

src/main/assembly/www/index.html

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

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

@@ -0,0 +1 @@
+

src/main/java/ch/psi/fda/DescriptorProvider.java

@@ -0,0 +1,17 @@
+package ch.psi.fda;
+
+import java.io.File;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.fda.vdescriptor.VDescriptor;
+
+public interface DescriptorProvider {
+
+	public void load(File ... files );
+	
+	public EDescriptor getEDescriptor();
+	public VDescriptor getVDescriptor();
+	
+	public Class<?> getEDescriptorClass();
+	
+}

src/main/java/ch/psi/fda/EContainer.java

@@ -0,0 +1,28 @@
+package ch.psi.fda;
+
+public interface EContainer {
+
+	/**
+	 * Initialize execution container like required resources, etc.
+	 */
+	public void initialize();
+	
+	/**
+	 * Executes the logic implemented by the ExecutionContainer
+	 * Execute is a blocking function and must not return before the actual logic is executed
+	 */
+	public void execute();
+	
+	/**
+	 * Try to abort the execution of the logic
+	 */
+	public void abort();
+	
+	public boolean isActive();
+	
+	/**
+	 * Destroy execution container and free all allocated resources
+	 */
+	public void destroy();
+	
+}

src/main/java/ch/psi/fda/EContainerFactory.java

@@ -0,0 +1,22 @@
+package ch.psi.fda;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+
+import com.google.common.eventbus.EventBus;
+
+public interface EContainerFactory {
+
+	/**
+	 * Check whether the factory supports 
+	 * @param descriptor
+	 * @return
+	 */
+	public boolean supportsEDescriptor(EDescriptor descriptor);
+	
+	/**
+	 * Create the execution container based on the passed descriptor
+	 * @param descriptor
+	 * @return
+	 */
+	public EContainer getEContainer(EDescriptor descriptor, EventBus bus);
+}

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

@@ -55,14 +55,10 @@ import ch.psi.fda.core.actors.PseudoActuatorSensor;
 import ch.psi.fda.core.guard.ChannelAccessGuard;
 import ch.psi.fda.core.guard.ChannelAccessGuardCondition;
 import ch.psi.fda.core.loops.ActorSensorLoop;
-import ch.psi.fda.core.loops.cr.CrlogicLoop;
+import ch.psi.fda.core.loops.cr.CrlogicLoopStream;
 import ch.psi.fda.core.loops.cr.CrlogicResource;
 import ch.psi.fda.core.loops.cr.ParallelCrlogic;
 import ch.psi.fda.core.loops.cr.ScrlogicLoop;
-import ch.psi.fda.core.loops.otf.OTFLoop;
-import ch.psi.fda.core.loops.otf.OTFNamedChannelSensor;
-import ch.psi.fda.core.loops.otf.OTFScalerChannelSensor;
-import ch.psi.fda.core.loops.otf.TemplateOTF;
 import ch.psi.fda.core.manipulator.JythonManipulation;
 import ch.psi.fda.core.scripting.JythonGlobalVariable;
 import ch.psi.fda.core.scripting.JythonParameterMapping;
@@ -106,7 +102,7 @@ import ch.psi.fda.model.v1.SimpleScalarDetector;
 import ch.psi.fda.model.v1.Timestamp;
 import ch.psi.fda.model.v1.Variable;
 import ch.psi.fda.model.v1.VariableParameterMapping;
-import ch.psi.fda.serializer.DataSerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.ChannelDescriptor;
 import ch.psi.jcae.ChannelException;
@@ -119,8 +115,6 @@ import ch.psi.jcae.util.ComparatorREGEX;
 /**
  * Data acquisition engine for performing scans
  * Mapping is specific to scan model version 1.0
- * @author ebner
- *
  */
 public class Acquisition {
 	
@@ -130,7 +124,7 @@ public class Acquisition {
 	
 	private ActionLoop actionLoop;
 	private Manipulator manipulator;
-	private DataSerializerTXT serializer;
+	private SerializerTXT serializer;
 	
 	private List<Manipulation> manipulations;
 	private volatile boolean active = false;
@@ -233,9 +227,13 @@ public class Acquisition {
 		
 		logger.fine("Map Model to internal logic");
 
-		if(smodel.getScan().getManipulation()!= null && smodel.getScan().getManipulation().size()>0){
+		if(smodel.getScan().getManipulation()!= null && smodel.getScan().getManipulation().size()>0){                        
 			// Setup optimized with manipulations
-			EventBus b = new AsyncEventBus(Executors.newCachedThreadPool());
+                        //EventBus b = new AsyncEventBus(Executors.newCachedThreadPool());
+                        EventBus b = new AsyncEventBus(Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors()));
+                        
+                        //EventBus b = new AsyncEventBus(Executors.newSingleThreadExecutor());
+                        
 			// Map scan to base model
 			// After this call actionLoop and collector will be initialized
 			Collector collector = new Collector(b);
@@ -250,7 +248,7 @@ public class Acquisition {
 			b.register(this.manipulator);
 			
 			
-			this.serializer = new DataSerializerTXT(datafile, true);
+			this.serializer = new SerializerTXT(datafile, true);
 			bus.register(serializer);
 		}
 		else{
@@ -259,7 +257,7 @@ public class Acquisition {
 			mapScan(collector, smodel);
 //			col = collector;
 			
-			this.serializer = new DataSerializerTXT(datafile, true);
+			this.serializer = new SerializerTXT(datafile, true);
 			bus.register(serializer);
 		}
 	}
@@ -269,7 +267,13 @@ public class Acquisition {
 	 * @throws InterruptedException 
 	 */
 	public void execute() throws InterruptedException {
-
+		String hostname;
+		try {
+			hostname = InetAddress.getLocalHost().getHostName();
+		} catch (UnknownHostException e) {
+			hostname="unknown";
+		}
+		
 		try{
 			active = true;
 	
@@ -277,38 +281,16 @@ public class Acquisition {
 			actionLoop.execute();
 			actionLoop.cleanup();
 	
-			// Send notifications out to all recipients that want to have success notifications
-			try {
-				String hostname = InetAddress.getLocalHost().getHostName();
-				notificationAgent.sendNotification("Notification - FDA Execution Finished", "The execution of the FDA on '"+hostname+"' for file '"+datafile.getName()+"' finished successfully\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", false,true);
-			} catch (UnknownHostException e1) {
-				logger.log(Level.WARNING, "Unable to send notification", e1);
-			}
+			notificationAgent.sendNotification("Notification - FDA Execution Finished", "The execution of the FDA on '"+hostname+"' for file '"+datafile.getName()+"' finished successfully\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", false,true);
 		}
 		catch(RuntimeException e){
 			logger.log(Level.WARNING, "Execution failed: ", e);
-			
-			try {
-				String hostname = InetAddress.getLocalHost().getHostName();
-				notificationAgent.sendNotification("Notification - FDA Execution Failed", "The execution of the FDA failed on '"+hostname+"' for file '"+datafile.getName()+"'\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", true,false);
-			} catch (UnknownHostException e1) {
-				logger.log(Level.WARNING, "Unable to send notification", e1);
-			}
-			
+			notificationAgent.sendNotification("Notification - FDA Execution Failed", "The execution of the FDA failed on '"+hostname+"' for file '"+datafile.getName()+"'\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", true,false);
 			throw e;
 		}
 		catch(InterruptedException e){
 			logger.log(Level.WARNING, "Execution interrupted: ", e);
-			
-			// Execution got aborted.
-			try {
-				String hostname = InetAddress.getLocalHost().getHostName();
-				notificationAgent.sendNotification("Notification - FDA Execution was aborted", "The execution of the FDA on '"+hostname+"' for file '"+datafile.getName()+"' was aborted\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", false, true);
-			} catch (UnknownHostException e1) {
-				logger.log(Level.WARNING, "Unable to send notification", e1);
-			}
-//			throw e;
-			
+			notificationAgent.sendNotification("Notification - FDA Execution was aborted", "The execution of the FDA on '"+hostname+"' for file '"+datafile.getName()+"' was aborted\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", false, true);
 		}
 		finally{
 			active = false;
@@ -340,10 +322,6 @@ public class Acquisition {
 		// Clear global variables Jython
 		jVariableDictionary.clear();
 		
-//		// Destroy the CA context
-//		cservice.destroy();
-//		logger.fine("ChannelService destroyed");
-		
 		// Remove log handler
 		if(logHandler!=null){
 			logger.fine("Close log handler");
@@ -352,15 +330,8 @@ public class Acquisition {
 		}
 	}
 
-	/**
-	 * Abort acquisition
-	 */
 	public void abort(){
-		
 		actionLoop.abort();
-//		if(acquisitionThread!=null){
-//			acquisitionThread.interrupt();
-//		}
 	}
 	
 	public String getDatafileName(){
@@ -399,6 +370,14 @@ public class Acquisition {
 		this.configModel = configuration;
 		Scan scan = configuration.getScan();
 		
+		for(Variable v: configuration.getVariable()){
+			JythonGlobalVariable var = new JythonGlobalVariable();
+			var.setName(v.getName());
+			var.setValue(v.getValue());
+			jVariableDictionary.put(v.getName(), var);
+			v.getValue();
+		}
+		
 		// Map continuous dimension
 		if(scan.getCdimension() != null){
 			ActionLoop aLoop = mapContinuousDimension(scan.getCdimension());
@@ -979,140 +958,93 @@ public class Acquisition {
 	 * @param dimension
 	 * @return
 	 */
-	private ActionLoop mapContinuousDimension(ContinuousDimension dimension){
-		
-		ActionLoop aLoop = null;
-		
-		if(!configuration.isOtfUseCrlogic()){
-			
-			// USE OTFLOGIC FOR CONTINUOUS "SCANS"
-			
-			// Create loop
-			boolean zigZag = dimension.isZigzag(); // default value is false
-			
-			Map<String,String> macros = new HashMap<>();
-			macros.put("PREFIX", configuration.getOtfChannelPrefix());
-			TemplateOTF template = new TemplateOTF();
-			createTemplateChannels(template, macros);
-			OTFLoop actionLoop = new OTFLoop(template, configuration.getOtfNfsServer(), configuration.getOtfNfsShare(), configuration.getOtfSmbShare(), zigZag);
-			
-			actionLoop.getPreActions().addAll(mapActions(dimension.getPreAction()));
-			
-			// Map positioner
-			ContinuousPositioner p = dimension.getPositioner();
-			double backlash = 0;
-			if(p.getAdditionalBacklash()!=null){
-				backlash = p.getAdditionalBacklash();
-			}
-			actionLoop.setActuator(p.getId(), p.getName(), p.getReadback(), p.getStart(), p.getEnd(), p.getStepSize(), p.getIntegrationTime(), backlash);
-			
-			// Map sensors 
-			// ATTENTION: the sequence of the mapping depends on the sequence in the schema file !
-			int cnt = 0;
-			for(SimpleScalarDetector detector: dimension.getDetector()){
-				if(cnt<8){ // Only up to 8 additional channels supported
-					actionLoop.getSensors().add(new OTFNamedChannelSensor(detector.getId(), detector.getName()));
-				}
-				cnt++;
-			}
-			
-			cnt = 0;
-			for(ScalerChannel detector: dimension.getScaler()){
-				if(cnt<16){ // Only up to 16 scaler channels supported
-					actionLoop.getSensors().add(new OTFScalerChannelSensor(detector.getId(), detector.getChannel()));
-				}
-				cnt++;
-			}
-			
-			Timestamp detector = dimension.getTimestamp();
-			if(detector != null){
-				actionLoop.getSensors().add(new TimestampSensor(detector.getId()));
-			}
-			
-			actionLoop.getPostActions().addAll(mapActions(dimension.getPostAction()));
-			
-			aLoop = actionLoop;
-		}
-		else{
-			// USE CRLOGIC FOR CONTINUOUS "SCANS"
-			
-			boolean hcrOnly = true;
-			for(SimpleScalarDetector detector: dimension.getDetector()){
-				if(detector.isScr()){
-					hcrOnly=false;
-					break;
-				}
-			}
-			
-			
-			// BEGIN configure HCRLOGIC
-			
-			// Create loop
-			boolean zigZag = dimension.isZigzag(); // default value is false
-			
-			CrlogicLoop actionLoop = new CrlogicLoop(cservice, configuration.getOtfCrlogicPrefix(), configuration.getOtfNfsServer(), configuration.getOtfNfsShare(), configuration.getOtfSmbShare(), zigZag);
-			actionLoop.setKeepTmpFiles(configuration.isOtfCrlogicKeepTmpFiles());
-			
-			actionLoop.getPreActions().addAll(mapActions(dimension.getPreAction()));
-			
-			// Map positioner
-			ContinuousPositioner p = dimension.getPositioner();
-			double backlash = 0;
-			if(p.getAdditionalBacklash()!=null){
-				backlash = p.getAdditionalBacklash();
-			}
-			actionLoop.setActuator(p.getId(), p.getName(), p.getReadback(), p.getStart(), p.getEnd(), p.getStepSize(), p.getIntegrationTime(), backlash);
-			
-			// Map sensors 
-			// ATTENTION: the sequence of the mapping depends on the sequence in the schema file !
-			for(SimpleScalarDetector detector: dimension.getDetector()){
-				if(!detector.isScr()){
-					actionLoop.getSensors().add(new CrlogicResource(detector.getId(), detector.getName()));
-				}
-			}
-			
-			for(ScalerChannel detector: dimension.getScaler()){
-				actionLoop.getSensors().add(new CrlogicResource(detector.getId(), "SCALER"+detector.getChannel(), true));
-			}
-			
-			Timestamp tdetector = dimension.getTimestamp();
-			if(tdetector != null){
-				actionLoop.getSensors().add(new CrlogicResource(tdetector.getId(), "TIMESTAMP"));
-			}
-			
-			actionLoop.getPostActions().addAll(mapActions(dimension.getPostAction()));
-			
-			// END Configure HCRLOGIC
-			
-			
-			if(hcrOnly){
-				// There are no additional channels to be read out while taking data via hcrlogic
-				// Therefor we just register the hcr loop as action loop
+	private ActionLoop mapContinuousDimension(ContinuousDimension dimension) {
 
-				aLoop = actionLoop;
+		ActionLoop aLoop = null;
+
+		boolean hcrOnly = true;
+		for (SimpleScalarDetector detector : dimension.getDetector()) {
+			if (detector.isScr()) {
+				hcrOnly = false;
+				break;
 			}
-			else{
-				List<Channel<DoubleTimestamp>> sensors = new ArrayList<>();
-				List<String> ids = new ArrayList<>();
-				
-				for(SimpleScalarDetector detector: dimension.getDetector()){
-					if(detector.isScr()){
-						ids.add(detector.getId());
-						sensors.add(createChannel(DoubleTimestamp.class, detector.getName()));
-					}
+		}
+
+		// Create loop
+		boolean zigZag = dimension.isZigzag(); // default value is false
+
+		CrlogicLoopStream actionLoop = new CrlogicLoopStream(cservice, configuration.getCrlogicPrefix(), configuration.getCrlogicIoc(), zigZag);
+
+		actionLoop.getPreActions().addAll(mapActions(dimension.getPreAction()));
+
+		// Map positioner
+		ContinuousPositioner p = dimension.getPositioner();
+		double backlash = 0;
+		if (p.getAdditionalBacklash() != null) {
+			backlash = p.getAdditionalBacklash();
+		}
+		actionLoop.setActuator(p.getId(), p.getName(), p.getReadback(), p.getStart(), p.getEnd(), p.getStepSize(), p.getIntegrationTime(), backlash);
+
+		// Map sensors
+		// ATTENTION: the sequence of the mapping depends on the sequence in the
+		// schema file !
+		for (SimpleScalarDetector detector : dimension.getDetector()) {
+			if (!detector.isScr()) {
+				actionLoop.getSensors().add(new CrlogicResource(detector.getId(), detector.getName()));
+			}
+		}
+
+		for (ScalerChannel detector : dimension.getScaler()) {
+			actionLoop.getSensors().add(new CrlogicResource(detector.getId(), "SCALER" + detector.getChannel(), true));
+		}
+
+		Timestamp tdetector = dimension.getTimestamp();
+		if (tdetector != null) {
+			actionLoop.getSensors().add(new CrlogicResource(tdetector.getId(), "TIMESTAMP"));
+		}
+
+		actionLoop.getPostActions().addAll(mapActions(dimension.getPostAction()));
+
+		if (hcrOnly) {
+			// There are no additional channels to be read out while taking data
+			// via hcrlogic
+			// Therefore we just register the hcr loop as action loop
+
+			aLoop = actionLoop;
+		} else {
+			List<Channel<DoubleTimestamp>> sensors = new ArrayList<>();
+			List<String> ids = new ArrayList<>();
+
+			for (SimpleScalarDetector detector : dimension.getDetector()) {
+				if (detector.isScr()) {
+					ids.add(detector.getId());
+					sensors.add(createChannel(DoubleTimestamp.class, detector.getName(), true));
 				}
-				// Create soft(ware) based crlogic
-				ScrlogicLoop scrlogic = new ScrlogicLoop(ids, sensors);
-				
-				// Create parallel logic
-				ParallelCrlogic pcrlogic = new ParallelCrlogic(actionLoop, scrlogic);
-				
-				aLoop = pcrlogic;
+			}
+			// Create soft(ware) based crlogic
+			ScrlogicLoop scrlogic = new ScrlogicLoop(ids, sensors);
+
+			// Create parallel logic
+			ParallelCrlogic pcrlogic = new ParallelCrlogic(actionLoop, scrlogic);
+
+			aLoop = pcrlogic;
+		}
+		return aLoop;
+	}
+	
+	private <T> Channel<T> createChannel(Class<T> type, String name, boolean monitor){
+		try {
+			if(name== null){
+				return null;
 			}
 			
+			Channel<T> c = cservice.createChannel(new ChannelDescriptor<T>(type, name, monitor) );
+			channels.add(c);
+			return c;
+		} catch (ChannelException | InterruptedException | TimeoutException e) {
+			throw new RuntimeException("Unable to create channel: "+name,e);
 		}
 		
-		return aLoop;
 	}
 	
 	/**
@@ -1149,17 +1081,5 @@ public class Acquisition {
 			throw new RuntimeException("Unable to create channel: "+name,e);
 		}
 		
-	}
-	
-	private void createTemplateChannels(Object o, Map<String,String> macro){
-		try {
-			cservice.createAnnotatedChannels(o, macro);
-			templates.add(o);
-		} catch (ChannelException | InterruptedException | TimeoutException e) {
-			throw new RuntimeException("Unable to initialize template: "+o.getClass().getName(),e);
-		}
-		
-	}
-	
-	
+	}	
 }

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

@@ -19,6 +19,7 @@
 
 package ch.psi.fda.aq;
 
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
@@ -29,27 +30,15 @@ import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import ch.psi.fda.install.ApplicationConfigurator;
-
-/**
- * @author ebner
- *
- */
 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";
+	public final static String FDA_CONFIG_FILE = "ch.psi.fda.xscan.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;
+	private String crlogicPrefix;
+	private String crlogicIoc;
 	
 	/**
 	 * Base directory for data. The directory may contain date macros. The string may contain any @see java.text.SimpleDateFormat
@@ -77,27 +66,21 @@ public class AcquisitionConfiguration {
 	 * The constructor will read the configuration from the /fda.properties file (resource) located in the classpath.
 	 */
 	public AcquisitionConfiguration(){
-		loadConfiguration();
-	}
-	
-	
-	public void loadConfiguration(){
-		loadConfiguration(null);
+		loadConfiguration(System.getProperty(FDA_CONFIG_FILE));
 	}
 	
 	/**
 	 * Load configuration from properties file
 	 */
 	public void loadConfiguration(String file) {
-		if(file == null){
-			file = System.getProperty(FDA_CONFIG_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(file));
+				properties.load(new FileReader(cfile));
 			} catch (FileNotFoundException e) {
 				throw new RuntimeException("Configuration file "+file+" not found", e);
 			} catch (IOException e) {
@@ -109,25 +92,16 @@ public class AcquisitionConfiguration {
 		}
 		
 		// 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", "");
+		crlogicPrefix = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".crlogic.prefix", "");
+		crlogicIoc= properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".crlogic.ioc", "");
 		
-		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"));
-		
-		if(System.getProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT)!=null){ // TODO remove
-			dataBaseDirectory = System.getProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT)+"/data";
+		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; 
 		}
-		else{
-			dataBaseDirectory = "./data";
-		}
-		
 		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");
@@ -162,71 +136,22 @@ public class AcquisitionConfiguration {
 		return newString;
 	}
 
-	// Getter and setter functions
+
+	public String getCrlogicPrefix() {
+		return crlogicPrefix;
+	}
+
+	public void setCrlogicPrefix(String crlogicPrefix) {
+		this.crlogicPrefix = crlogicPrefix;
+	}
 	
-	public String getOtfChannelPrefix() {
-		return otfChannelPrefix;
+	public void setCrlogicIoc(String crlogicIoc) {
+		this.crlogicIoc = crlogicIoc;
 	}
-
-	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 getCrlogicIoc() {
+		return crlogicIoc;
 	}
+	
 
 	public String getDataBaseDirectory() {
 		return dataBaseDirectory;
@@ -259,5 +184,4 @@ public class AcquisitionConfiguration {
 	public void setSmptServer(String smptServer) {
 		this.smptServer = smptServer;
 	}
-	
 }

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

@@ -25,11 +25,11 @@ import java.util.List;
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
+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.

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

@@ -26,9 +26,9 @@ import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
 import ch.psi.fda.core.Manipulation;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
 
 /**
  * Applies manipulations to the data stream
@@ -66,12 +66,14 @@ public class Manipulator {
 			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));
+//                          ((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);
 			}
-			// Need to update the metadata of the message
-			dm.setMetadata(this.metadata);
-		}
+		}                
 		bus.post(message);
+                //System.out.println(Thread.currentThread());
 	}
 }

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

@@ -0,0 +1,50 @@
+package ch.psi.fda.aq;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.EContainer;
+import ch.psi.fda.model.v1.Configuration;
+import ch.psi.jcae.ChannelService;
+
+public class XScanContainer implements EContainer {
+
+	private final Acquisition acquisition;
+	
+	private EventBus bus;
+	private Configuration xscanConfiguration;
+	
+	public XScanContainer(ChannelService cservice, AcquisitionConfiguration config, EventBus bus, Configuration xscanConfiguration){
+		acquisition = new Acquisition(cservice, config);
+		this.bus = bus;
+		this.xscanConfiguration = xscanConfiguration;
+	}
+	
+	@Override
+	public void initialize() {
+		acquisition.initalize(bus, xscanConfiguration);
+	}
+
+	@Override
+	public void execute() {
+		try {
+			acquisition.execute();
+		} catch (InterruptedException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	@Override
+	public void abort() {
+		acquisition.abort();
+	}
+
+	@Override
+	public void destroy() {
+		acquisition.destroy();
+	}
+
+	@Override
+	public boolean isActive() {
+		return acquisition.isActive();
+	}
+}

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

@@ -0,0 +1,29 @@
+package ch.psi.fda.aq;
+
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.fda.model.v1.Configuration;
+
+@XmlRootElement(name="edescriptor")
+@XmlType(name="edescriptor")
+public class XScanDescriptor implements EDescriptor {
+
+	private Configuration configuration;
+
+	public XScanDescriptor(){
+	}
+	
+	public XScanDescriptor(Configuration configuration){
+		this.configuration = configuration;
+	}
+
+	
+	public Configuration getConfiguration() {
+		return configuration;
+	}
+	public void setConfiguration(Configuration configuration) {
+		this.configuration = configuration;
+	}
+}

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

@@ -1,114 +1,128 @@
-/**
- * 
- * 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.io.File;
 import java.util.List;
+import java.util.logging.Logger;
 
+import ch.psi.fda.DescriptorProvider;
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.fda.model.ModelManager;
 import ch.psi.fda.model.v1.ArrayDetector;
+import ch.psi.fda.model.v1.Configuration;
 import ch.psi.fda.model.v1.ContinuousPositioner;
+import ch.psi.fda.model.v1.Data;
 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;
+import ch.psi.fda.vdescriptor.LinePlot;
+import ch.psi.fda.vdescriptor.VDescriptor;
+import ch.psi.fda.vdescriptor.XYSeries;
+import ch.psi.fda.vdescriptor.XYZSeries;
+import ch.psi.fda.vdescriptor.YSeries;
+import ch.psi.fda.vdescriptor.YZSeries;
 
-/**
- * @author ebner
- *
- */
-public class VisualizationMapper {
+public class XScanDescriptorProvider implements DescriptorProvider {
 	
+	private static final Logger logger = Logger.getLogger(XScanDescriptorProvider.class.getName());
+
+	private EDescriptor edescriptor;
+	private VDescriptor vdescriptor;
 	
-	/**
-	 * 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();
+	@Override
+	public void load(File... files) {
+		
+		if(files.length<1 || files[0]==null){
+			throw new IllegalArgumentException("There need to be at lease one file specified");
 		}
-		else if (object instanceof Detector){
-			id = ((Detector)object).getId();
+		File file = files[0];
+		
+		if(!file.exists()){
+			throw new IllegalArgumentException("File "+file.getAbsolutePath()+" does not exist");
 		}
-		else if (object instanceof ch.psi.fda.model.v1.Manipulation){
-			id = ((ch.psi.fda.model.v1.Manipulation)object).getId();
+		
+		Configuration c;
+		try {
+			c = ModelManager.unmarshall(file);
+		} catch (Exception e) {
+			throw new UnsupportedOperationException("Unable to deserialize configuration: "+e.getMessage(), e);
 		}
-		// For testing purposes
-		else if(object instanceof String){
-			id = (String) object;
+		
+		// Set data file name
+		// Determine name used for the data file
+		String name = file.getName();
+		name = name.replaceAll("\\.xml$", "");
+		
+		if(c.getData()!=null){
+			Data data = c.getData();
+			// Only update filename if no name is specified in xml file
+			if(data.getFileName()==null){
+				data.setFileName(name);
+			}
 		}
 		else{
-			throw new RuntimeException("Unable to identify id of object reference "+object);
+			Data data = new Data();
+			data.setFileName(name);
+			c.setData(data);
 		}
-		return id;
+		
+		
+//		// Override number of executions
+//		if(iterations != null){
+//			c.setNumberOfExecution(iterations);
+//		}
+		// Fix configuration if iterations is specified with 0 and no iterations option is specified
+		if(c.getNumberOfExecution()==0){
+			c.setNumberOfExecution(1);
+		}
+		
+		this.edescriptor = new XScanDescriptor(c);
+		this.vdescriptor = mapVisualizations(c.getVisualization());
+		
 	}
 	
-	public static List<SeriesDataFilter> mapVisualizations(List<Visualization> vl){
-		List<SeriesDataFilter> filters = new ArrayList<SeriesDataFilter>();
+	/**
+	 * Create a vdescriptor out of the scan description
+	 * @param vl
+	 * @return
+	 */
+	public static VDescriptor mapVisualizations(List<Visualization> vl){
+		VDescriptor vd = new VDescriptor();
+		
 		
 		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());
+				String x = getId(lp.getX());
 				
+				LinePlot lineplot = new LinePlot(lp.getTitle());
 				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);
+					String y = getId(o);
+					lineplot.getData().add(new XYSeries(x, y));
 				}
+				
+				vd.getPlots().add(lineplot);
 			}
 			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());
-				
+				LinePlot lineplot = new 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);
+					// TODO Need to actually check if minX of 
+					lineplot.setMinX(new Double(lp.getOffset()));
+					lineplot.setMaxX(new Double(lp.getOffset()+lp.getSize()));
+                                        lineplot.setMaxSeries(lp.getMaxSeries());
+					lineplot.getData().add(new YSeries(idY));
 				}
+                                vd.getPlots().add(lineplot);
 			}
 			else if(v instanceof ch.psi.fda.model.v1.MatrixPlot){
 				
@@ -178,12 +192,18 @@ public class VisualizationMapper {
 				// 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);
+				ch.psi.fda.vdescriptor.MatrixPlot matrixplot = new ch.psi.fda.vdescriptor.MatrixPlot(mp.getTitle());
+				matrixplot.setMinX(minX);
+				matrixplot.setMaxX(maxX);
+				matrixplot.setnX(nX);
+				matrixplot.setMinY(minY);
+				matrixplot.setMaxY(maxY);
+				matrixplot.setnY(nY);
+                                matrixplot.setType(mp.getType());
+				
+				matrixplot.getData().add(new XYZSeries(idX, idY, idZ));
+				vd.getPlots().add(matrixplot);
 			}
 			else if(v instanceof ch.psi.fda.model.v1.MatrixPlotArray){
 				// Support for 2D waveform plots
@@ -254,18 +274,66 @@ public class VisualizationMapper {
 				// 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);
+				ch.psi.fda.vdescriptor.MatrixPlot matrixplot = new ch.psi.fda.vdescriptor.MatrixPlot(mp.getTitle());
+				matrixplot.setMinX(minX);
+				matrixplot.setMaxX(maxX);
+				matrixplot.setnX(nX);
+				matrixplot.setMinY(minY);
+				matrixplot.setMaxY(maxY);
+				matrixplot.setnY(nY);
+                                matrixplot.setType(mp.getType());
+				
+				matrixplot.getData().add(new YZSeries(idY, idZ));
+				vd.getPlots().add(matrixplot);
 				
-				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");
+				logger.warning(v.getClass().getName()+" is not supported as visualization type");
 			}
 		}
-		return filters;
+		return vd;
 	}
+	
+	/**
+	 * 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;
+	}
+	
+
+	@Override
+	public EDescriptor getEDescriptor() {
+		return edescriptor;
+	}
+
+	@Override
+	public VDescriptor getVDescriptor() {
+		return vdescriptor;
+	}
+
+	@Override
+	public Class<?> getEDescriptorClass() {
+		return XScanDescriptor.class;
+	}
+
 }

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

@@ -0,0 +1,36 @@
+package ch.psi.fda.aq;
+
+import javax.inject.Inject;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.EContainer;
+import ch.psi.fda.EContainerFactory;
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.jcae.ChannelService;
+
+public class XScanFactory implements EContainerFactory {
+
+	@Inject
+	private ChannelService cservice;
+	
+	private AcquisitionConfiguration config = new AcquisitionConfiguration();
+	
+	@Override
+	public boolean supportsEDescriptor(EDescriptor descriptor) {
+		return (descriptor instanceof XScanDescriptor);
+	}
+
+	@Override
+	public EContainer getEContainer(EDescriptor descriptor, EventBus bus) {
+		
+		if(! (descriptor instanceof XScanDescriptor)){
+			throw new IllegalArgumentException("Descriptor of type "+descriptor.getClass().getName()+" is not supported - descriptor need to be of type "+XScanDescriptor.class);
+		}
+		
+		XScanDescriptor xdescriptor = (XScanDescriptor) descriptor;
+		
+		return new XScanContainer(cservice, config, bus, xdescriptor.getConfiguration());
+	}
+
+}

src/main/java/ch/psi/fda/cdump/Cdump.java

@@ -0,0 +1,151 @@
+/**
+ * 
+ * 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.cdump;
+
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.TimeoutException;
+import java.util.logging.Logger;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.jcae.Channel;
+import ch.psi.jcae.ChannelDescriptor;
+import ch.psi.jcae.ChannelException;
+import ch.psi.jcae.ChannelService;
+
+/**
+ * Cdump readout logic - i.e. put monitor on a data waveform channel of the fast
+ * ADC and send data to the eventbus
+ */
+public class Cdump {
+	
+	private static final Logger logger = Logger.getLogger(Cdump.class.getName());
+	
+	public final static String[] SAMPLING_RATES = new String[] {"1Hz","2Hz", "5Hz", "10Hz", "20Hz", "50Hz", "100Hz", "200Hz", "500Hz",
+		"1kHz", "2kHz", "5kHz", "10kHz", "20kHz", "50kHz", "100kHz"};
+	
+	private Channel<int[]> adcData;
+
+	private enum AdcCmd {
+		READY, GO
+	};
+
+	private Channel<Integer> adcCmd;
+
+	private CdumpListener listener;
+	private ChannelService cservice;
+	private CdumpConfiguration configuration;
+
+	public Cdump(ChannelService cservice, EventBus ebus, CdumpConfiguration configuration) {
+		this.cservice = cservice;
+		this.configuration = configuration;
+		this.listener = new CdumpListener(ebus, configuration.getNelements());
+	}
+
+	/**
+	 * Acquire data with the given sampling rate
+	 * @param samplingRate
+	 */
+	public void acquire(String samplingRate) {
+		
+		logger.info("Start acquisition with sampling rate "+ samplingRate);
+		
+		try {
+			// Set ADC sampling rate
+			Channel<Integer> smplRate = cservice.createChannel(new ChannelDescriptor<>(Integer.class, configuration.getSamplingRateChannel(), false));
+			smplRate.setValue(getIntSamplingRate(samplingRate));
+			smplRate.destroy();
+
+			adcData = cservice.createChannel(new ChannelDescriptor<>(int[].class, configuration.getDataChannel(), true));
+			adcCmd = cservice.createChannel(new ChannelDescriptor<>(Integer.class, configuration.getControlChannel(), false));
+
+			adcCmd.setValue(AdcCmd.GO.ordinal());
+			adcData.addPropertyChangeListener(listener);
+		} catch (ChannelException | TimeoutException | InterruptedException | ExecutionException e) {
+			throw new RuntimeException(e);
+		}
+	}
+	
+	/**
+	 * Wait until acquire is done
+	 */
+	public void waitAcquireDone(){
+		try {
+			adcCmd.waitForValue(AdcCmd.READY.ordinal());
+		} catch (InterruptedException | ExecutionException | ChannelException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	public void stop() {
+		
+		logger.info("Stop acquisition");
+		
+		try {
+			// Detach listener from channel - i.e. stop data acquisition
+			adcData.removePropertyChangeListener(listener);
+			adcCmd.setValue(AdcCmd.READY.ordinal());
+	
+			listener.terminate();
+		
+			adcCmd.destroy();
+			adcData.destroy();
+		} catch (ChannelException | InterruptedException | ExecutionException e) {
+			throw new RuntimeException(e);
+		}
+	}
+	
+	/**
+	 * Get sampling rate int value based on the passed rate string.
+	 * If the string does not match any of the strings specified in the rates variable
+	 * this function will set the rate to 1Hz
+	 * 
+	 * 0  = 1Hz 
+	 * 1  = 2Hz
+	 * 2  = 5Hz
+	 * 3  = 10Hz
+	 * 4  = 20Hz
+	 * 5  = 50Hz
+	 * 6  = 100Hz
+	 * 7  = 200Hz
+	 * 8  = 500Hz
+	 * 9  = 1000Hz
+	 * 10 = 2000Hz
+	 * 11 = 5000Hz
+	 * 12 = 10000Hz
+	 * 13 = 20000Hz
+	 * 14 = 50000Hz
+	 * 15 = 100000Hz
+	 *  
+	 * @param rate
+	 */
+	private int getIntSamplingRate(String rate){
+		
+		for(int i=0;i<SAMPLING_RATES.length; i++){
+			if(rate.equals(SAMPLING_RATES[i])){
+				return i;
+			}
+		}
+		
+		// Default sampling rate 10kHz
+		logger.info("Using default sampling rate 12");
+		return 12;
+	}
+}

src/main/java/ch/psi/fda/cdump/CdumpConfiguration.java

@@ -0,0 +1,87 @@
+/**
+ * 
+ * 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.cdump;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Properties;
+
+
+public class CdumpConfiguration {
+	
+	public final static String CDUMP_CONFIG = "ch.psi.fda.cdump.config.file";
+	
+	private String dataChannel;
+	private int nelements = 65536;
+	private String controlChannel;
+	private String samplingRateChannel;
+
+	public CdumpConfiguration(){
+		String config = System.getProperty(CDUMP_CONFIG);
+		
+		if(config != null){
+			loadFile(new File(config));
+		}
+		else{
+			throw new RuntimeException("No configuration file specified via -D"+CDUMP_CONFIG+"=...");
+		}
+	}
+
+	public void loadFile(File file) {
+		Properties properties = new Properties();
+		
+		if(file!=null){
+			try {
+				properties.load(new FileReader(file));
+			} catch (IOException e) {
+				throw new RuntimeException("Cannot read file "+file, e);
+			}
+		}
+		
+		dataChannel = properties.getProperty(CdumpConfiguration.class.getPackage().getName()+".dataChannel", "");
+		controlChannel = properties.getProperty(CdumpConfiguration.class.getPackage().getName()+".controlChannel", "");
+		samplingRateChannel = properties.getProperty(CdumpConfiguration.class.getPackage().getName()+".samplingRateChannel", "");
+		nelements = Integer.parseInt(properties.getProperty(CdumpConfiguration.class.getPackage().getName()+".nelements", "65536"));
+		
+	}
+	
+	public String getDataChannel() {
+		return dataChannel;
+	}
+	public void setDataChannel(String dataChannel) {
+		this.dataChannel = dataChannel;
+	}
+	public String getControlChannel() {
+		return controlChannel;
+	}
+	public void setControlChannel(String controlChannel) {
+		this.controlChannel = controlChannel;
+	}
+	public String getSamplingRateChannel() {
+		return samplingRateChannel;
+	}
+	public void setSamplingRateChannel(String samplingRateChannel) {
+		this.samplingRateChannel = samplingRateChannel;
+	}
+	public int getNelements() {
+		return nelements;
+	}
+}

src/main/java/ch/psi/fda/cdump/CdumpEContainer.java

@@ -0,0 +1,73 @@
+package ch.psi.fda.cdump;
+
+import java.io.File;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.EContainer;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.jcae.ChannelService;
+
+public class CdumpEContainer implements EContainer {
+
+	private final ChannelService cservice;
+	private final CdumpEDescriptor edescriptor;
+	private final EventBus eventbus;
+
+	private Cdump cdump;
+	private SerializerTXT serializer;
+
+	private volatile boolean running = false;
+	
+	public CdumpEContainer(ChannelService cservice, EventBus eventbus, CdumpEDescriptor edescriptor) {
+		this.cservice = cservice;
+		this.eventbus = eventbus;
+		this.edescriptor = edescriptor;
+	}
+
+	@Override
+	public void initialize() {
+		cdump = new Cdump(cservice, eventbus, new CdumpConfiguration());
+
+		File file = new File(edescriptor.getFileName());
+		file.getParentFile().mkdirs(); // Create data base directory
+		
+		serializer = new SerializerTXT(file);
+		serializer.setShowDimensionHeader(false);
+
+		eventbus.register(serializer);
+	}
+
+	@Override
+	public void execute() {
+		running = true;
+		try{
+			cdump.acquire(edescriptor.getSamplingRate());
+			cdump.waitAcquireDone();
+		}
+		finally{
+			running=false;
+		}
+	}
+
+	@Override
+	public void abort() {
+		eventbus.post(new EndOfStreamMessage());
+		cdump.stop();
+		running = false;
+		
+		eventbus.unregister(serializer);
+	}
+
+	@Override
+	public boolean isActive() {
+		return running;
+	}
+
+	@Override
+	public void destroy() {
+		abort();
+	}
+
+}

src/main/java/ch/psi/fda/cdump/CdumpEContainerFactory.java

@@ -0,0 +1,26 @@
+package ch.psi.fda.cdump;
+
+import javax.inject.Inject;
+
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.EContainer;
+import ch.psi.fda.EContainerFactory;
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.jcae.ChannelService;
+
+public class CdumpEContainerFactory implements EContainerFactory {
+
+	@Inject
+	private ChannelService cservice;
+	
+	@Override
+	public boolean supportsEDescriptor(EDescriptor descriptor) {
+		return descriptor instanceof CdumpEDescriptor;
+	}
+
+	@Override
+	public EContainer getEContainer(EDescriptor descriptor, EventBus bus) {
+		return new CdumpEContainer(cservice, bus, (CdumpEDescriptor) descriptor);
+	}
+}

src/main/java/ch/psi/fda/cdump/CdumpEDescriptor.java

@@ -0,0 +1,25 @@
+package ch.psi.fda.cdump;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+
+@XmlRootElement(name="cdump")
+public class CdumpEDescriptor implements EDescriptor {
+
+	private String samplingRate;
+	private String fileName;
+	
+	public String getSamplingRate() {
+		return samplingRate;
+	}
+	public void setSamplingRate(String samplingRate) {
+		this.samplingRate = samplingRate;
+	}
+	public String getFileName() {
+		return fileName;
+	}
+	public void setFileName(String fileName) {
+		this.fileName = fileName;
+	}
+}

src/main/java/ch/psi/fda/cdump/CdumpEDescriptorProvider.java

@@ -0,0 +1,44 @@
+package ch.psi.fda.cdump;
+
+import java.io.File;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+import ch.psi.fda.DescriptorProvider;
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.fda.vdescriptor.VDescriptor;
+
+public class CdumpEDescriptorProvider implements DescriptorProvider {
+
+	private EDescriptor edescriptor;
+	
+	@Override
+	public void load(File... files) {
+		try {
+			JAXBContext context = JAXBContext.newInstance(CdumpEDescriptor.class);
+			Unmarshaller u = context.createUnmarshaller();
+			edescriptor = (EDescriptor) u.unmarshal(files[0]);
+		} catch (JAXBException e) {
+			throw new RuntimeException(e);
+		}
+		
+	}
+
+	@Override
+	public EDescriptor getEDescriptor() {
+		return edescriptor;
+	}
+
+	@Override
+	public VDescriptor getVDescriptor() {
+		return null;
+	}
+
+	@Override
+	public Class<?> getEDescriptorClass() {
+		return CdumpEDescriptor.class;
+	}
+
+}

src/main/java/ch/psi/fda/cdump/CdumpListener.java

@@ -0,0 +1,102 @@
+/**
+ * 
+ * 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.cdump;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
+
+import com.google.common.eventbus.EventBus;
+
+/**
+ * Listener that monitors the adc data channel and splitting up the data
+ */
+public class CdumpListener implements PropertyChangeListener {
+	
+	private final EventBus bus;
+	private final int numberOfElements;
+
+	private boolean first = true;
+	private int numberOfWaveforms = 0;
+	private final List<Metadata> metadata = new ArrayList<>();
+	
+	public CdumpListener(EventBus bus, int numberOfElements){
+		this.bus = bus;
+		this.numberOfElements = numberOfElements;
+	}
+	
+	@Override
+	public void propertyChange(PropertyChangeEvent evt) {
+		if(evt.getPropertyName().equals("value")){
+			transform((int[]) evt.getNewValue());
+		}
+	}
+	
+	
+	/**
+	 * Transform received waveform
+	 * 1. Take channel waveform
+	 * [wavefrom .......................................................]
+	 * 2. Split up waveform
+	 * [1-number of elements][2-number of elements][3-number of elements]
+	 * 3. Rotate splitted waveforms
+	 * [1-0,2-0,3-0]   thats one message
+	 * [1-1,2-1,3-1]
+	 * ...
+	 * [1-noe, 2-noe, 3-noe]
+	 * 
+	 */
+	public void transform(int[] value){
+		
+		// The first time check whether received waveform is a multiple of the specified number of elements number
+		// Calculate how many waveforms are within the received waveform
+		if(first){
+			first=false;
+			int nelements = value.length;
+			int n = nelements % numberOfElements;
+			if (n != 0) {
+				throw new RuntimeException("Array size is not a multiple of "+numberOfElements);
+			}
+			numberOfWaveforms = nelements / numberOfElements;
+			for(int i=0;i<numberOfWaveforms;i++){
+				metadata.add(new Metadata("waveform-"+i));
+			}
+		}
+		
+
+		// Split and rotate waveform
+		for (int x = 0; x < numberOfElements; x++) {
+			
+			DataMessage m = new DataMessage(metadata);
+			for (int t = 0; t < numberOfWaveforms; t++) {
+				m.getData().add(value[x + t * numberOfElements]);
+			}
+			bus.post(m);
+		}
+	}
+
+	public void terminate(){
+		bus.post(new EndOfStreamMessage());
+	}
+}

src/main/java/ch/psi/fda/cdump/ui/CdumpMain.java

@@ -0,0 +1,107 @@
+/**
+ * 
+ * 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.cdump.ui;
+
+import java.io.File;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import com.google.common.eventbus.AsyncEventBus;
+import com.google.common.eventbus.EventBus;
+
+import ch.psi.fda.cdump.Cdump;
+import ch.psi.fda.cdump.CdumpConfiguration;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.jcae.ChannelService;
+import ch.psi.jcae.impl.DefaultChannelService;
+import sun.misc.Signal;
+import sun.misc.SignalHandler;
+
+@SuppressWarnings("restriction")
+public class CdumpMain {
+	
+	public static void main(String[] args){
+		
+		final ChannelService cservice = new DefaultChannelService();
+		
+		if(args.length != 2){
+			System.err.println("Usage: cdump <samplingRate> <datafilename>");
+			StringBuilder b = new StringBuilder();
+			for(String s: Cdump.SAMPLING_RATES){
+				b.append(s);
+				b.append(" ");
+			}
+			System.err.println("Supported rates: "+b.toString());
+			System.exit(1);
+		}
+		
+		String samplingRate = args[0];
+		
+		// Calculate data file location/name
+		String fname = args[1];
+		
+		File f = new File(fname);
+		f.getParentFile().mkdirs(); // Create data base directory
+		
+		// Create execution service
+		EventBus eventbus = new AsyncEventBus(Executors.newSingleThreadExecutor());
+		final Cdump service = new Cdump(cservice, eventbus, new CdumpConfiguration());
+		
+		SerializerTXT serializer = new SerializerTXT(f);
+		serializer.setShowDimensionHeader(false);
+		
+		eventbus.register(serializer);
+	
+		// Stop/abort handling of acquisition
+		Signal.handle(new Signal("INT"), new SignalHandler() {
+			/**
+			 * Thread save signal counter
+			 */
+			private AtomicInteger signalCount= new AtomicInteger(0);
+			
+			/**
+			 * Testing signal handler (in Eclipse) use this after starting scan:
+			 *
+			 * SL5: A=`ps -ef | tail -10 | grep jav[a] | awk '{printf $2}'`;kill -2 $A
+			 * MacOS X: A=`ps -ef | grep AcquisitionMai[n] | awk '{printf $2}'`;kill -2 $A
+			 * 
+			 * on the command line use CTRL-C
+			 */
+			@Override
+			public void handle(Signal signal) {
+				
+				
+				int count = signalCount.incrementAndGet();
+				
+				// If signal is received more than 1 time forcefully abort application
+				if(count>1){
+					System.exit(2);
+				}
+
+				service.stop();
+				
+				cservice.destroy();
+			}
+		});
+		
+		service.acquire(samplingRate);
+	}
+
+}

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

@@ -21,8 +21,8 @@ package ch.psi.fda.core;
 
 import java.util.List;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Metadata;
 
 public interface Manipulation {
 

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

@@ -16,25 +16,21 @@
  * along with this code. If not, see <http://www.gnu.org/licenses/>.
  * 
  */
-package ch.psi.fda;
+package ch.psi.fda.core;
 
-/**
- * @author ebner
- *
- */
 public class TestConfiguration {
 	private static final TestConfiguration instance = new TestConfiguration();
 	
 	private final String otfPrefix = "MTEST-HW3-OTFX";
 	private final String crlogicPrefix = "MTEST-HW3-CRL";
 	private final String prefixScaler = "MTEST-HW3:JS";
-	private final String server = "yoke.psi.ch";
-	private final String share = "/usr/nfs";
-	private final String smbShare = "smb://test:test@"+server+"/nfs/"; // It is important to have the last slash / !
+	private final String server = "MTEST-VME-HW3";
 	
 	private final String motor1 = "MTEST-HW3:MOT1";
 	private final String analogIn1 = "MTEST-HW3-AI1:AI_01";
 	
+	private final String ioc = "MTEST-VME-HW3.psi.ch";
+	
 	private TestConfiguration(){
 	}
 	
@@ -63,20 +59,6 @@ public class TestConfiguration {
 		return server;
 	}
 
-	/**
-	 * @return the share
-	 */
-	public String getShare() {
-		return share;
-	}
-
-	/**
-	 * @return the smbShare
-	 */
-	public String getSmbShare() {
-		return smbShare;
-	}
-
 	/**
 	 * @return the motor1
 	 */
@@ -98,5 +80,8 @@ public class TestConfiguration {
 		return otfPrefix;
 	}
 
+	public String getIoc() {
+		return ioc;
+	}
 	
 }