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-1.6">
-		<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.jdt.core.prefs

@@ -1,5 +0,0 @@
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
-org.eclipse.jdt.core.compiler.compliance=1.6
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.6

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

@@ -1,205 +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>1.1.40</version>
-
-	<dependencies>
-		<dependency>
-			<groupId>ch.psi</groupId>
-			<artifactId>jcae</artifactId>
-			<version>1.0.30</version>
-		</dependency>
-		<!-- Plotting library -->
-		<dependency>
-			<groupId>ch.psi</groupId>
-			<artifactId>plot</artifactId>
-			<version>1.1.30</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>javax.mail</groupId>
-			<artifactId>mail</artifactId>
-			<version>1.4.1</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>
-					<source>1.6</source>
-					<target>1.6</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>
-			</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/aq/AcquisitionEngineConfiguration.java

@@ -1,299 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.aq;
-
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-import java.util.Properties;
-import java.util.logging.Logger;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import ch.psi.fda.install.ApplicationConfigurator;
-
-/**
- * @author ebner
- *
- */
-public class AcquisitionEngineConfiguration {
-	
-	
-	private static final Logger logger = Logger.getLogger(AcquisitionEngineConfiguration.class.getName());
-	private static final AcquisitionEngineConfiguration instance = new AcquisitionEngineConfiguration();
-	
-	private String otfChannelPrefix;
-	private String otfNfsServer;
-	private String otfNfsShare;
-	private String otfSmbShare;
-	private String otfScalerPrefix;
-	private boolean otfUseCrlogic;
-	private String otfCrlogicPrefix;
-	private boolean otfCrlogicKeepTmpFiles;
-	
-	/**
-	 * Base directory for data. The directory may contain date macros. The string may contain any @see java.text.SimpleDateFormat
-	 * patterns within ${ } brackets. The macros are resolved with the actual time while the get method
-	 * of this property is called.
-	 */
-	private String dataBaseDirectory = System.getProperty("user.home");
-	/**
-	 * Prefix of the data file. The prefix may contain date macros. The string may contain any @see java.text.SimpleDateFormat
-	 * patterns within ${ } brackets. The macros are resolved with the actual time while the get method
-	 * of this property is called.
-	 */
-	private String dataFilePrefix = "";
-	
-	/**
-	 * Maximum time for a actor move
-	 */
-	private Long actorMoveTimeout = 600000l; // 10 Minutes maximum move time 
-	
-	private String smptServer;
-	
-	/**
-	 * Default Constructor
-	 * The constructor will read the configuration from the /fda.properties file (resource) located in the classpath.
-	 */
-	private AcquisitionEngineConfiguration(){
-		loadConfiguration();
-	}
-	
-	/**
-	 * Get instance of this configuration
-	 * @return configuration
-	 */
-	public static AcquisitionEngineConfiguration getInstance(){
-		return(instance);
-	}
-	
-	/**
-	 * Load configuration from properties file
-	 */
-	private void loadConfiguration() {
-		String config = System.getProperty(ApplicationConfigurator.FDA_CONFIG_FILE_ARGUMENT);
-		
-		Properties properties = new Properties();
-		
-		if(config != null){
-			try {
-				properties.load(new FileReader(config));
-			} catch (FileNotFoundException e) {
-				throw new RuntimeException("Configuration file "+config+" not found", e);
-			} catch (IOException e) {
-				throw new RuntimeException("Cannot read configuration file "+config, e);
-			}
-		}
-		else{
-			logger.warning("No configfile specified !");
-		}
-		
-		// The defaults are set here
-		otfChannelPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.channelPrefix", "");
-		otfScalerPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.scalerPrefix", "");
-		otfNfsServer = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.nfsServer", "");
-		otfNfsShare = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.nfsShare", "");
-		otfSmbShare = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.smbShare", "");
-		otfUseCrlogic = new Boolean(properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.useCrlogic", "false"));
-		otfCrlogicPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.crlogicPrefix", "");
-		otfCrlogicKeepTmpFiles = new Boolean(properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.crlogicKeepTmpFiles", "false"));
-		
-		// Workaround
-//		dataBaseDirectory = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".data.baseDirectory", ".");
-		if(System.getProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT)!=null){
-			dataBaseDirectory = System.getProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT)+"/data";
-		}
-		else{
-			dataBaseDirectory = "./data";
-		}
-		
-		dataFilePrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".data.filePrefix","");
-		
-		actorMoveTimeout = new Long(properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".actorMoveTimeout","600000"));
-		
-		smptServer= properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".notification.host","mail.psi.ch");
-		
-	}
-	
-	/**
-	 * Reload this configuration from the corresponding properties file
-	 * @throws IOException 
-	 */
-	public void reloadConfiguration() throws IOException{
-		loadConfiguration();
-	}
-
-	/**
-	 * @return the otfChannelPrefix
-	 */
-	public String getOtfChannelPrefix() {
-		return otfChannelPrefix;
-	}
-
-	/**
-	 * @return the otfScalerPrefix
-	 */
-	public String getOtfScalerPrefix() {
-		return otfScalerPrefix;
-	}
-
-	/**
-	 * @return the otfNfsServer
-	 */
-	public String getOtfNfsServer() {
-		return otfNfsServer;
-	}
-
-	/**
-	 * @return the otfNfsShare
-	 */
-	public String getOtfNfsShare() {
-		return otfNfsShare;
-	}
-
-	/**
-	 * @return the otfSmbShare
-	 */
-	public String getOtfSmbShare() {
-		return otfSmbShare;
-	}
-
-	/**
-	 * @return the otfUseCrlogic
-	 */
-	public boolean isOtfUseCrlogic() {
-		return otfUseCrlogic;
-	}
-
-	/**
-	 * @return the dataBaseDirectory
-	 */
-	public String getDataBaseDirectory() {
-		return dataBaseDirectory;
-	}
-
-	/**
-	 * @return the dataFilePrefix
-	 */
-	public String getDataFilePrefix() {
-		return dataFilePrefix;
-	}
-
-	/**
-	 * @return the smptServer
-	 */
-	public String getSmptServer() {
-		return smptServer;
-	}
-
-	
-	/**
-	 * @return the otfCrlogicPrefix
-	 */
-	public String getOtfCrlogicPrefix() {
-		return otfCrlogicPrefix;
-	}
-
-	/**
-	 * @return the otfCrlogicKeepTmpFiles
-	 */
-	public boolean isOtfCrlogicKeepTmpFiles() {
-		return otfCrlogicKeepTmpFiles;
-	}
-
-	/**
-	 * @return the actorMoveTimeout
-	 */
-	public Long getActorMoveTimeout() {
-		return actorMoveTimeout;
-	}
-
-	public String replaceMacros(String string, Date date, String name){
-		String newString = string;
-		
-		// Replace scan name macros
-		newString = newString.replaceAll("\\$\\{name\\}", name);
-		
-		
-		// Replace date macros
-		Pattern pattern = Pattern.compile("\\$\\{[a-z,A-Z,-,_,:]*\\}");
-        Matcher matcher = pattern.matcher(newString);
-        while(matcher.find()){
-        	String datePattern = matcher.group();
-        	datePattern = datePattern.replaceAll("\\$\\{", "");
-        	datePattern = datePattern.replaceAll("\\}", "");
-        	SimpleDateFormat datef = new SimpleDateFormat(datePattern);
-        	newString = matcher.replaceFirst(datef.format(date));
-        	matcher = pattern.matcher(newString);
-        }
-		return newString;
-	}
-
-	public void setOtfChannelPrefix(String otfChannelPrefix) {
-		this.otfChannelPrefix = otfChannelPrefix;
-	}
-
-	public void setOtfNfsServer(String otfNfsServer) {
-		this.otfNfsServer = otfNfsServer;
-	}
-
-	public void setOtfNfsShare(String otfNfsShare) {
-		this.otfNfsShare = otfNfsShare;
-	}
-
-	public void setOtfSmbShare(String otfSmbShare) {
-		this.otfSmbShare = otfSmbShare;
-	}
-
-	public void setOtfScalerPrefix(String otfScalerPrefix) {
-		this.otfScalerPrefix = otfScalerPrefix;
-	}
-
-	public void setOtfUseCrlogic(boolean otfUseCrlogic) {
-		this.otfUseCrlogic = otfUseCrlogic;
-	}
-
-	public void setOtfCrlogicPrefix(String otfCrlogicPrefix) {
-		this.otfCrlogicPrefix = otfCrlogicPrefix;
-	}
-
-	public void setOtfCrlogicKeepTmpFiles(boolean otfCrlogicKeepTmpFiles) {
-		this.otfCrlogicKeepTmpFiles = otfCrlogicKeepTmpFiles;
-	}
-
-	public void setDataBaseDirectory(String dataBaseDirectory) {
-		this.dataBaseDirectory = dataBaseDirectory;
-	}
-
-	public void setDataFilePrefix(String dataFilePrefix) {
-		this.dataFilePrefix = dataFilePrefix;
-	}
-
-	public void setActorMoveTimeout(Long actorMoveTimeout) {
-		this.actorMoveTimeout = actorMoveTimeout;
-	}
-
-	public void setSmptServer(String smptServer) {
-		this.smptServer = smptServer;
-	}
-	
-}

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

@@ -1,87 +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;
-
-/**
- * Singleton object for holing the core engine configuration
- * 
- * @author ebner
- */
-public class EngineConfiguration {
-
-	/**
-	 * Flag to indicate whether the engine should fail if there is an error while reading out a sensor.
-	 */
-	private boolean failOnSensorError = true;
-	
-	/**
-	 * Flag to indicate whether the set value of the actor should be verified after the set operation.
-	 * Having this flag on true will enable detecting for example that a motor hit the end switch or
-	 * did not move correctly.
-	 */
-	private boolean checkActorSet = true;
-	
-	/**
-	 * Singleton instance
-	 */
-	private final static EngineConfiguration instance = new EngineConfiguration(); 
-
-	
-	
-	private EngineConfiguration(){
-	}
-	
-	/**
-	 * Get singleton instance of this class
-	 * @return Engine configuration
-	 */
-	public static EngineConfiguration getInstance(){
-		return instance;
-	}
-
-	/**
-	 * @return the failOnSensorError
-	 */
-	public boolean isFailOnSensorError() {
-		return failOnSensorError;
-	}
-
-	/**
-	 * @param failOnSensorError the failOnSensorError to set
-	 */
-	public void setFailOnSensorError(boolean failOnSensorError) {
-		this.failOnSensorError = failOnSensorError;
-	}
-
-	/**
-	 * @return the checkActorSet
-	 */
-	public boolean isCheckActorSet() {
-		return checkActorSet;
-	}
-
-	/**
-	 * @param checkActorSet the checkActorSet to set
-	 */
-	public void setCheckActorSet(boolean checkActorSet) {
-		this.checkActorSet = checkActorSet;
-	}
-	
-}

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

@@ -1,155 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.actions;
-
-import java.util.Comparator;
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- * @author ebner
- *
- */
-public class ChannelAccessConditionAnd<E extends Integer> implements Action {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessConditionAnd.class.getName());
-	
-	/**
-	 * Channel to set
-	 */
-	private final ChannelBean<E> channel;
-	/**
-	 * Value to wait for
-	 */
-	private final E expectedValue;
-	
-	private final Long timeout;
-	
-	private volatile boolean abort = false;
-	private volatile Thread waitT = null;
-	
-	/**
-	 * Constructor
-	 * @param channelName		Name of the channel to set the value
-	 * @param expectedValue		Value to wait for
-	 * @param timeout			Timeout of the condition in milliseconds (null accepted - will take default wait timeout for channels ch.psi.jcae.ChannelBeanFactory.waitTimeout)
-	 * 
-	 * @throws	IllegalArgumentException	Unable to initialize channel,
-	 * 										Timeout specified is not >=0
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessConditionAnd(String channelName, E expectedValue, Long timeout){
-
-		if(timeout !=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-		
-		try {
-			this.channel = (ChannelBean<E>) ChannelBeanFactory.getFactory().createChannelBean( (Class<E>) expectedValue.getClass(), channelName, false);
-		} catch (CAException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		
-		this.expectedValue = expectedValue;
-		
-		if(timeout==null){
-			this.timeout = channel.getWaitTimeout();
-		}
-		else{
-			this.timeout = timeout;
-		}
-	}
-
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException 
-	 * @throws RuntimeException		Channel value did not reach expected value (within the specified timeout period)
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort=false;
-		logger.finest("Checking channel "+channel.getName()+" for value "+expectedValue+" [timeout: "+timeout+"]" );
-		try{
-			waitT = Thread.currentThread();
-			channel.waitForValue(expectedValue, new Comparator<E>() {
-
-				@Override
-				public int compare(E o1, E o2) {
-					int one = o1;
-					int two = o2;
-					if((one & two) != 0){
-						return 0;
-					}
-					return 1;
-				}
-			}
-			, timeout); // Workaround use 10seconds default set timeout to check several times whether the channel has reached the value
-		} catch (CAException e) {
-			throw new RuntimeException("Channel [name:"+channel.getName()+"] did not reach expected value "+expectedValue+" ", e);
-		} catch(InterruptedException e){
-			if(!abort){
-				throw e;
-			}
-		}
-		finally{
-			waitT=null;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort=true;
-		if(waitT!=null){
-			waitT.interrupt();
-		}
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy action channel: "+channel.getName());
-			channel.destroy();
-		} catch (CAException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

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

@@ -1,155 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.actions;
-
-import java.util.Comparator;
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- * @author ebner
- *
- */
-public class ChannelAccessConditionOr<E extends Integer> implements Action {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessConditionOr.class.getName());
-	
-	/**
-	 * Channel to set
-	 */
-	private final ChannelBean<E> channel;
-	/**
-	 * Value to wait for
-	 */
-	private final E expectedValue;
-	
-	private final Long timeout;
-	
-	private volatile boolean abort = false;
-	private volatile Thread waitT = null;
-	
-	/**
-	 * Constructor
-	 * @param channelName		Name of the channel to set the value
-	 * @param expectedValue		Value to wait for
-	 * @param timeout			Timeout of the condition in milliseconds (null accepted - will take default wait timeout for channels ch.psi.jcae.ChannelBeanFactory.waitTimeout)
-	 * 
-	 * @throws	IllegalArgumentException	Unable to initialize channel,
-	 * 										Timeout specified is not >=0
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessConditionOr(String channelName, E expectedValue, Long timeout){
-
-		if(timeout !=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-		
-		try {
-			this.channel = (ChannelBean<E>) ChannelBeanFactory.getFactory().createChannelBean( (Class<E>) expectedValue.getClass(), channelName, false);
-		} catch (CAException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		
-		this.expectedValue = expectedValue;
-		
-		if(timeout==null){
-			this.timeout = channel.getWaitTimeout();
-		}
-		else{
-			this.timeout = timeout;
-		}
-	}
-
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException 
-	 * @throws RuntimeException		Channel value did not reach expected value (within the specified timeout period)
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort=false;
-		logger.finest("Checking channel "+channel.getName()+" for value "+expectedValue+" [timeout: "+timeout+"]" );
-		try{
-			waitT = Thread.currentThread();
-			channel.waitForValue(expectedValue, new Comparator<E>() {
-
-				@Override
-				public int compare(E o1, E o2) {
-					int one = o1;
-					int two = o2;
-					if((one | two) != 0){
-						return 0;
-					}
-					return 1;
-				}
-			}
-			, timeout); // Workaround use 10seconds default set timeout to check several times whether the channel has reached the value
-		} catch (CAException e) {
-			throw new RuntimeException("Channel [name:"+channel.getName()+"] did not reach expected value "+expectedValue+" ", e);
-		} catch(InterruptedException e){
-			if(!abort){
-				throw e;
-			}
-		}
-		finally{
-			waitT=null;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort=true;
-		if(waitT!=null){
-			waitT.interrupt();
-		}
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy action channel: "+channel.getName());
-			channel.destroy();
-		} catch (CAException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

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

@@ -1,149 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.actions;
-
-import java.util.Comparator;
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- * @author ebner
- *
- */
-public class ChannelAccessConditionRegex<E extends String> implements Action {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessConditionRegex.class.getName());
-	
-	/**
-	 * Channel to set
-	 */
-	private final ChannelBean<E> channel;
-	/**
-	 * Value to wait for
-	 */
-	private final E expectedValue;
-	
-	private final Long timeout;
-	
-	private volatile boolean abort = false;
-	private volatile Thread waitT = null;
-	
-	/**
-	 * Constructor
-	 * @param channelName		Name of the channel to set the value
-	 * @param expectedValue		Value to wait for
-	 * @param timeout			Timeout of the condition in milliseconds (null accepted - will take default wait timeout for channels ch.psi.jcae.ChannelBeanFactory.waitTimeout)
-	 * 
-	 * @throws	IllegalArgumentException	Unable to initialize channel,
-	 * 										Timeout specified is not >=0
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessConditionRegex(String channelName, E expectedValue, Long timeout){
-
-		if(timeout !=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-		
-		try {
-			this.channel = (ChannelBean<E>) ChannelBeanFactory.getFactory().createChannelBean( (Class<E>) expectedValue.getClass(), channelName, false);
-		} catch (CAException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		
-		this.expectedValue = expectedValue;
-		
-		if(timeout==null){
-			this.timeout = channel.getWaitTimeout();
-		}
-		else{
-			this.timeout = timeout;
-		}
-	}
-
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException 
-	 * @throws RuntimeException		Channel value did not reach expected value (within the specified timeout period)
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort=false;
-		logger.finest("Checking channel "+channel.getName()+" for value "+expectedValue+" [timeout: "+timeout+"]" );
-		try{
-			waitT = Thread.currentThread();
-			channel.waitForValue(expectedValue, new Comparator<E>() {
-
-				@Override
-				public int compare(E o1, E o2) {
-					return o1.matches(o2) ? 0:1;
-				}
-			}, timeout); // Workaround use 10seconds default set timeout to check several times whether the channel has reached the value
-		} catch (CAException e) {
-			throw new RuntimeException("Channel [name:"+channel.getName()+"] did not reach expected value "+expectedValue+" ", e);
-		} catch(InterruptedException e){
-			if(!abort){
-				throw e;
-			}
-		}
-		finally{
-			waitT=null;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort=true;
-		if(waitT!=null){
-			waitT.interrupt();
-		}
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy action channel: "+channel.getName());
-			channel.destroy();
-		} catch (CAException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

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

@@ -1,188 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.actors;
-
-import ch.psi.fda.core.Actor;
-
-/**
- * Special actuator for the OTFLoop. This type of actor must not be used in any other
- * type of loop than OTFLoop. If it is used it will, depending on the loop, immediately stop the loop
- * as it no single step.
- * @author ebner
- *
- */
-public class OTFActuator implements Actor {
-
-	/**
-	 * Name of the motor channel
-	 */
-	private final String name;
-	
-	/**
-	 * Channel name of the encoder;
-	 */
-	private final String readback;
-	
-	private  double start;
-	private  double end;
-	private final double stepSize;
-	private final double integrationTime;
-	
-	private final String id;
-	
-	/**
-	 * Additional backlash for the motor
-	 */
-	private final double additionalBacklash;
-	
-	
-	public OTFActuator(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;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#set()
-	 */
-	@Override
-	public void set() {
-		// Do nothing
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#hasNext()
-	 */
-	@Override
-	public boolean hasNext() {
-		return false;
-	}
-
-	
-	
-	/**
-	 * @return the name
-	 */
-	public String getName() {
-		return name;
-	}
-
-	/**
-	 * @return the readback
-	 */
-	public String getReadback() {
-		return readback;
-	}
-
-	/**
-	 * @return the start
-	 */
-	public double getStart() {
-		return start;
-	}
-
-	/**
-	 * @return the end
-	 */
-	public double getEnd() {
-		return end;
-	}
-
-	/**
-	 * @return the stepSize
-	 */
-	public double getStepSize() {
-		return stepSize;
-	}
-
-	/**
-	 * @return the integrationTime
-	 */
-	public double getIntegrationTime() {
-		return integrationTime;
-	}
-
-	/**
-	 * @return the additionalBacklash
-	 */
-	public double getAdditionalBacklash() {
-		return additionalBacklash;
-	}
-
-	/**
-	 * @return the id
-	 */
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#init()
-	 */
-	@Override
-	public void init() {
-		// Not implemented
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reverse()
-	 */
-	@Override
-	public void reverse() {
-		// Not implemented
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reset()
-	 */
-	@Override
-	public void reset() {
-		// Not implemented
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-		
-	}
-
-	/**
-	 * @param start the start to set
-	 */
-	public void setStart(double start) {
-		this.start = start;
-	}
-
-	/**
-	 * @param end the end to set
-	 */
-	public void setEnd(double end) {
-		this.end = end;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/collector/Collector.java

@@ -1,165 +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.collector;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Collector class that is collecting and merging data from different Queues.
- * @author ebner
- *
- */
-public class Collector implements Runnable{
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(Collector.class.getName());
-	
-	/**
-	 * List of queues and their metadata this collector is responsible to readout.
-	 * The logic is as follows:
-	 * Read out the last queue until the first queue in the list has the EndOfLoopMessage.
-	 */
-	private List<DataQueue> queues;
-	
-	/**
-	 * Outgoing queue of this collector
-	 */
-	private BlockingQueue<Message> outQueue;
-	
-	/**
-	 * Constructor
-	 */
-	public Collector(){
-		queues = new ArrayList<DataQueue>();
-		outQueue = new LinkedBlockingQueue<Message>(1000); // Create bounded queue to prevent running out of memory ...
-	}
-	
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		
-		if(queues.size()>0){
-			try{
-				readQueue(0, null);
-			}
-			catch(InterruptedException e){
-				// Readout aborted through interrupt
-			}
-		}
-		else{
-			// No queue registered for reading
-		}
-		
-		try {
-			
-			outQueue.put(new EndOfStreamMessage());
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Unable to terminate stream with and End of Stream Message",e);
-		}
-		
-		logger.info("END");
-		
-	}
-
-	
-	private void readQueue(int index, DataMessage m) throws InterruptedException{
-		
-		BlockingQueue<Message> q = queues.get(index).getQueue();
-		
-		// Read Message
-		Message message = q.take();
-		while(message instanceof DataMessage){
-			// Create new data message 
-			DataMessage dm = new DataMessage();
-			if(m!=null){
-				dm.getData().addAll(m.getData());
-			}
-			
-			dm.getData().addAll(((DataMessage)message).getData());
-			
-			if(index<(queues.size()-1)){
-				readQueue(index+1, dm);
-			}
-			else{
-				// Write message to outgoing queue
-				outQueue.put(dm);
-			}
-			
-			// Read next message
-			message = q.take();
-		}
-		
-		if(message instanceof EndOfStreamMessage){
-			// Translate EndOfStream to StreamDelimiter message
-			StreamDelimiterMessage ddm = new StreamDelimiterMessage(queues.size()-1-index, ((EndOfStreamMessage)message).isIflag());
-			// Write message to outgoing queue
-			outQueue.put(ddm);
-		}
-	}
-	
-
-	/**
-	 * @return the queues
-	 */
-	public List<DataQueue> getQueues() {
-		return queues;
-	}
-	
-	
-	/**
-	 * Get the outgoing data queue.
-	 * Attention, only call this method after all ingoing queues were registered! Otherwise the data returned
-	 * by this method is not accurate.
-	 * @return	output queue of collector
-	 */
-	public DataQueue getOutQueue(){
-		DataMessageMetadata dataMessageMetadata = new DataMessageMetadata();
-		dataMessageMetadata.getComponents();
-		
-		// Generate new combined metadata and add dimension information to the components
-		int nq = queues.size();
-		for(int i=0;i<nq;i++){
-			DataQueue q = queues.get(i);
-			for(ComponentMetadata cm: q.getDataMessageMetadata().getComponents()){
-				// The dimension number is the number of queues minus the index of the current queue minus 1 (because dimension index starts at 0)
-				dataMessageMetadata.getComponents().add(new ComponentMetadata(cm.getId(), nq-i-1));
-			}
-		}
-		
-		return(new DataQueue(outQueue, dataMessageMetadata));
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/collector/DataDispatcher.java

@@ -1,88 +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.collector;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Serialize data received by a DataQueue
- * @author ebner
- *
- */
-public class DataDispatcher implements Runnable{
-	
-	private DataQueue queue;
-	private List<DataQueue> outQueues;
-	
-	public DataDispatcher(DataQueue queue){
-		this.queue = queue;
-		this.outQueues = new ArrayList<DataQueue>();
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-
-			// TODO Need to synchronize message metadata
-//			for(DataQueue q: outQueues){
-//			}
-			
-			// Dispatch Messages
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				
-				// Clone message ...
-				for(DataQueue q: outQueues){
-					q.getQueue().put(message);
-				}
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			// Write end of stream message
-			for(DataQueue q: outQueues){
-				q.getQueue().put(message);
-			}
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data serializer was interrupted while writing data to file",e);
-		} 
-	}
-
-	/**
-	 * @return the outQueues
-	 */
-	public List<DataQueue> getOutQueues() {
-		return outQueues;
-	}
-	
-	
-	
-}

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

@@ -1,96 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.guard;
-
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * Channel and condition that need to be met. 
- * @author ebner
- *
- */
-public class ChannelAccessGuardCondition {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessGuardCondition.class.getName());
-	
-	/**
-	 * Channel name
-	 */
-	private final ChannelBean<?> channel;
-	
-	/**
-	 * Value of the channel to meet condition
-	 */
-	private final Object value;
-
-	/**
-	 * Constructor
-	 * @param channel	Name of the channel that contributes to a guard
-	 * @param value
-	 */
-	public ChannelAccessGuardCondition(String channel, Object value){
-		try {
-			this.channel = ChannelBeanFactory.getFactory().createChannelBean(value.getClass(), channel, true);
-		} catch (CAException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channel+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channel+"]",e);
-		}
-		this.value = value;
-	}
-	
-	/**
-	 * @return the channel
-	 */
-	public ChannelBean<?> getChannel() {
-		return channel;
-	}
-
-	/**
-	 * @return the value
-	 */
-	public Object getValue() {
-		return value;
-	}
-	
-	/**
-	 * Destroy guard condition. 
-	 * Can be used for the cleanup of used resources of the guard condition (e.g. to close connections, ...) if
-	 * this cannot be done automatically by the GarbageCollector.
-	 * 
-	 * After calling this method the guard condition must not be used any more!
-	 */
-	public void destroy(){
-		// Destroy channel
-		try {
-			logger.finest("Destroy guard condition channel: "+channel.getName());
-			channel.destroy();
-		} catch (CAException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-	
-}

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

@@ -1,162 +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 java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-
-import jcifs.smb.SmbFile;
-
-/**
- * @author ebner
- *
- */
-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/OTFBean.java

@@ -1,770 +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 gov.aps.jca.CAException;
-
-import java.util.List;
-
-import ch.psi.jcae.annotation.CaChannel;
-import ch.psi.jcae.ChannelBean;
-
-/**
- * Bean holding all OTF channels and functionality
- * @author ebner
- *
- */
-public class OTFBean {
-
-	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 =":UMOT")
-	private ChannelBean<String> motor;
-	
-	@CaChannel(type=String.class, name=":MENC")
-	private ChannelBean<String> encoder;
-	
-	@CaChannel(type=Double.class, name=":UBEG")
-	private ChannelBean<Double> begin;
-	
-	@CaChannel(type=Double.class, name=":UBEG.DRVL")
-	private ChannelBean<Double> beginMin;
-	
-	@CaChannel(type=Double.class, name=":UBEG.DRVH")
-	private ChannelBean<Double> beginMax;
-	
-	@CaChannel(type=Double.class, name=":UEND")
-	private ChannelBean<Double> end;
-	
-	@CaChannel(type=Double.class, name=":UEND.DRVL")
-	private ChannelBean<Double> endMin;
-	
-	@CaChannel(type=Double.class, name=":UEND.DRVH")
-	private ChannelBean<Double> endMax;
-	
-	@CaChannel(type=Double.class, name=":USSIZ")
-	private ChannelBean<Double> stepSize;
-	
-	@CaChannel(type=Double.class, name=":USSIZ.DRVL")
-	private ChannelBean<Double> stepSizeMin;
-	
-	@CaChannel(type=Double.class, name=":UITIM")
-	private ChannelBean<Double> integrationTime;
-	
-	@CaChannel(type=Double.class, name=":UITIM.DRVL")
-	private ChannelBean<Double> integrationTimeMin;
-	
-	@CaChannel(type=Double.class, name=":UITIM.DRVH")
-	private ChannelBean<Double> integrationTimeMax;
-	
-	@CaChannel(type=Double.class, name=":UBCL")
-	private ChannelBean<Double> userBacklash;
-	
-	@CaChannel(type=String.class, name=":NFSSE")
-	private ChannelBean<String> nfsServer;
-	
-	@CaChannel(type=String.class, name=":NFSSH")
-	private ChannelBean<String> nfsShare;
-	
-	@CaChannel(type=String.class, name=":DFNAM")
-	private ChannelBean<String> fileName;
-	
-	@CaChannel(type=String.class, name=":FFORM")
-	private ChannelBean<String> fileNameFormat;
-	
-	@CaChannel(type=Integer.class, name=":FCNT")
-	private ChannelBean<Integer> fileCount;
-	
-	@CaChannel(type=Integer.class, name=":FCNT.B")
-	private ChannelBean<Integer> resetFileCounter;
-	
-	@CaChannel(type=Boolean.class, name=":FAPPE")
-	private ChannelBean<Boolean> appendFile;
-
-	@CaChannel(type=Boolean.class, name=":FUSE")
-	private ChannelBean<Boolean> fileNameGeneration;
-	
-	@CaChannel(type=Boolean.class, name=":UZIGZ")
-	private ChannelBean<Boolean> zigZag;
-	
-	@CaChannel(type=Integer.class, name=":UCOM")
-	private ChannelBean<Integer> command;
-	
-	@CaChannel(type=Boolean.class, name=":SCRU", monitor=true)
-	private ChannelBean<Boolean> scanRunning;
-	
-	@CaChannel(type=Boolean.class, name=":MUENC")
-	private ChannelBean<Boolean> useEncoder;
-	
-	@CaChannel(type=String.class, name={":CTM0",":CTM1",":CTM2",":CTM3",":CTM4",":CTM5",":CTM6",":CTM7"})
-	private List<ChannelBean<String>> monitoredChannels;
-	
-	@CaChannel(type=Boolean.class, name=":OTF", monitor=true)
-	private ChannelBean<Boolean> running;
-	
-	@CaChannel(type=Integer.class, name=":USTAT", monitor=true)
-	private ChannelBean<Integer> status;
-	
-	@CaChannel(type=Boolean.class, name=":MOK", monitor=true)
-	private ChannelBean<Boolean> motorOk;
-	
-	@CaChannel(type=Boolean.class, name=":EOK", monitor=true)
-	private ChannelBean<Boolean> encoderOk;
-	
-	@CaChannel(type=String.class, name=":MSG")
-	private ChannelBean<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 (CAException 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 (CAException 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 CAException, InterruptedException{
-		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);
-	}
-
-	/**
-	 * Get motor of the OTFScan axis
-	 * @return	Name of the OTF motor
-	 * @throws CAException
-	 */
-	public String getMotor() throws CAException, InterruptedException {
-		return(this.motor.getValue());
-	}
-	
-	/**
-	 * Set motor of the OTFScan axis
-	 * @param motor
-	 * @throws CAException
-	 */
-	public void setMotor(String motor) throws CAException, InterruptedException {
-		this.motor.setValue(motor);
-	}
-	
-	/**
-	 * Get encoder of the OTFScan axis
-	 * @return	Name of the used encoder
-	 * @throws CAException
-	 */
-	public String getEncoder() throws CAException, InterruptedException {
-		return(this.encoder.getValue());
-	}
-	
-	/**
-	 * Set encoder to use of the OTFScan axis
-	 * @param encoder
-	 * @throws CAException
-	 */
-	public void setEncoder(String encoder) throws CAException, InterruptedException {
-		this.encoder.setValue(encoder);
-	}
-	
-	/**
-	 * Get begin position of the scan
-	 * @return Begin position scan
-	 * @throws CAException
-	 */
-	public Double getBegin() throws CAException, InterruptedException {
-		return(this.begin.getValue());
-	}
-	
-	/**
-	 * Set begin position of scan
-	 * @param begin
-	 * @throws Exception
-	 */
-	public void setBegin(Double begin) throws CAException, InterruptedException {
-		
-		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);
-	}
-	
-	/**
-	 * Get minimum value of the begin position
-	 * @return	Min value for begin
-	 * @throws CAException
-	 */
-	public Double getMinBegin() throws CAException, InterruptedException {
-		return(this.beginMin.getValue());
-	}
-	
-	/**
-	 * Get maximum value of the begin position
-	 * @return	Max value for begin
-	 * @throws CAException
-	 */
-	public Double getMaxBegin() throws CAException, InterruptedException {
-		return(this.beginMax.getValue());
-	}
-	
-	/**
-	 * Get end position of the scan
-	 * @return End position scan
-	 * @throws CAException
-	 */
-	public Double getEnd() throws CAException, InterruptedException {
-		return(this.end.getValue());
-	}
-	
-	/**
-	 * Set end positon of scan
-	 * @param end
-	 * @throws CAException
-	 */
-	public void setEnd(Double end) throws CAException, InterruptedException {
-		
-		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);
-	}
-	
-	/**
-	 * Get minimum value of end position
-	 * @return	Min value for end
-	 * @throws CAException
-	 */
-	public Double getMinEnd() throws CAException, InterruptedException {
-		return(this.endMin.getValue());
-	}
-	/**
-	 * Get maximum value of end position
-	 * @return 	Max value for end
-	 * @throws CAException
-	 */
-	public Double getMaxEnd() throws CAException, InterruptedException {
-		return(this.endMax.getValue());
-	}
-	
-	/**
-	 * Get scan step size
-	 * @return Step size
-	 * @throws CAException
-	 */
-	public Double getStepSize() throws CAException, InterruptedException {
-		return(this.stepSize.getValue());
-	}
-	
-	/**
-	 * Set step size of scan
-	 * @param stepSize
-	 * @throws CAException
-	 */
-	public void setStepSize(Double stepSize) throws CAException, InterruptedException {
-
-		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);
-	}
-	
-	/**
-	 * Get minimum integration time
-	 * @return	Min value for step size
-	 * @throws CAException
-	 */
-	public double getMinStepSize() throws CAException, InterruptedException {
-		return(this.stepSizeMin.getValue());
-	}
-	
-	/**
-	 * Get scan integration time (time that is spend in one step)
-	 * @return	Integration time
-	 * @throws CAException
-	 */
-	public Double getIntegrationTime() throws CAException, InterruptedException {
-		return(this.integrationTime.getValue());
-	}
-
-	/**
-	 * Set integration time of scan
-	 * @param integrationTime
-	 * @throws CAException
-	 */
-	public void setIntegrationTime(Double integrationTime) throws CAException, InterruptedException {
-		
-		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);
-	}
-	
-	/**
-	 * Get minimum integration time
-	 * @return	Min value for integration time
-	 * @throws CAException
-	 */
-	public Double getMinIntegrationTime() throws CAException, InterruptedException {
-		return(this.integrationTimeMin.getValue());
-	}
-	/**
-	 * Get maximum integration time
-	 * @return	Max value for integration time
-	 * @throws CAException
-	 */
-	public Double getMaxIntegrationTime() throws CAException, InterruptedException {
-		return(this.integrationTimeMax.getValue());
-	}
-	
-	/**
-	 * Get additional user defined backlash
-	 * @return	User backlash
-	 * @throws CAException 
-	 */
-	public Double getUserBacklash() throws CAException, InterruptedException {
-		return(this.userBacklash.getValue());
-	}
-
-	/**
-	 * Set additional user defined backlash
-	 * @param userBacklash
-	 * @throws CAException
-	 */
-	public void setUserBacklash(Double userBacklash) throws CAException, InterruptedException {
-		if(userBacklash==null){
-			throw new IllegalArgumentException("User backlash must not be null");
-		}
-		
-		this.userBacklash.setValue(userBacklash);
-	}
-	
-	/**
-	 * Get the current NFS server the data is written to
-	 * @return	Name of NFS server
-	 * @throws CAException
-	 */
-	public String getNfsServer() throws CAException, InterruptedException {
-		return(this.nfsServer.getValue());
-	}
-	
-	/**
-	 * Set name of the NFS server the data is written to
-	 * @param nfsServer
-	 * @throws CAException
-	 */
-	public void setNfsServer(String nfsServer) throws CAException, InterruptedException {
-		this.nfsServer.setValue(nfsServer);
-	}
-	
-	/**
-	 * Get the NFS share the data is written to
-	 * @return	Name of NFS share
-	 * @throws CAException
-	 */
-	public String getNfsShare() throws CAException, InterruptedException {
-		return(this.nfsShare.getValue());
-	}
-	
-	/**
-	 * Set name of the NFS share the data is written to
-	 * @param nfsShare
-	 * @throws CAException
-	 */
-	public void setNfsShare(String nfsShare) throws CAException, InterruptedException {
-		this.nfsShare.setValue(nfsShare);
-	}
-	
-	/**
-	 * Get the name of the data file
-	 * @return	Name of data file name
-	 * @throws CAException
-	 */
-	public String getFileName() throws CAException, InterruptedException {
-		return(this.fileName.getValue());
-	}
-
-	/**
-	 * Set name of the data file
-	 * @param filename
-	 * @throws CAException
-	 */
-	public void setFileName(String filename) throws CAException, InterruptedException {
-		this.fileName.setValue(filename);
-	}
-	
-	/**
-	 * Get File name formate
-	 * @return	Get format for file name
-	 * @throws CAException
-	 */
-	public String getFileNameFormat() throws CAException, InterruptedException {
-		return(this.fileNameFormat.getValue());
-	}
-	
-	/**
-	 * Set file name formate of the data file
-	 * @param fileNameFormat
-	 * @throws Exception
-	 */
-	public void setFileNameFormat(String fileNameFormat) throws CAException, InterruptedException {
-		this.fileNameFormat.setValue(fileNameFormat);
-	}
-	
-	/**
-	 * Get value of the IOC based file name counter
-	 * @return	File counter
-	 * @throws CAException
-	 */
-	public int getFileCounter() throws CAException, InterruptedException {
-		return(this.fileCount.getValue());
-	}
-	
-	/**
-	 * Reset the IOC based file counter
-	 * @throws CAException
-	 */
-	public void resetFileCounter() throws CAException, InterruptedException {
-		this.resetFileCounter.setValue(1);
-	}
-	
-	/**
-	 * Get if append file option is activated
-	 * @return	Append file flag
-	 * @throws CAException
-	 */
-	public boolean isAppendFile() throws CAException, InterruptedException {
-		return(this.appendFile.getValue());
-	}
-	
-	/**
-	 * Set whether to append the specified file if the file exists
-	 * @param append
-	 * @throws CAException
-	 */
-	public void setAppendFile(boolean append) throws CAException, InterruptedException {
-		this.appendFile.setValue(append);
-	}
-	
-	/**
-	 * Get if file name generation is on or off
-	 * @return	File name generation flag
-	 * @throws CAException
-	 */
-	public boolean isFileNameGeneration() throws CAException, InterruptedException {
-		return(this.fileNameGeneration.getValue());
-	}
-	
-	/**
-	 * 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 CAException, InterruptedException {
-		this.fileNameGeneration.setValue(generation);
-	}
-	
-	/**
-	 * Get if ZigZag scan option is on or off
-	 * @return	ZigZag flag
-	 * @throws CAException
-	 */
-	public boolean isZigZag() throws CAException, InterruptedException {
-		return(this.zigZag.getValue());
-	}
-	
-	/**
-	 * Set ZigZag scan mode on/off
-	 * @param zigZag	ZigZag mode on = true, ZigZag mode off = false
-	 * @throws CAException
-	 */
-	public void setZigZag(boolean zigZag) throws CAException, InterruptedException {
-		this.zigZag.setValue(zigZag);
-	}
-	
-	/**
-	 * Get whether encoder is used
-	 */
-	public boolean isUseEncoder() throws CAException, InterruptedException {
-		return(this.useEncoder.getValue());
-	}
-	
-	/**
-	 * Set flag to use encoder
-	 * @throws CAException
-	 */
-	public void setUseEncoder(boolean flag) throws CAException, InterruptedException {
-		this.useEncoder.setValue(flag);
-	}
-	
-	/**
-	 * Get the channels that are currently monitored by the OTFScan logic
-	 * @return	Names of the monitored channels
-	 * @throws CAException
-	 */
-	public String[] getMonitoredChannels() throws CAException, InterruptedException {
-		String[] values = new String[this.monitoredChannels.size()];
-		
-		for(int i=0; i<this.monitoredChannels.size();i++){
-			values[i] = monitoredChannels.get(i).getValue();
-		}
-		
-		return(values);
-	}
-	
-	/**
-	 * 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 CAException, InterruptedException {
-		
-		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("");
-			}
-		}
-	}
-	
-	/**
-	 * Returns whether an scan is running
-	 * @return	Running flag
-	 * @throws CAException 
-	 */
-	public boolean isRunning() throws CAException, InterruptedException {
-		return(running.getValue());
-	}
-	
-	/**
-	 * Get status of the scan
-	 * @return Status of the scan
-	 * @throws CAException 
-	 */
-	public Status getStatus() throws CAException, InterruptedException {
-		return(Status.values()[this.status.getValue()]);
-	}
-	
-	/**
-	 * Get the (error) message from the OTF records
-	 * @return	Message from OTF C logic
-	 * @throws CAException
-	 */
-	public String getMessage() throws CAException, InterruptedException {
-		return(message.getValue());
-	}
-	
-	/**
-	 * 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 CAException, InterruptedException {
-		return(motorOk.getValue());
-	}
-	
-	/**
-	 * 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 CAException, InterruptedException {
-		motorOk.waitForValue(true, timeout);
-	}
-	
-	/**
-	 * 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 CAException, InterruptedException {
-		motorOk.waitForValue(false, timeout);
-	}
-	
-	
-	public void waitUntilEncoderOk(long timeout) throws CAException, InterruptedException {
-		if(!useEncoder.getValue()){
-			return;
-		}
-		encoderOk.waitForValue(true, timeout);
-	}
-}

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

@@ -1,521 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.loops;
-
-import java.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.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Logger;
-
-//import jcifs.smb.SmbException;
-//import jcifs.smb.SmbFile;
-
-import gov.aps.jca.CAException;
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.actors.OTFActuator;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.MillisecondTimestampSensor;
-import ch.psi.fda.core.sensors.OTFNamedChannelSensor;
-import ch.psi.fda.core.sensors.OTFReadbackSensor;
-import ch.psi.fda.core.sensors.OTFScalerChannelSensor;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * ActionLoop that is implementing the OTF Scan logic.
- * While executing the loop a full OTF scan procedure is executed.
- * @author ebner
- *
- */
-public class OTFLoop implements ActionLoop {
-	
-	// Get Logger
-	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;
-	
-	// Constants
-	/**
-	 * 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 OTFBean 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;
-	
-	/**
-	 * Special OTF Actuator
-	 */
-	private OTFActuator actor = null;
-	
-	/**
-	 * 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;
-	
-	/**
-	 * 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 BlockingQueue<Message> dataQueue;
-	
-	/**
-	 * Flag that indicates that the loop was requested to abort.
-	 */
-	private volatile boolean abort = false;
-	
-	/**
-	 * Constructor
-	 * @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(String channelPrefix, String server, String share, String smbShare, boolean zigZag){
-		
-		// Initialize connection to the OTF records
-		try {
-			this.obean = new OTFBean();
-			ChannelBeanFactory.getFactory().createChannelBeans(obean, channelPrefix);
-		} catch (CAException e) {
-			throw new IllegalArgumentException("Unable to connect to the OTF channels",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to connect to the OTF channels",e);
-		}
-		
-		// 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>();
-		
-		this.dataQueue = new LinkedBlockingQueue<Message>(2000);
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@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
-		dataQueue.put(new EndOfStreamMessage(dataGroup));
-		
-		// Increase execution count
-		executionCount++;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		// Abort otf scan logic
-		obean.abort();
-		
-		abort=true;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#prepare()
-	 */
-	@Override
-	public void prepare() {
-		executionCount = 0;
-		
-		// Set abort flag to false
-		abort=false;
-		
-		// Check whether actor is set for the loop
-		if(actor == null){
-			throw new IllegalStateException("No actor specified for this loop");
-		}
-		
-		// list with all monitored channels
-		List<String> monitoredChannels = new ArrayList<String>();
-		dataIndexes = new ArrayList<Integer>();
-		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 MillisecondTimestampSensor){
-				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(actor.getName());
-			obean.waitUntilMotorOk(timeout);
-	
-			obean.setBegin(actor.getStart());
-			obean.setEnd(actor.getEnd());
-			obean.setStepSize(actor.getStepSize());
-			obean.setIntegrationTime(actor.getIntegrationTime());
-			
-			// Override encoder if specified
-			if(actor.getReadback()!=null){
-				obean.setUseEncoder(true);
-				obean.setEncoder(actor.getReadback());
-				obean.waitUntilEncoderOk(timeout);
-			}
-			
-			// Set user backlash
-			obean.setUserBacklash(actor.getAdditionalBacklash());
-			
-			
-			// 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(CAException e){
-			throw new RuntimeException("Unable to set OTF configuration parameters",e);
-		} catch (InterruptedException 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);
-		}
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#cleanup()
-	 */
-	@Override
-	public void cleanup() {
-		// TODO Auto-generated method stub
-		
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Close all connections used by the OTFBean
-		try {
-			ChannelBeanFactory.getFactory().destroyChannelBeans(obean);
-		} catch (CAException e) {
-			throw new RuntimeException("Unable to destroy channels",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to destroy channels",e);
-		}		
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPreActions()
-	 */
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPostActions()
-	 */
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	/**
-	 * The structure of the data message depends on the sensors registered at this loop 
-	 * at the time this method is called.
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-		
-		// Build up data message metadata based on the sensors currently registered.
-		for(Sensor s: sensors){
-			m.getComponents().add(new ComponentMetadata(s.getId()));
-		}
-		return new DataQueue(dataQueue, m);
-	}
-	
-	/**
-	 * 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();
-						// 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));
-							}
-						}
-						dataQueue.put(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);
-		}
-	}
-	
-	
-	// Getter functions for variable parts
-
-
-	
-	/**
-	 * @return the sensors
-	 */
-	public List<Sensor> getSensors() {
-		return sensors;
-	}
-	
-	/**
-	 * @return the actor
-	 */
-	public OTFActuator getActor() {
-		return actor;
-	}
-
-	/**
-	 * @param actor the actor to set
-	 */
-	public void setActor(OTFActuator actor) {
-		this.actor = actor;
-	}
-
-	/**
-	 * @return the dataGroup
-	 */
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-	/**
-	 * @param dataGroup the dataGroup to set
-	 */
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-	
-}

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

@@ -1,157 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.loops.cr;
-
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.annotation.CaChannel;
-
-/**
- * @author ebner
- *
- */
-public class CrlogicChannelsTemplate {
-
-	/**
-	 * Status of the OTFSCAN IOC logic
-	 */
-	public enum Status { SETUP, INACTIVE, INITIALIZE, ACTIVE, STOP, FAULT, ERROR };
-	
-	/**
-	 * Ticks per second - IOC setting
-	 * ATTENTION - This field must only be set bu the IOC - ATTENTION
-	 */
-	@CaChannel(type=Integer.class, name =":TPS")
-	private ChannelBean<Integer> ticksPerSecond;
-
-	/**
-	 * Status of the OTFSCAN IOC logic
-	 */
-	@CaChannel(type=String.class, name =":STATUS")
-	private ChannelBean<String> status;
-	
-	/**
-	 * Message from the OTFSCAN IOC logic
-	 */
-	@CaChannel(type=String.class, name =":MSG")
-	private ChannelBean<String> message;
-
-	/**
-	 * IOC ticks between data acquisition interrupts
-	 */
-	@CaChannel(type=Integer.class, name =":TBINT")
-	private ChannelBean<Integer> ticksBetweenInterrupts;
-
-	/**
-	 * Name or ip address of the NFS server to save the data to
-	 * (depending on the IOC setup)
-	 */
-	@CaChannel(type=String.class, name =":NFSSE")
-	private ChannelBean<String> nfsServer;
-	
-	/**
-	 * Name of the NFS share on the NFS server
-	 */
-	@CaChannel(type=String.class, name =":NFSSH")
-	private ChannelBean<String> nfsShare;
-
-	/**
-	 * Name of the data file
-	 */
-	@CaChannel(type=String.class, name =":DFNAM")
-	private ChannelBean<String> dataFile;
-	
-	/**
-	 * Flag to identify whether the data file should be appended
-	 */
-	@CaChannel(type=Boolean.class, name =":FAPPE")
-	private ChannelBean<Boolean> appendFile;
-
-	
-	/**
-	 * Readout resources
-	 */
-	@CaChannel(type=String[].class, name =":RRES")
-	private ChannelBean<String[]> readoutResources;
-	
-	
-	/**
-	 * @return the ticksPerSecond
-	 */
-	public ChannelBean<Integer> getTicksPerSecond() {
-		return ticksPerSecond;
-	}
-
-	/**
-	 * @return the status
-	 */
-	public ChannelBean<String> getStatus() {
-		return status;
-	}
-
-	/**
-	 * @return the message
-	 */
-	public ChannelBean<String> getMessage() {
-		return message;
-	}
-
-	/**
-	 * @return the ticksBetweenInterrupts
-	 */
-	public ChannelBean<Integer> getTicksBetweenInterrupts() {
-		return ticksBetweenInterrupts;
-	}
-
-	/**
-	 * @return the nfsServer
-	 */
-	public ChannelBean<String> getNfsServer() {
-		return nfsServer;
-	}
-
-	/**
-	 * @return the nfsShare
-	 */
-	public ChannelBean<String> getNfsShare() {
-		return nfsShare;
-	}
-
-	/**
-	 * @return the dataFile
-	 */
-	public ChannelBean<String> getDataFile() {
-		return dataFile;
-	}
-
-	/**
-	 * @return the appendFile
-	 */
-	public ChannelBean<Boolean> getAppendFile() {
-		return appendFile;
-	}
-
-	/**
-	 * @return the readoutResources
-	 */
-	public ChannelBean<String[]> getReadoutResources() {
-		return readoutResources;
-	}
-	
-}

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

@@ -1,898 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.loops.cr;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.Semaphore;
-import java.util.logging.Logger;
-
-import jcifs.smb.SmbFile;
-import gov.aps.jca.CAException;
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.actors.OTFActuator;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.MillisecondTimestampSensor;
-import ch.psi.fda.core.sensors.OTFNamedChannelSensor;
-import ch.psi.fda.core.sensors.OTFScalerChannelSensor;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * @author ebner
- * 
- * While using Crlogic the IOC system clock rate should/must be set to 1000 (default 60)
- * 
- * sysClkRateSet 1000
- *
- */
-public class CrlogicLoop implements ActionLoop {
-	
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(CrlogicLoop.class.getName());
-	
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	private boolean keepTmpFiles = false;
-	
-	private BlockingQueue<String> readQueue = new LinkedBlockingQueue<String>();
-	private volatile boolean stopReadoutThread = false;
-	private Thread readoutThread;
-	
-	// Constants
-	
-	/**
-	 * Default timeout (in milliseconds) for wait operations
-	 */
-	private long startStopTimeout = 8000;
-	
-	/**
-	 * Name of the NFS server to place the data of the OTF logic
-	 */
-	private final String server;
-	/**
-	 * Share on the NFS server to put the OTF data on to
-	 */
-	private final String share;
-	/**
-	 * SMB share  to access the data written by the OTF C logic
-	 */
-	private final String smbShare;
-	
-	/**
-	 * Flag whether the actor of this loop should move in zig zag mode
-	 */
-	private final boolean zigZag;
-	
-	boolean useReadback;
-	boolean useEncoder;
-	
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	/**
-	 * Prefix for the CRLOGIC channels
-	 */
-	private String prefix;
-	
-	private CrlogicChannelsTemplate template;
-	private MotorChannelsTemplate motortemplate;
-	
-	/**
-	 * Semaphore to ensure that data is read in correct sequence
-	 */
-	private Semaphore semaphore = new Semaphore(1);
-	
-	/**
-	 * Special OTF Actuator
-	 */
-	private OTFActuator actuator = null;
-	
-	/**
-	 * List of sensors of this loop
-	 */
-	private List<Sensor> sensors;
-	
-	private List<String> readoutResources;
-	private Map<Integer, CrlogicDeltaDataFilter> scalerIndices;
-	private CrlogicRangeDataFilter crlogicDataFilter;
-	
-	/**
-	 * 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 BlockingQueue<Message> dataQueue;
-	
-	/**
-	 * Abort status
-	 */
-	private boolean abort = false;
-	private boolean abortForce = false;
-	private Thread executionThread = null;
-	
-	
-	public CrlogicLoop(String prefix, String server, String share, String smbShare, boolean zigZag){
-		this.prefix = prefix;
-		this.server = server;
-		this.share = share;
-		this.smbShare = smbShare;
-		this.zigZag = zigZag;
-		
-		// Initialize lists used by the loop
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		this.sensors = new ArrayList<Sensor>();
-		this.readoutResources = new ArrayList<String>();
-		this.scalerIndices = new HashMap<Integer, CrlogicDeltaDataFilter>();
-		
-		this.crlogicDataFilter = new CrlogicRangeDataFilter();
-		this.dataQueue = new LinkedBlockingQueue<Message>(2000);
-	}
-	
-		
-	/**
-	 * Collect data from share
-	 * @param tmpFileName	Name of the temporary file
-	 * @throws InterruptedException 
-	 * @throws IOException 
-	 */
-	private void collectData(String tmpDir, String tmpFileName) throws InterruptedException, IOException {
-		semaphore.acquire();
-		if (tmpDir.startsWith("smb:")) {
-
-			SmbFile tmpFile = new SmbFile(tmpDir, tmpFileName);
-			logger.info("Collect data from " + tmpFile.getCanonicalPath());
-
-			SmbFile lockfile = new SmbFile(tmpFile.getCanonicalPath() + ".lock");
-
-			logger.info("Wait until file is written [lock file: " + lockfile.getCanonicalPath() + "]");
-			// Wait until file is created
-			while ((!tmpFile.exists()) || lockfile.exists()) {
-				try{
-					Thread.sleep(100);
-				}
-				catch(InterruptedException e){
-					abort=true;
-				}
-				 if(abort){
-					 // If abort is issued while waiting for data immediately return without
-					 // trying to read the data
-					 return;
-				 }
-			}
-
-			InputStreamReader inreader = new InputStreamReader(tmpFile.getInputStream());
-			BufferedReader in = new BufferedReader(inreader);
-			String line;
-			boolean firstline = true;
-			int linecount=0;
-			int mcounter=0;
-			
-//			boolean wasInRangeBefore = false;
-			boolean discardAnyway = false;
-			
-			while (true) {
-				line = in.readLine();
-				linecount++;
-				if (line == null) {
-					break;
-				} else {
-					// if(line.matches("^\\[.*")){
-					if (line.matches("^ *#.*")) {
-						// Skip header/comment lines
-//						logger.info("HEADER: " + line);
-					} else {
-						if (firstline) {
-							firstline = false;
-							continue;
-						}
-
-//						logger.info(line);
-
-						// Write into queue
-						DataMessage message = new DataMessage();
-						String[] tokens = line.split("\t");
-						boolean use = true;
-						
-						for(int i=0;i<tokens.length;i++){
-							String t = tokens[i];
-							Double val;
-							
-							if(i==0){
-								Double raw = new Double(t);
-								
-								if(useEncoder){
-									val = crlogicDataFilter.calculatePositionMotorUseEncoder(raw);
-								}
-								else if(useReadback){
-									val = crlogicDataFilter.calculatePositionMotorUseReadback(raw);
-								}
-								else{
-									val = crlogicDataFilter.calculatePositionMotor(raw);
-								}
-								
-								// Check whether data is within the configured range - otherwise drop data
-								use = crlogicDataFilter.filter(val);
-//								if(!use){
-//									break;
-//								}
-							}
-							else if(scalerIndices.containsKey(i)){
-								CrlogicDeltaDataFilter f = scalerIndices.get(i); 
-								val = f.delta(new Double(t));
-							}
-							else{
-								val = new Double(t);
-							}
-							
-							
-							message.getData().add(val);
-						}
-						
-						// Does not work if zigzag, ... 
-//						// Use this to filter out motor retry movements at the end of the scan
-//						wasInRangeBefore = wasInRangeBefore | use;
-//						if(!use && wasInRangeBefore){
-//							discardAnyway=true;
-//							// Optimization - terminate read loop once range is left
-//							logger.info("Terminate read loop because point is outside range");
-//							break;
-//						}
-						
-						// Filter data
-						if(use && !discardAnyway){
-							dataQueue.put(message);
-							mcounter++;
-						}
-						
-						
-					}
-				}
-			}
-			in.close();
-			inreader.close();
-			
-			logger.info("Lines read: "+linecount+" Messages generated (after filtering): "+mcounter);
-			
-			// Remove temporary file
-			if(!keepTmpFiles){
-				tmpFile.delete();
-			}
-		}
-		else{
-			// TODO - File in local file system
-		}
-		
-		// Issue end of loop control message
-		dataQueue.put(new EndOfStreamMessage(dataGroup));
-		semaphore.release();
-	}
-	
-	
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		try{
-		
-			double stepSize = actuator.getStepSize();
-			double start = actuator.getStart();
-			double end = actuator.getEnd();
-			double integrationTime = actuator.getIntegrationTime();
-			double ubacklash = actuator.getAdditionalBacklash();
-			
-			// Set values for the datafilter
-			crlogicDataFilter.setStart(actuator.getStart());
-			crlogicDataFilter.setEnd(actuator.getEnd());
-			
-			// Reset data filter
-			for(Integer k: scalerIndices.keySet()){
-				scalerIndices.get(k).reset();
-			}
-			
-			synchronized(this){
-				// Set abort state to false
-				abort = false;
-				abortForce = false;
-			
-			// Set execution thread to current thread
-				executionThread = Thread.currentThread();
-			}
-			
-			
-			// TODO each actuator will result in an additional sensor (at the beginning)
-			// Dependent on actuator settings (readback use encoder, ...)
-			
-			
-			// TODO filename generation?
-			final String tmpFileName = "tmp-"+System.currentTimeMillis()+".txt";
-			
-			Long timeout = 600000l; // 10 minutes move timeout
-			
-			// Check if logic is inactive, otherwise return early
-			if(!template.getStatus().getValue().equals(CrlogicChannelsTemplate.Status.INACTIVE.toString())){
-				logger.info("CRLOGIC is not inactive!");
-				// TODO Decide what to do in this situation
-				
-				if(template.getStatus().getValue().equals(CrlogicChannelsTemplate.Status.FAULT.toString())){
-					// If in fault show message and recover
-					logger.info("CRLOGIC in FAULT state");
-					logger.info("Error message: "+template.getMessage().getValue());
-					logger.info("Recover logic and set it to INACTIVE");
-					template.getStatus().setValue(CrlogicChannelsTemplate.Status.INACTIVE.toString());
-				}
-				else if(template.getStatus().getValue().equals(CrlogicChannelsTemplate.Status.ACTIVE.toString())){
-					template.getStatus().setValue(CrlogicChannelsTemplate.Status.STOP.toString());
-					template.getStatus().waitForValue(CrlogicChannelsTemplate.Status.INACTIVE.toString(), startStopTimeout);
-				}
-				else{
-					throw new RuntimeException("CRLOGIC is not inactive");
-				}
-			}
-			
-			
-			logger.info("Set parameters");
-			template.getNfsServer().setValue(server);
-			template.getNfsShare().setValue(share);
-			template.getDataFile().setValue(tmpFileName);
-			
-			int tps = template.getTicksPerSecond().getValue();
-			logger.info("Ticks per second: "+tps);
-			
-			logger.info("Set readout resources");
-			
-			template.getReadoutResources().setValue(readoutResources.toArray(new String[readoutResources.size()]));
-			
-			
-			
-			// Set ticks between interrupt to integration time
-			int ticks = (int)(tps*integrationTime);
-			template.getTicksBetweenInterrupts().setValue(ticks);
-			
-			// Prepare motor
-			double totalTimeSeconds = Math.abs((end-start)/stepSize*integrationTime);
-			int hours = (int) Math.floor(totalTimeSeconds/60/60);
-			int minutes = (int) Math.floor(totalTimeSeconds/60-hours*60);
-			int seconds = (int) Math.floor(totalTimeSeconds-hours*60*60-minutes*60);
-			
-			logger.info("Estimated time: "+hours+":"+minutes+":"+seconds);
-			
-			int direction = 1;
-			if(end-start<0){
-				direction = -1;
-			}
-			
-			double motorBaseSpeed = motortemplate.getBaseSpeed().getValue();
-			double motorHighLimit = motortemplate.getHighLimit().getValue();
-			double motorLowLimit = motortemplate.getLowLimit().getValue();
-			double motorBacklash = motortemplate.getBacklashDistance().getValue();
-			
-			boolean respectMotorMinSpeed = false; // if false set min speed to 0
-			double motorMinSpeed = 0;
-			if(respectMotorMinSpeed){
-				motorMinSpeed = motorBaseSpeed;
-			}
-			
-			// Check user parameters
-			// TODO start and end values must be between the motor high and low value - otherwise fail
-			if(start>motorHighLimit || start<motorLowLimit){
-				// Start value is outside motor high and/or low value
-				logger.info("Start value is outside motor high and/or low value");
-				throw new IllegalArgumentException("Start value is outside motor high and/or low value");
-			}
-			if(end>motorHighLimit || end<motorLowLimit){
-				// End value is outside motor high and/or low value
-				logger.info("End value is outside motor high and/or low value");
-				throw new IllegalArgumentException("End value is outside motor high and/or low value");
-			}
-			// TODO Check minimum step size
-			int minimumTicks = 10;
-			double minStepSize = motorMinSpeed*(minimumTicks/tps);
-			if(stepSize<minStepSize){
-				// Step size is too small
-				logger.info("Step size is too small");
-				throw new IllegalArgumentException("Step size is too small");
-			}
-			// TODO Check integration time
-			if(motorMinSpeed>0){
-				double maxIntegrationTime = stepSize/motorMinSpeed;
-				if(integrationTime>maxIntegrationTime){
-					logger.info("Integration time is too big");
-					// Integration time is too big
-					throw new IllegalArgumentException("Integration time is too big");
-				}
-			}
-			double motorMaxSpeed = motortemplate.getVelocity().getValue();
-			double minIntegrationTime = Math.min( (stepSize/motorMaxSpeed), ((double)minimumTicks/(double)tps) );
-			if(integrationTime<minIntegrationTime){
-				// Integration time is too small
-				logger.info("Integration time is too small [min integration time: "+minIntegrationTime+"]");
-				throw new IllegalArgumentException("Integration time is too small [min integration time: "+minIntegrationTime+"]");
-			}
-			
-			
-			// TODO Calculate and set motor speed, backlash, etc.
-			double motorSpeed = stepSize/integrationTime;
-			double backlash = (0.5*motorSpeed*motortemplate.getAccelerationTime().getValue())+motorBacklash+ubacklash;
-			double realEnd = end+(backlash*direction);
-			double realStart = start-(backlash*direction);
-	
-			
-			// Move to start
-			logger.info("Move motor to start ["+realStart+"]");
-			motortemplate.getSetValue().setValue(realStart, timeout); // Will block until move is done
-			
-			
-			// Set motor paramters
-			// Backup settings
-			logger.info("Backup motor settings");
-			double backupSpeed = motortemplate.getVelocity().getValue();
-			double backupBacklash = motorBacklash;
-			double backupMinSpeed = motorBaseSpeed;
-			
-			try{
-				// Set motor settings
-				logger.info("Update motor settings");
-//				if(!respectMotorMinSpeed){
-//					motortemplate.getBaseSpeed().setValue(0d);
-//				}
-				// Set base speed as fast as possible but not faster than the original base speed.
-				double base = motorBaseSpeed;
-				if(motorSpeed<base){
-					base = motorSpeed;
-				}
-				motortemplate.getBaseSpeed().setValue(base);
-				motortemplate.getVelocity().setValue(motorSpeed);
-				motortemplate.getBacklashDistance().setValue(0d);
-				
-				
-				// Execute pre actions
-				for(Action action: preActions){
-					action.execute();
-				}
-				
-				
-				// Start crlogic logic
-				logger.info("Start CRLOGIC");
-				template.getStatus().setValue(CrlogicChannelsTemplate.Status.INITIALIZE.toString());
-				try{
-					template.getStatus().waitForValue(CrlogicChannelsTemplate.Status.ACTIVE.toString(), startStopTimeout);
-				}
-				catch(CAException e){
-					logger.info( "Failed to start CRLOGIC. Logic in status: "+template.getStatus().getValue() );
-					if(template.getStatus().getValue().equals(CrlogicChannelsTemplate.Status.FAULT.toString())){
-						logger.info("Error message: "+template.getMessage().getValue());
-					}
-					// Recover to inactive
-					template.getStatus().setValue(CrlogicChannelsTemplate.Status.INACTIVE.toString());
-					// TODO Improve error handling
-					throw new RuntimeException("Failed to start CRLOGIC. Logic in status: "+template.getStatus().getValue()+ " Error message: "+template.getMessage().getValue(), e);
-					
-				}
-
-				// Move motor(s) to end / wait until motor is stopped
-				logger.info("Move motor to end ["+realEnd+"]");
-				try{
-					motortemplate.getSetValue().setValue(realEnd, timeout); // Will block until move is done
-				}
-				catch (InterruptedException e) {
-					if(abort & (!abortForce)){
-						// Abort motor move 
-						motortemplate.getCommand().setValue(MotorChannelsTemplate.Commands.Stop.ordinal());
-						motortemplate.getCommand().setValue(MotorChannelsTemplate.Commands.Go.ordinal());
-					}
-					else{
-						throw e;
-					}
-				}
-				logger.info("Motor reached end position");
-				
-				// Stop crlogic logic
-				logger.info("Stop CRLOGIC");
-				template.getStatus().setValue(CrlogicChannelsTemplate.Status.STOP.toString());
-				// Wait until stopped
-				logger.info("Wait until stopped");
-				try{
-					template.getStatus().waitForValue(CrlogicChannelsTemplate.Status.INACTIVE.toString(), startStopTimeout);
-				}
-				catch(CAException e){
-					logger.info( "Failed to stop CRLOGIC. Logic in status: "+template.getStatus().getValue() );
-					// TODO Improve error handling
-					throw new RuntimeException("Failed to stop CRLOGIC.  Logic in status: "+template.getStatus().getValue(), e);
-				}
-				logger.info("CRLOGIC is now stopped");
-				
-				
-				// Execute post actions
-				for(Action action: postActions){
-					action.execute();
-				}
-				
-				
-			}
-			finally{
-				logger.info("Restore motor settings");
-				motortemplate.getBaseSpeed().setValue(backupMinSpeed);
-				motortemplate.getVelocity().setValue(backupSpeed);
-				motortemplate.getBacklashDistance().setValue(backupBacklash);
-			}
-			
-			// Request read of data file
-			readQueue.put(tmpFileName);
-			
-//			// Read data
-//			Thread t = new Thread(new Runnable() {
-//				
-//				@Override
-//				public void run() {
-//					try {
-//						collectData(smbShare, tmpFileName);
-//					} catch (InterruptedException e) {
-//						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-//					} catch (IOException e) {
-//						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-//					}
-//				}
-//			});
-//			t.start();
-			
-			if(zigZag){
-				// Swap start and end
-				double aend = actuator.getEnd();
-				actuator.setEnd(actuator.getStart());
-				actuator.setStart(aend);
-			}
-			
-			synchronized(this){
-				executionThread = null;
-			}
-		}
-		catch(CAException e){
-			throw new RuntimeException("Unable to execute crloop", e);
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort(false);
-	}
-	
-	/**
-	 * Abort logic
-	 * @param force
-	 */
-	public synchronized void abort(boolean force){
-		abort = true;
-		abortForce = force;
-		
-		// executionThread variable guarded by "this"
-		if(executionThread != null){
-			executionThread.interrupt();
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		stopReadoutThread = true;
-		readoutThread.interrupt();
-		// TODO eventually interrupt readout thread
-		
-		try {
-			
-			ChannelBeanFactory.getFactory().destroyChannelBeans(template);
-			ChannelBeanFactory.getFactory().destroyChannelBeans(motortemplate);
-			template = null;
-			motortemplate = null;
-			
-		} catch (Exception e) {
-			throw new RuntimeException("Unable to destroy CrlogicLoop", e);
-		}
-		
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#prepare()
-	 */
-	@Override
-	public void prepare() {
-		
-		stopReadoutThread = false;
-		// Start readout Thread
-		readoutThread = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				while(!stopReadoutThread){
-					String file;
-					try {
-						file = readQueue.take();
-					} catch (InterruptedException e) {
-						break;
-					}
-					// TODO Read file and 
-					try {
-						collectData(smbShare, file);
-					} catch (InterruptedException e) {
-						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-					} catch (IOException e) {
-						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-					}
-					
-				}
-				
-			}
-		});
-		readoutThread.start();
-		
-		try{
-			// Connect crlogic channels
-			template = new CrlogicChannelsTemplate();
-			logger.info("Connect channels");
-			ChannelBeanFactory.getFactory().createChannelBeans(template, prefix);
-			
-			// Connect motor channels
-			motortemplate = new MotorChannelsTemplate();
-			ChannelBeanFactory.getFactory().createChannelBeans(motortemplate, actuator.getName());
-			
-			useReadback = motortemplate.getUseReadback().getValue();
-			useEncoder = motortemplate.getUseEncoder().getValue();
-			
-			logger.info("Motor type: "+ MotorChannelsTemplate.Type.values()[motortemplate.getType().getValue()]);
-			logger.info("Motor use readback: "+useReadback);
-			logger.info("Motor use encoder: "+useEncoder);
-			
-			// TODO build up list of readout resources (based on sensors)
-			readoutResources.clear();
-			// first sensor is the actuator
-			
-			// Determine mode of motor
-			if((!useReadback) && (!useEncoder)){
-				// Open loop
-				if(actuator.getReadback()!=null){
-					throw new IllegalArgumentException("Readback not supported if motor is configured in open loop");
-				}
-				else{
-					readoutResources.add(actuator.getName());
-				}
-				
-			}
-			else if(useReadback && (!useEncoder)){
-				String readback;
-				// use readback link
-				if(actuator.getReadback()!=null){
-					// Use specified readback
-					readback = (actuator.getReadback());
-				}
-				else{
-					// Set resouce to readback link
-					readback = (motortemplate.getReadbackLink().getValue());
-					readback = readback.replaceAll(" +.*", ""); // remove NPP etc at the end
-				}
-				
-				readoutResources.add(readback);
-				
-				// Fill readback encoder settings
-				// Connect to encoder
-				EncoderChannelsTemplate encodertemplate = new EncoderChannelsTemplate();
-				ChannelBeanFactory.getFactory().createChannelBeans(encodertemplate, readback);
-				
-				// Read encoder settings
-				if(encodertemplate.getDirection().getValue()==EncoderChannelsTemplate.Direction.Positive.ordinal()){
-					crlogicDataFilter.setEncoderDirection(1);
-				}
-				else{
-					crlogicDataFilter.setEncoderDirection(-1);
-				}
-				crlogicDataFilter.setEncoderOffset(encodertemplate.getOffset().getValue());
-				crlogicDataFilter.setEncoderResolution(encodertemplate.getResolution().getValue());
-				
-				// Disconnect from encoder
-				ChannelBeanFactory.getFactory().destroyChannelBeans(encodertemplate);
-				
-			}
-			else if (useEncoder && (!useReadback)){
-				// use readback link
-				if(actuator.getReadback()!=null){
-					throw new IllegalArgumentException("Readback not supported if motor is configured to use encoder");
-				}
-				else{
-					// Set resouce to readback link
-					readoutResources.add(actuator.getName()+"_ENC");
-				}
-			}
-			else{
-				throw new IllegalArgumentException("Motor configuration not supportet: use readback - "+useReadback+" use encoder - "+useEncoder);
-			}
-			
-			// Fill Motor specific settings
-			if(motortemplate.getDirection().getValue()==MotorChannelsTemplate.Direction.Positive.ordinal()){
-				crlogicDataFilter.setMotorDirection(1);
-			}
-			else{
-				crlogicDataFilter.setMotorDirection(-1);
-			}
-			crlogicDataFilter.setMotorEncoderResolution(motortemplate.getEncoderResolution().getValue());
-			crlogicDataFilter.setMotorOffset(motortemplate.getOffset().getValue());
-			crlogicDataFilter.setMotorReadbackResolution(motortemplate.getReadbackResolution().getValue());
-			crlogicDataFilter.setMotorResolution(motortemplate.getMotorResolution().getValue());
-			
-			// Clear all indices
-			scalerIndices.clear();
-			
-			int c = 1; // We start at 1 because the actuator right now is an implicit sensor 
-			for(Sensor s: sensors){
-					if(s instanceof OTFNamedChannelSensor){
-						// Monitored channel (MUST be configured MODULE ID'S)
-						OTFNamedChannelSensor so = (OTFNamedChannelSensor) s;
-						readoutResources.add(so.getName());
-					}
-					else if (s instanceof OTFScalerChannelSensor){
-						OTFScalerChannelSensor so = (OTFScalerChannelSensor) s;
-						readoutResources.add("SCALER"+so.getIndex());
-						scalerIndices.put(c, new CrlogicDeltaDataFilter());
-					}
-					else if (s instanceof MillisecondTimestampSensor){
-						readoutResources.add("TIMESTAMP");
-					}
-					else{
-						throw new IllegalArgumentException("Sensor type "+s.getClass()+" is not supported by this loop");
-					}
-					c++;
-			}
-			
-			// Workaround - somehow one has to add an empty thing to the value otherwise the c logic 
-			// does not pick up the end
-			readoutResources.add("");
-		}
-		catch(Exception e){
-			throw new RuntimeException("Unable to prepare crloop: ",e);
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#cleanup()
-	 */
-	@Override
-	public void cleanup() {
-		// TODO Auto-generated method stub
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPreActions()
-	 */
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPostActions()
-	 */
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#isDataGroup()
-	 */
-	@Override
-	public boolean isDataGroup() {
-		// TODO Auto-generated method stub
-		return dataGroup;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#setDataGroup(boolean)
-	 */
-	@Override
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-	
-	/**
-	 * @return the sensors
-	 */
-	public List<Sensor> getSensors() {
-		return sensors;
-	}
-	
-	/**
-	 * @return the actor
-	 */
-	public OTFActuator getActor() {
-		return actuator;
-	}
-
-	/**
-	 * @param actor the actor to set
-	 */
-	public void setActor(OTFActuator actor) {
-		this.actuator = actor;
-	}
-
-	/**
-	 * The structure of the data message depends on the sensors registered at this loop 
-	 * at the time this method is called.
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-		
-		// Build up data message metadata based on the sensors currently registered.
-		m.getComponents().add(new ComponentMetadata(actuator.getId()));
-		for(Sensor s: sensors){
-			m.getComponents().add(new ComponentMetadata(s.getId()));
-		}
-		return new DataQueue(dataQueue, m);
-	}
-
-
-	/**
-	 * @return the keepTmpFiles
-	 */
-	public boolean isKeepTmpFiles() {
-		return keepTmpFiles;
-	}
-
-
-	/**
-	 * @param keepTmpFiles the keepTmpFiles to set
-	 */
-	public void setKeepTmpFiles(boolean keepTmpFiles) {
-		this.keepTmpFiles = keepTmpFiles;
-	}
-	
-	
-	
-}

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

@@ -1,652 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.loops.cr;
-
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.annotation.CaChannel;
-
-/**
- * @author ebner
- *
- */
-public class MotorChannelsTemplate {
-
-	public enum Type {SOFT_CHANNEL, MOTOR_SIMULATION, OMS_VME58, OMS_MAXv};
-	
-	/**
-	 * ## Drive section ##
-	 * # User coordinates #
-	 */
-	
-	/**
-	 * .HLM	High limit	- double
-	 */
-	@CaChannel(type=Double.class, name =".HLM")
-	private ChannelBean<Double> highLimit;
-	
-	/**
-	 * .LLM	Low limit	- double
-	 */
-	@CaChannel(type=Double.class, name =".LLM")
-	private ChannelBean<Double> lowLimit;
-	
-	/**
-	 * .RBV	Readback value	- double
-	 */
-	@CaChannel(type=Double.class, name =".RBV", monitor=true)
-	private ChannelBean<Double> readbackValue;
-	
-	/**
-	 * .VAL	Set value	- double
-	 */
-	@CaChannel(type=Double.class, name =".VAL", monitor=true)
-	private ChannelBean<Double> setValue;
-
-	/**
-	 * .RLV	Relative move value	- double
-	 */
-	@CaChannel(type=Double.class, name =".RLV")
-	private ChannelBean<Double> relativeMoveValue;
-	
-	/**
-	 * .TWV	Teak value	- double
-	 */
-	@CaChannel(type=Double.class, name =".TWV")
-	private ChannelBean<Double> tweakValue;
-	
-	/**
-	 * .TWR	Tweak reverse - move left	- int
-	 */
-	@CaChannel(type=Integer.class, name =".TWR")
-	private ChannelBean<Integer> tweakReverse;
-	
-	/**
-	 * .TWF	Tweak forward - move right	- int
-	 */
-	@CaChannel(type=Integer.class, name =".TWF")
-	private ChannelBean<Integer> tweakForward;
-	
-	/**
-	 * .JOGR	Jog reverse	- int
-	 */
-	@CaChannel(type=Integer.class, name =".JOGR")
-	private ChannelBean<Integer> jogReverse;
-	
-	/**
-	 * .JOGF	Jog forward	- int
-	 */
-	@CaChannel(type=Integer.class, name =".JOGF")
-	private ChannelBean<Integer> jogForward;
-	
-	/**
-	 * .HOMR	Home reverse	- int
-	 */
-	@CaChannel(type=Integer.class, name =".HOMR")
-	private ChannelBean<Integer> homeReverse;
-	
-	/**
-	 * .HOMF	Home forward	- int
-	 */
-	@CaChannel(type=Integer.class, name =".HOMF")
-	private ChannelBean<Integer> homeForward;
-
-	/**
-	 * .EGU	Engineering unit	- String
-	 */
-	@CaChannel(type=String.class, name =".EGU")
-	private ChannelBean<String> engineeringUnit;
-
-	/**
-	 * .DTYP	Type	- String (e.g. "OMS MAXv") see enum Type
-	 */
-	@CaChannel(type=Integer.class, name =".DTYP")
-	private ChannelBean<Integer> type;
-	
-	/**
-	 * .DESC	Description	- String
-	 */
-	@CaChannel(type=String.class, name =".DESC")
-	private ChannelBean<String> description;
-
-	
-	/**
-	 * # Dial coordinates #
-	 */
-	
-	/**
-	 * .DHLM	Dial high limit	- double
-	 */
-	@CaChannel(type=Double.class, name =".DHLM")
-	private ChannelBean<Double> dialHighLimit;
-	
-	/**
-	 * .DLLM	Dial low limit	- double
-	 */
-	@CaChannel(type=Double.class, name =".DLLM")
-	private ChannelBean<Double> dialLowLimit;
-	
-	/**
-	 * .DRBV	Dial readback value	- double
-	 */
-	@CaChannel(type=Double.class, name =".DRBV", monitor=true)
-	private ChannelBean<Double> dialReadbackValue;
-	
-	/**
-	 * .DVAL	Dial set value	- double
-	 */
-	@CaChannel(type=Double.class, name =".DVAL", monitor=true)
-	private ChannelBean<Double> dialSetValue;
-
-	/**
-	 * .RVAL	Raw value	- int
-	 */
-	@CaChannel(type=Integer.class, name =".RVAL", monitor=true)
-	private ChannelBean<Integer> rawValue;
-	
-	/**
-	 * .RRBV	Raw readback value	- int
-	 */
-	@CaChannel(type=Integer.class, name =".RRBV", monitor=true)
-	private ChannelBean<Integer> rawReadbackValue;
-
-	/**
-	 * .SPMG	Stop/Pause/Move/Go	- (0:"Stop", 1:"Pause", 2:"Move", 3:"Go")	- 3
-	 */
-	public enum Commands { Stop, Pause, Move, Go };
-	@CaChannel(type=Integer.class, name =".SPMG")
-	private ChannelBean<Integer> command;
-	
-
-	/**
-	 * ## Calibration section ##
-	 */
-	
-	/**
-	 * .SET	Set/Use Switch	- (0:"Use", 1:"Set")	- 0
-	 */
-	public enum Calibration {Use, Set};
-	@CaChannel(type=Integer.class, name =".SET")
-	private ChannelBean<Integer> calibration;
-	
-	/**
-	 * .OFF	User offset (EGU)	- double
-	 */
-	@CaChannel(type=Double.class, name =".OFF")
-	private ChannelBean<Double> offset;
-	
-	/**
-	 * .FOFF	Offset-Freeze Switch	- (0:"Variable", 1:"Frozen") - 1
-	 */
-	public enum OffsetMode {Variable, Frozen};
-	@CaChannel(type=Integer.class, name =".FOFF")
-	private ChannelBean<Integer> offsetMode;
-	
-	/**
-	 * .DIR	User direction	- (0:"Pos", 1:"Neg")
-	 */
-	public enum Direction {Positive, Negative};
-	@CaChannel(type=Integer.class, name =".DIR")
-	private ChannelBean<Integer> direction;
-
-	
-	/**
-	 * ## Dynamics ##
-	 */
-	
-	/**
-	 * .VELO	Velocity (EGU/s)	- double
-	 */
-	@CaChannel(type=Double.class, name =".VELO")
-	private ChannelBean<Double> velocity;
-	
-	/**
-	 * .BVEL	Backlash velocity (EGU/s) - double
-	 */
-	@CaChannel(type=Double.class, name =".BVEL")
-	private ChannelBean<Double> backlashVelocity;
-	
-	/**
-	 * .VBAS	Base speed (EGU/s) - double
-	 */
-	@CaChannel(type=Double.class, name =".VBAS")
-	private ChannelBean<Double> baseSpeed;
-	
-	/**
-	 * .ACCL	Acceleration time / seconds to velocity	- double
-	 */
-	@CaChannel(type=Double.class, name =".ACCL")
-	private ChannelBean<Double> accelerationTime;
-	
-	/**
-	 * .BACC	Backlash acceleration time / seconds to velocity	- double
-	 */
-	@CaChannel(type=Double.class, name =".BACC")
-	private ChannelBean<Double> backlashAccelerationTime;
-	
-	/**
-	 * .BDST	Backlash distance (EGU)	- double 
-	 */
-	@CaChannel(type=Double.class, name =".BDST")
-	private ChannelBean<Double> backlashDistance;
-	
-	/**
-	 * .FRAC	Move fraction	- double
-	 */
-	@CaChannel(type=Double.class, name =".FRAC")
-	private ChannelBean<Double> moveFracion;
-	
-
-	/**
-	 * ## Resolution ##
-	 */
-	
-	/**
-	 * .MRES	Motor resolution	- double
-	 */
-	@CaChannel(type=Double.class, name =".MRES")
-	private ChannelBean<Double> motorResolution;
-	
-	/**
-	 * .ERES	Encoder resolution	- double
-	 */
-	@CaChannel(type=Double.class, name =".ERES")
-	private ChannelBean<Double> encoderResolution;
-	
-	/**
-	 * .RRES	Readback resolution	- double
-	 */
-	@CaChannel(type=Double.class, name =".RRES")
-	private ChannelBean<Double> readbackResolution;
-	
-	/**
-	 * .RDBD	Retry deadband (EGU)	- double
-	 */
-	@CaChannel(type=Double.class, name =".RDBD")
-	private ChannelBean<Double> retryDeadband;
-	
-	/**
-	 * .RTRY	Max retry count	- int
-	 */
-	@CaChannel(type=Integer.class, name =".RTRY")
-	private ChannelBean<Integer> maxRetryCount;
-	
-	/**
-	 * .RCNT	Retry count	- int
-	 */
-	@CaChannel(type=Integer.class, name =".RCNT", monitor=true)
-	private ChannelBean<Integer> retryCount;
-	
-	/**
-	 * .UEIP	Use encoder (if present) - (0:"No", 1:"Yes")
-	 */
-	@CaChannel(type=Boolean.class, name =".UEIP")
-	private ChannelBean<Boolean> useEncoder;
-	
-	/**
-	 * .URIP	Use readback link (if present)	- (0:"No", 1:"Yes")
-	 */
-	@CaChannel(type=Boolean.class, name =".URIP")
-	private ChannelBean<Boolean> useReadback;
-	
-	/**
-	 * .DLY	Readback delay (s)	- double
-	 */
-	@CaChannel(type=Double.class, name =".DLY")
-	private ChannelBean<Double> readbackDelay;
-	
-	/**
-	 * .RDBL	Readback link	- String
-	 */
-	@CaChannel(type=String.class, name =".RDBL")
-	private ChannelBean<String> readbackLink;
-	
-	/**
-	 * .OMSL	Output mode select	- (0:"supervisory", 1:"closed_loop")
-	 */
-	public enum OutputMode {Supervisory, Closed_Loop};
-	@CaChannel(type=Integer.class, name =".OMSL")
-	private ChannelBean<Integer> outputMode;
-	
-	/**
-	 * ## Status ## 
-	 */
-	
-	/**
-	 * .DMOV	Done move	- int
-	 */
-	@CaChannel(type=Boolean.class, name =".DMOV", monitor=true)
-	private ChannelBean<Boolean> moveDone;
-
-	/**
-	 * @return the highLimit
-	 */
-	public ChannelBean<Double> getHighLimit() {
-		return highLimit;
-	}
-
-	/**
-	 * @return the lowLimit
-	 */
-	public ChannelBean<Double> getLowLimit() {
-		return lowLimit;
-	}
-
-	/**
-	 * @return the readbackValue
-	 */
-	public ChannelBean<Double> getReadbackValue() {
-		return readbackValue;
-	}
-
-	/**
-	 * @return the setValue
-	 */
-	public ChannelBean<Double> getSetValue() {
-		return setValue;
-	}
-
-	/**
-	 * @return the relativeMoveValue
-	 */
-	public ChannelBean<Double> getRelativeMoveValue() {
-		return relativeMoveValue;
-	}
-
-	/**
-	 * @return the tweakValue
-	 */
-	public ChannelBean<Double> getTweakValue() {
-		return tweakValue;
-	}
-
-	/**
-	 * @return the tweakReverse
-	 */
-	public ChannelBean<Integer> getTweakReverse() {
-		return tweakReverse;
-	}
-
-	/**
-	 * @return the tweakForward
-	 */
-	public ChannelBean<Integer> getTweakForward() {
-		return tweakForward;
-	}
-
-	/**
-	 * @return the jogReverse
-	 */
-	public ChannelBean<Integer> getJogReverse() {
-		return jogReverse;
-	}
-
-	/**
-	 * @return the jogForward
-	 */
-	public ChannelBean<Integer> getJogForward() {
-		return jogForward;
-	}
-
-	/**
-	 * @return the homeReverse
-	 */
-	public ChannelBean<Integer> getHomeReverse() {
-		return homeReverse;
-	}
-
-	/**
-	 * @return the homeForward
-	 */
-	public ChannelBean<Integer> getHomeForward() {
-		return homeForward;
-	}
-
-	/**
-	 * @return the engineeringUnit
-	 */
-	public ChannelBean<String> getEngineeringUnit() {
-		return engineeringUnit;
-	}
-
-	/**
-	 * @return the type
-	 */
-	public ChannelBean<Integer> getType() {
-		return type;
-	}
-
-	/**
-	 * @return the description
-	 */
-	public ChannelBean<String> getDescription() {
-		return description;
-	}
-
-	/**
-	 * @return the dialHighLimit
-	 */
-	public ChannelBean<Double> getDialHighLimit() {
-		return dialHighLimit;
-	}
-
-	/**
-	 * @return the dialLowLimit
-	 */
-	public ChannelBean<Double> getDialLowLimit() {
-		return dialLowLimit;
-	}
-
-	/**
-	 * @return the dialReadbackValue
-	 */
-	public ChannelBean<Double> getDialReadbackValue() {
-		return dialReadbackValue;
-	}
-
-	/**
-	 * @return the dialSetValue
-	 */
-	public ChannelBean<Double> getDialSetValue() {
-		return dialSetValue;
-	}
-
-	/**
-	 * @return the rawValue
-	 */
-	public ChannelBean<Integer> getRawValue() {
-		return rawValue;
-	}
-
-	/**
-	 * @return the rawReadbackValue
-	 */
-	public ChannelBean<Integer> getRawReadbackValue() {
-		return rawReadbackValue;
-	}
-
-	/**
-	 * @return the command
-	 */
-	public ChannelBean<Integer> getCommand() {
-		return command;
-	}
-
-	/**
-	 * @return the calibration
-	 */
-	public ChannelBean<Integer> getCalibration() {
-		return calibration;
-	}
-
-	/**
-	 * @return the userOffset
-	 */
-	public ChannelBean<Double> getOffset() {
-		return offset;
-	}
-
-	/**
-	 * @return the offsetMode
-	 */
-	public ChannelBean<Integer> getOffsetMode() {
-		return offsetMode;
-	}
-
-	/**
-	 * @return the direction
-	 */
-	public ChannelBean<Integer> getDirection() {
-		return direction;
-	}
-
-	/**
-	 * @return the velocity
-	 */
-	public ChannelBean<Double> getVelocity() {
-		return velocity;
-	}
-
-	/**
-	 * @return the backlashVelocity
-	 */
-	public ChannelBean<Double> getBacklashVelocity() {
-		return backlashVelocity;
-	}
-
-	/**
-	 * @return the baseSpeed
-	 */
-	public ChannelBean<Double> getBaseSpeed() {
-		return baseSpeed;
-	}
-
-	/**
-	 * @return the accelerationTime
-	 */
-	public ChannelBean<Double> getAccelerationTime() {
-		return accelerationTime;
-	}
-
-	/**
-	 * @return the backlashAccelerationTime
-	 */
-	public ChannelBean<Double> getBacklashAccelerationTime() {
-		return backlashAccelerationTime;
-	}
-
-	/**
-	 * @return the backlashDistance
-	 */
-	public ChannelBean<Double> getBacklashDistance() {
-		return backlashDistance;
-	}
-
-	/**
-	 * @return the moveFracion
-	 */
-	public ChannelBean<Double> getMoveFracion() {
-		return moveFracion;
-	}
-
-	/**
-	 * @return the motorResolution
-	 */
-	public ChannelBean<Double> getMotorResolution() {
-		return motorResolution;
-	}
-
-	/**
-	 * @return the encoderResolution
-	 */
-	public ChannelBean<Double> getEncoderResolution() {
-		return encoderResolution;
-	}
-
-	/**
-	 * @return the readbackResolution
-	 */
-	public ChannelBean<Double> getReadbackResolution() {
-		return readbackResolution;
-	}
-
-	/**
-	 * @return the retryDeadband
-	 */
-	public ChannelBean<Double> getRetryDeadband() {
-		return retryDeadband;
-	}
-
-	/**
-	 * @return the maxRetryCount
-	 */
-	public ChannelBean<Integer> getMaxRetryCount() {
-		return maxRetryCount;
-	}
-
-	/**
-	 * @return the retryCount
-	 */
-	public ChannelBean<Integer> getRetryCount() {
-		return retryCount;
-	}
-
-	/**
-	 * @return the useEncoder
-	 */
-	public ChannelBean<Boolean> getUseEncoder() {
-		return useEncoder;
-	}
-
-	/**
-	 * @return the useReadback
-	 */
-	public ChannelBean<Boolean> getUseReadback() {
-		return useReadback;
-	}
-
-	/**
-	 * @return the readbackDelay
-	 */
-	public ChannelBean<Double> getReadbackDelay() {
-		return readbackDelay;
-	}
-
-	/**
-	 * @return the readbackLink
-	 */
-	public ChannelBean<String> getReadbackLink() {
-		return readbackLink;
-	}
-
-	/**
-	 * @return the outputMode
-	 */
-	public ChannelBean<Integer> getOutputMode() {
-		return outputMode;
-	}
-
-	/**
-	 * @return the moveDone
-	 */
-	public ChannelBean<Boolean> getMoveDone() {
-		return moveDone;
-	}
-	
-}

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

@@ -1,169 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.loops.cr;
-
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * @author ebner
- *
- */
-public class ParallelCrlogicStreamMerge {
-
-	private BlockingQueue<Message> dataQueue;
-	
-	private DataQueue primaryQueue;
-	private DataQueue secondaryQueue;
-	
-	/**
-	 * 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.
-	 * 
-	 * @param pqueue	Primary/master queue
-	 * @param squeue	Secondary queue
-	 */
-	public ParallelCrlogicStreamMerge(DataQueue pqueue, DataQueue squeue){
-		this.primaryQueue = pqueue;
-		this.secondaryQueue = squeue;
-		
-		this.dataQueue = new LinkedBlockingQueue<Message>();
-	}
-	
-	/**
-	 * Merge the streams based on the timestamp
-	 * @throws InterruptedException 
-	 */
-	public void merge() throws InterruptedException{
-		
-		// 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.getQueue().take();
-		
-		while(! (m instanceof EndOfStreamMessage)){
-			
-			if(m instanceof DataMessage){
-				
-				DataMessage dm = (DataMessage) m;
-				
-				// 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);
-				
-//				System.out.println("timestamp: "+new Date(milliseconds)+" "+milliseconds+" ."+nanoOffset);
-				
-				while(true){
-					// Assumption: the secondary Queue holds at least the data up to the 
-					// timestamp of the primary queue
-					Message mess = secondaryQueue.getQueue().peek();
-//					Message mess = secondaryQueue.getQueue().take();
-					
-					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;
-						
-//						System.out.println("Mess: "+mess);
-						
-						long currMilliCheck = ((Double) msCheck.getData().get(0)).longValue();
-						long currNanoCheck = ((Double) msCheck.getData().get(1)).longValue();
-	
-						// Check
-						if(currMilliCheck>milliseconds || (currMilliCheck==milliseconds && currNanoCheck>nanoOffset)){
-							break;
-						}
-						
-						DataMessage ms = (DataMessage) secondaryQueue.getQueue().take();
-						
-//						System.out.println("Ms: "+ms);
-						
-						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);
-				
-				dataQueue.add(dm);
-			}
-			
-			
-			m = primaryQueue.getQueue().take();
-		}
-		
-		// Add the end of stream message of the primary queue
-		dataQueue.add(m);
-		
-		// Clear all remaining messages in secondary queue  
-		secondaryQueue.getQueue().clear();
-	}
-	
-	
-	/**
-	 * The structure of the data message depends on the sensors registered at this loop 
-	 * at the time this method is called.
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-		
-		DataMessageMetadata pqm = primaryQueue.getDataMessageMetadata();
-		m.getComponents().add(pqm.getComponents().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.getComponents().size();i++){
-			m.getComponents().add(pqm.getComponents().get(i));
-		}
-		
-		DataMessageMetadata sqm = secondaryQueue.getDataMessageMetadata();
-		// Skip first two components of the message as this is the timestamp
-		for(int i=2;i<sqm.getComponents().size();i++){
-			m.getComponents().add(sqm.getComponents().get(i));
-		}
-		
-		return new DataQueue(dataQueue, m);
-	}
-	
-}

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

@@ -1,397 +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 gov.aps.jca.CAException;
-import gov.aps.jca.Monitor;
-
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.CountDownLatch;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.ChannelAccessDoubleSensor;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.MonitorListenerDoubleTimestamp;
-
-/**
- * @author ebner
- * 
- *         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>();
-
-	/**
-	 * Sensors to read out
-	 */
-	private List<Sensor> sensors;
-
-	/**
-	 * List of monitors that were attached to the sensor channels (i.e
-	 * workaround)
-	 */
-	private final List<Monitor> monitors = new ArrayList<Monitor>();
-
-	/**
-	 * 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;
-
-	public ScrlogicLoop(List<Sensor> sensors) {
-		this.sensors = sensors;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-
-		// Clear all queues
-		queues.clear();
-		latch = new CountDownLatch(1);
-
-		try {
-			// Attach monitors to the channels (this is actually a workaround)
-			for (Sensor sensor : sensors) {
-				if (sensor instanceof ChannelAccessDoubleSensor) {
-					ChannelAccessDoubleSensor s = (ChannelAccessDoubleSensor) sensor;
-					ChannelBean<Double> b = s.getChannel();
-					// Create data queue for the channel
-					final BlockingQueue<TimestampedValue> q = new LinkedBlockingQueue<TimestampedValue>();
-					queues.add(q);
-
-					Monitor m = b
-							.attachMonitor(new MonitorListenerDoubleTimestamp() {
-
-								@Override
-								public void valueChanged(Double value, Date timestamp, long nanosecondsOffset) {
-									// Add values to channel queue
-									q.add(new TimestampedValue(value, timestamp.getTime(), nanosecondsOffset));
-								}
-							});
-					monitors.add(m);
-				}
-			}
-		} catch (CAException e) {
-			new RuntimeException("Unable to create monitor for channels", e);
-		}
-
-		logger.info("Start data acquisition");
-
-		latch.await();
-
-		// Remove monitors
-		try {
-			for (int i = 0; i < sensors.size(); i++) {
-				Sensor sensor = sensors.get(i);
-				if (sensor instanceof ChannelAccessDoubleSensor) {
-					ChannelAccessDoubleSensor s = (ChannelAccessDoubleSensor) sensor;
-					ChannelBean<Double> b = s.getChannel();
-					try{
-						b.removeMonitor(monitors.get(i));
-					}
-					catch(IllegalArgumentException e){
-						logger.log(Level.SEVERE, "Unable to detach monitor", e);
-					}
-				}
-			}
-		} catch (CAException e) {
-			new RuntimeException(e);
-		}
-		finally{
-			// Clear all monitors in the list
-			monitors.clear();
-		}
-
-		// Merge data
-		merge();
-
-		// Clear data queues
-		for (BlockingQueue<TimestampedValue> q : queues) {
-			q.clear();
-		}
-		queues.clear();
-
-		// Put end of stream to the queue
-		dataQueue.add(new EndOfStreamMessage(dataGroup));
-		
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		latch.countDown();
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy all sensors
-		for (Sensor s : sensors) {
-			s.destroy();
-		}
-		sensors.clear();
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#prepare()
-	 */
-	@Override
-	public void prepare() {
-		// do nothing
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#cleanup()
-	 */
-	@Override
-	public void cleanup() {
-		// Do nothing
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#getPreActions()
-	 */
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#getPostActions()
-	 */
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#isDataGroup()
-	 */
-	@Override
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#setDataGroup(boolean)
-	 */
-	@Override
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-
-	/**
-	 * The structure of the data message depends on the sensors registered at
-	 * this loop at the time this method is called.
-	 * 
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-
-		// Build up data message metadata based on the channels registered.
-		m.getComponents().add(new ComponentMetadata(ID_TIMESTAMP_MILLISECONDS));
-		m.getComponents().add(
-				new ComponentMetadata(ID_TIMESTAMP_OFFSET_NANOSECONDS));
-		for (Sensor s : sensors) {
-			m.getComponents().add(new ComponentMetadata(s.getId()));
-		}
-		return new DataQueue(dataQueue, m);
-	}
-
-	private boolean hasNext(){
-		for (int i = 0; i < queues.size(); i++) {
-			if(!queues.get(i).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()) {
-
-//			semaphore.acquire();
-			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();
-
-				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);
-				dataQueue.add(message);
-			}
-
-		}
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/VSC16ScalerChannelsTemplate.java

@@ -1,103 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.loops.cr;
-
-import java.util.List;
-
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.annotation.CaChannel;
-
-/**
- * @author ebner
- *
- */
-public class VSC16ScalerChannelsTemplate {
-
-	
-	public enum Command {Done, Count};
-	/**
-	 * Command
-	 */
-	@CaChannel(type=Integer.class, name =".CNT")
-	private ChannelBean<Integer> command;
-	
-	
-	public enum Mode {OneShot, AutoCount};
-	/**
-	 * Count mode
-	 */
-	@CaChannel(type=Integer.class, name =".CONT")
-	private ChannelBean<Integer> mode;
-	
-	/**
-	 * Channel description
-	 */
-	@CaChannel(type=Boolean.class, name={".NM1", ".NM2", ".NM3", ".NM4", ".NM5", ".NM6", ".NM7", ".NM8", ".NM9", ".NM10", ".NM11", ".NM12", ".NM13", ".NM14", ".NM15", ".NM16"})
-	private List<ChannelBean<Boolean>> channelDescription;
-	
-	/**
-	 * Channel gate
-	 */
-	@CaChannel(type=Boolean.class, name={".G1", ".G2", ".G3", ".G4", ".G5", ".G6", ".G7", ".G8", ".G9", ".G10", ".G11", ".G12", ".G13", ".G14", ".G15", ".G16"})
-	private List<ChannelBean<Boolean>> channelGate;
-	
-	/**
-	 * Channel preset count
-	 * If gate is on scaler will only count until this value
-	 */
-	@CaChannel(type=Integer.class, name={".PR1", ".PR2", ".PR3", ".PR4", ".PR5", ".PR6", ".PR7", ".PR8", ".PR9", ".PR10", ".PR11", ".PR12", ".PR13", ".PR14", ".PR15", ".PR16"})
-	private List<ChannelBean<Integer>> channelPresetCount;
-
-	/**
-	 * @return the command
-	 */
-	public ChannelBean<Integer> getCommand() {
-		return command;
-	}
-
-	/**
-	 * @return the mode
-	 */
-	public ChannelBean<Integer> getMode() {
-		return mode;
-	}
-
-	/**
-	 * @return the channelDescription
-	 */
-	public List<ChannelBean<Boolean>> getChannelDescription() {
-		return channelDescription;
-	}
-
-	/**
-	 * @return the channelGate
-	 */
-	public List<ChannelBean<Boolean>> getChannelGate() {
-		return channelGate;
-	}
-
-	/**
-	 * @return the channelPresetCount
-	 */
-	public List<ChannelBean<Integer>> getChannelPresetCount() {
-		return channelPresetCount;
-	}
-	
-}

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

@@ -1,123 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.manipulator;
-
-import java.util.List;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * @author ebner
- *
- */
-public class Manipulator implements Runnable{
-	
-	/**
-	 * Outgoing data queue
-	 */
-	private final DataQueue outQueue;
-	
-	/**
-	 * Incomming data queue
-	 */
-	private final DataQueue queue;
-	
-	/**
-	 * List of manipulations
-	 */
-	private final List<Manipulation> manipulations;
-	
-	/**
-	 * Constructor
-	 * @param queue
-	 * @param manipulations
-	 */
-	// TODO need to support multiple (a list of) manipulation(s)
-	public Manipulator(DataQueue queue, List<Manipulation> manipulations){
-
-		this.manipulations = manipulations;
-		
-		// Create outgoing data metadata
-		DataMessageMetadata dmetadata = queue.getDataMessageMetadata().clone();
-		
-		// Initialize manipulations and create outgoing metadata
-		for(Manipulation manipulation: this.manipulations){
-			// Initialize manipulation
-//			manipulation.initialize(queue.getDataMessageMetadata());
-			manipulation.initialize(dmetadata);
-			
-			// Add manipulation id to metadata
-			dmetadata.getComponents().add(new ComponentMetadata(manipulation.getId(),0)); // Calculated component always belongs to lowes dimension
-		}
-		
-		this.queue = queue;
-		this.outQueue = new DataQueue(new LinkedBlockingQueue<Message>(1000) , dmetadata ); // Create bounded queue to prevent running out of memory ...
-	}
-
-	/**
-	 * @return the outQueue
-	 */
-	public DataQueue getOutQueue() {
-		return outQueue;
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-			
-			// Dispatch Messages
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				if(message instanceof DataMessage){
-					DataMessage dm = (DataMessage) message;
-					
-					for(Manipulation manipulation: manipulations){
-						dm.getData().add(manipulation.execute(dm));
-					}
-				}
-				
-				// Put message to outgoing queue ...
-				outQueue.getQueue().put(message);
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			// Write end of stream message
-			outQueue.getQueue().put(message);
-
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data manipulator was interrupted while writing data to file",e);
-		}
-	}
-	
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/messages/DataMessageMetadata.java

@@ -1,81 +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.messages;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Structure to hold the metadata of a component of a message.
- * @author ebner
- *
- */
-public class DataMessageMetadata {
-
-	/**
-	 * List of the metadata of the message components
-	 */
-	private List<ComponentMetadata> components;
-	
-	/**
-	 * Default constructor
-	 */
-	public DataMessageMetadata(){
-		components = new ArrayList<ComponentMetadata>();
-	}
-
-	/**
-	 * @return the list of component metadata of a message described by this object.
-	 */
-	public List<ComponentMetadata> getComponents() {
-		return components;
-	}
-	
-	/**
-	 * Get the index of the component with the specified Id
-	 * @param componentId	Id of the component to look for
-	 * @return Index of the component
-	 * @throws IllegalArgumentException	There is no component with the specified Id
-	 */
-	public int getIndex(String componentId) throws IllegalArgumentException {
-		for(int i=0;i<components.size();i++){
-			ComponentMetadata c =components.get(i);
-			if(c.getId().equals(componentId)){
-				return(i);
-			}
-		}
-		throw new IllegalArgumentException("There is no message component with Id "+ componentId);
-	}
-	
-	/**
-	 * Clone data structure
-	 * @return Cloned data structure
-	 */
-	public DataMessageMetadata clone(){
-		DataMessageMetadata metadata = new DataMessageMetadata();
-		
-		for(int i=0;i<components.size();i++){
-			ComponentMetadata c =components.get(i);
-			metadata.getComponents().add(new ComponentMetadata(c.getId(), c.getDimension()));
-		}
-		
-		return(metadata);
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/messages/DataQueue.java

@@ -1,66 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.messages;
-
-import java.util.concurrent.BlockingQueue;
-
-
-/**
- * Container holding for holding a queue and the metadata of the 
- * data messages of that queue.
- * @author ebner
- *
- */
-public class DataQueue {
-	
-	/**
-	 * Queue serving the messages
-	 */
-	private final BlockingQueue<Message> queue;
-	/**
-	 * Metadata of the data messages of the queue
-	 */
-	private final DataMessageMetadata dataMessageMetadata;
-	
-	/**
-	 * Constructor
-	 * @param queue		Data queue
-	 * @param dataMessageMetadata	Metadata of the data messages of the queue
-	 */
-	public DataQueue(BlockingQueue<Message> queue, DataMessageMetadata dataMessageMetadata){
-		this.queue = queue;
-		this.dataMessageMetadata = dataMessageMetadata;
-	}
-
-	/**
-	 * @return the queue
-	 */
-	public BlockingQueue<Message> getQueue() {
-		return queue;
-	}
-
-	/**
-	 * @return the metadata
-	 */
-	public DataMessageMetadata getDataMessageMetadata() {
-		return dataMessageMetadata;
-	}
-	
-}

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

@@ -1,75 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.scripting;
-
-import java.util.HashMap;
-
-/**
- * Singleton dictionary class
- * 
- * @author ebner
- *
- */
-public class JythonGlobalVariableDictionary {
-	
-	private static JythonGlobalVariableDictionary instance = new JythonGlobalVariableDictionary();
-	private HashMap<String, JythonGlobalVariable> dictionary = new HashMap<String, JythonGlobalVariable>();
-	
-	/**
-	 * Private constructor
-	 */
-	private JythonGlobalVariableDictionary(){
-	}
-	
-	/**
-	 * Get singleton instance of the dictionary
-	 * @return
-	 */
-	public static JythonGlobalVariableDictionary getInstance(){
-		return instance;
-	}
-
-	
-	/**
-	 * Get variable from dictionary. If the variable does not exist it will be created.
-	 * @param name
-	 * @return
-	 */
-	public JythonGlobalVariable getVariable(String name){
-		JythonGlobalVariable variable;
-		if(dictionary.containsKey(name)){
-			variable = dictionary.get(name);
-		}
-		else{
-			variable = new JythonGlobalVariable();
-			variable.setName(name);
-			dictionary.put(name, variable);
-		}
-		
-		return variable;
-	}
-	
-	/**
-	 * Clear variable dictionary
-	 */
-	public void clear(){
-		dictionary.clear();
-	}
-}

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

@@ -1,75 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.scripting;
-
-
-/**
- * Mapping of a script parameter to a channel bean.
- * @author ebner
- *
- */
-public class JythonParameterMappingChannel extends JythonParameterMapping {
-	
-	/**
-	 * Id of the component to map to this variable
-	 */
-	private String channel;
-	private Class<?> type;
-	
-	/**
-	 * Constructor accepting varible/id pair
-	 * @param variable
-	 * @param channel
-	 * @param type
-	 */
-	public JythonParameterMappingChannel(String variable, String channel, Class<?> type){
-		super(variable);
-		this.channel = channel;
-		this.type = type;
-	}
-	
-	/**
-	 * @return the channel
-	 */
-	public String getChannel() {
-		return channel;
-	}
-	/**
-	 * @param channel
-	 */
-	public void setChannel(String channel) {
-		this.channel = channel;
-	}
-
-	/**
-	 * @return the type
-	 */
-	public Class<?> getType() {
-		return type;
-	}
-
-	/**
-	 * @param type the type to set
-	 */
-	public void setType(Class<?> type) {
-		this.type = type;
-	}
-	
-}

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

@@ -1,144 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-import ch.psi.fda.core.EngineConfiguration;
-import ch.psi.fda.core.Sensor;
-import ch.psi.jcae.ChannelBeanFactory;
-import ch.psi.jcae.ChannelBean;
-
-/**
- * Scalar sensor that reads a double form a Channel Access channel
- * @author ebner
- *
- */
-public class ChannelAccessDoubleArraySensor implements Sensor {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessDoubleArraySensor.class.getName());
-	
-	/**
-	 * Channel Access channel of this sensor
-	 */
-	private final ChannelBean<double[]> channel;
-	
-	/**
-	 * Number of elements to read from the waveform
-	 */
-	private final int numberOfElements;
-	
-	/**
-	 * Global id of the sensor
-	 */
-	private final String id;
-	
-	/**
-	 * Constructor
-	 * @param id				Global id of the sensor
-	 * @param channelName		Name of the Channel Access channel of this sensor
-	 * @param numberOfElements	Number of elements to read out of the waveform
-	 */
-	public ChannelAccessDoubleArraySensor(String id, String channelName, int numberOfElements){
-		try {
-			this.channel = ChannelBeanFactory.getFactory().createChannelBean(double[].class, channelName, false);
-			this.numberOfElements = numberOfElements;
-			this.id = id;
-		} catch (CAException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize sensor channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize sensor channel [name:"+channelName+"]",e);
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#readout()
-	 */
-	@Override
-	public Object read() throws InterruptedException {
-		logger.finest("Read sensor "+channel.getName());
-		
-		double[] v;
-		try {
-			v = channel.getValue(numberOfElements);
-		} catch (IllegalStateException e) {
-			// Only fail during data acquisition if fail on error sensor flag is on true. Otherwise
-			// return NaN (Not a Number)
-			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-				throw e;
-			}
-			v = new double[numberOfElements];
-			for(int i =0;i<v.length;i++){
-				v[i] = Double.NaN;
-			}
-		} catch (CAException e) {
-			// Only fail during data acquisition if fail on error sensor flag is on true. Otherwise
-			// return NaN (Not a Number)
-			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-				// Convert Exception into unchecked RuntimeException
-				throw new RuntimeException("Unable to get value from channel [name:"+channel.getName()+"]",e);
-			}
-			
-			v = new double[numberOfElements];
-			for(int i =0;i<v.length;i++){
-				v[i] = Double.NaN;
-			}
-			
-//		} catch (InterruptedException e) {
-//			// Only fail during data acquisition if fail on error sensor flag is on true. Otherwise
-//			// return NaN (Not a Number)
-//			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-//				throw new RuntimeException("Unable to get value from channel [name:"+channel.getName()+"]",e);
-//			}
-//			
-//			v = new double[numberOfElements];
-//			for(int i =0;i<v.length;i++){
-//				v[i] = Double.NaN;
-//			}
-		}
-		return(v);
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#getId()
-	 */
-	@Override
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy sensor channel: "+channel.getName());
-			channel.destroy();
-		} catch (CAException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

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

@@ -1,132 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-import ch.psi.fda.core.EngineConfiguration;
-import ch.psi.fda.core.Sensor;
-import ch.psi.jcae.ChannelBeanFactory;
-import ch.psi.jcae.ChannelBean;
-
-/**
- * Scalar sensor that reads a double form a Channel Access channel
- * @author ebner
- *
- */
-public class ChannelAccessDoubleSensor implements Sensor {
-
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessDoubleSensor.class.getName());
-	
-	/**
-	 * Channel Access channel of this sensor
-	 */
-	private ChannelBean<Double> channel;
-	
-	/**
-	 * Global id of the sensor
-	 */
-	private final String id;
-	
-	/**
-	 * Constructor
-	 * @param id			Global id of the sensor
-	 * @param channelName	Name of the Channel Access channel of this sensor
-	 */
-	public ChannelAccessDoubleSensor(String id, String channelName){
-		try {
-			channel = ChannelBeanFactory.getFactory().createChannelBean(Double.class, channelName, false);
-			this.id = id;
-		} catch (CAException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize sensor channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize sensor channel [name:"+channelName+"]",e);
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#readout()
-	 */
-	@Override
-	public Object read() throws InterruptedException {
-		logger.finest("Read sensor "+channel.getName());
-		
-		Double v;
-		try {
-			v = channel.getValue();
-		} catch (IllegalStateException e) {
-			// Only fail during data acquisition if fail on error sensor flag is on true. Otherwise
-			// return NaN (Not a Number)
-			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-				throw e;
-			}
-			v = Double.NaN;
-		} catch (CAException e) {
-			// Only fail during data acquisition if fail on error sensor flag is on true. Otherwise
-			// return NaN (Not a Number)
-			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-				// Convert Exception into unchecked RuntimeException
-				throw new RuntimeException("Unable to get value from channel [name:"+channel.getName()+"]",e);
-			}
-			v = Double.NaN;
-//		} catch (InterruptedException e) {
-//			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-//				throw new RuntimeException("Unable to get value from channel [name:"+channel.getName()+"]",e);
-//			}
-//			v = Double.NaN;
-		}
-		return(v);
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#getId()
-	 */
-	@Override
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy sensor channel: "+channel.getName());
-			channel.destroy();
-		} catch (CAException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-	
-	/**
-	 * Get channel object of sensor
-	 * @return
-	 */
-	public ChannelBean<Double> getChannel(){
-		return channel;
-	}
-
-}

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

@@ -1,124 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-import ch.psi.fda.core.EngineConfiguration;
-import ch.psi.fda.core.Sensor;
-import ch.psi.jcae.ChannelBeanFactory;
-import ch.psi.jcae.ChannelBean;
-
-/**
- * Scalar sensor that reads a double form a Channel Access channel
- * @author ebner
- *
- */
-public class ChannelAccessStringSensor implements Sensor {
-
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessStringSensor.class.getName());
-	
-	/**
-	 * Channel Access channel of this sensor
-	 */
-	private ChannelBean<String> channel;
-	
-	/**
-	 * Global id of the sensor
-	 */
-	private final String id;
-	
-	/**
-	 * Constructor
-	 * @param id			Global id of the sensor
-	 * @param channelName	Name of the Channel Access channel of this sensor
-	 */
-	public ChannelAccessStringSensor(String id, String channelName){
-		try {
-			channel = ChannelBeanFactory.getFactory().createChannelBean(String.class, channelName, false);
-			this.id = id;
-		} catch (CAException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize sensor channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize sensor channel [name:"+channelName+"]",e);
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#readout()
-	 */
-	@Override
-	public Object read() throws InterruptedException {
-		logger.finest("Read sensor "+channel.getName());
-		
-		String v;
-		try {
-			v = channel.getValue();
-		} catch (IllegalStateException e) {
-			// Only fail during data acquisition if fail on error sensor flag is on true. Otherwise
-			// return NaN (Not a Number)
-			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-				throw e;
-			}
-			v = null;
-		} catch (CAException e) {
-			// Only fail during data acquisition if fail on error sensor flag is on true. Otherwise
-			// return NaN (Not a Number)
-			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-				// Convert Exception into unchecked RuntimeException
-				throw new RuntimeException("Unable to get value from channel [name:"+channel.getName()+"]",e);
-			}
-			v = null;
-//		} catch (InterruptedException e) {
-//			if(EngineConfiguration.getInstance().isFailOnSensorError()){
-//				throw new RuntimeException("Unable to get value from channel [name:"+channel.getName()+"]",e);
-//			}
-//			v = null;
-		}
-		return(v);
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#getId()
-	 */
-	@Override
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy sensor channel: "+channel.getName());
-			channel.destroy();
-		} catch (CAException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

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

@@ -1,136 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.Sensor;
-
-/**
- * Complex sensor that complements an other sensor with pre and post actions.
- * Before reading out the complemented sensor the pre actions are executed. After the
- * readout the post actions.
- * 
- * @author ebner
- *
- */
-public class ComplexSensor implements Sensor {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ComplexSensor.class.getName());
-	
-	/**
-	 * Id of the sensor
-	 */
-	private String id;
-	
-	/**
-	 * Sensor to complement
-	 */
-	private final Sensor sensor;
-	
-	/**
-	 * Actions that are executed directly before the first step of this actor
-	 */
-	private final List<Action> preActions;
-	
-	/**
-	 * Actions that are executed directly after the last step of this actor
-	 */
-	private final List<Action> postActions;
-
-	/**
-	 * Constructor
-	 */
-	public ComplexSensor(String id, Sensor sensor){
-		this.id = id;
-
-		this.sensor = sensor;
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#read()
-	 */
-	@Override
-	public Object read() throws InterruptedException {
-		// Execute pre actions
-		logger.finest("Execute pre actions");
-		for(Action action: preActions){
-			action.execute();
-		}
-		
-		// Readout sensor
-		Object value = sensor.read();
-		
-		// Execute post actions
-		logger.finest("Execute post actions");
-		for(Action action: postActions){
-			action.execute();
-		}
-		
-		return value;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#getId()
-	 */
-	@Override
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy preActions
-		for(Action a: preActions){
-			a.destroy();
-		}
-		
-		sensor.destroy();
-		
-		// Destroy postActions
-		for(Action a: postActions){
-			a.destroy();
-		}
-	}
-
-	/**
-	 * @return the preActions
-	 */
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/**
-	 * @return the postActions
-	 */
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-}

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

@@ -1,84 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import ch.psi.fda.core.Sensor;
-
-/**
- * Sensor to read 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;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#read()
-	 */
-	@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;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#getId()
-	 */
-	@Override
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-	}
-	
-}

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

@@ -1,70 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import ch.psi.fda.core.Sensor;
-
-/**
- * Sensor to read actuator readback. This sensor must only be used within the 
- * OTFLoop. If it is used in other loops, the read value will always be 0.
- * @author ebner
- *
- */
-public class OTFReadbackSensor implements Sensor {
-
-	/**
-	 * Global id of the sensor
-	 */
-	private final String id;
-	
-	/**
-	 * Constructor
-	 * @param id	Global id of the sensor
-	 */
-	public OTFReadbackSensor(String id){
-		this.id = id;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#read()
-	 */
-	@Override
-	public Object read() {
-		// Always return 0 if read() method is called.
-		return 0d;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#getId()
-	 */
-	@Override
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-	}
-
-}

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

@@ -1,84 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import ch.psi.fda.core.Sensor;
-
-/**
- * Sensor to read 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.
- * @author ebner
- *
- */
-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;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#read()
-	 */
-	@Override
-	public Object read() {
-		// Always return 0 if read() method is called.
-		return 0d;
-	}
-
-	/**
-	 * @return the index of the scaler channel
-	 */
-	public int getIndex() {
-		return index;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#getId()
-	 */
-	@Override
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-	}
-	
-}

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

@@ -1,205 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.model;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.IOException;
-import java.util.HashMap;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.UnmarshalException;
-import javax.xml.bind.Unmarshaller;
-import javax.xml.namespace.QName;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.Source;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.TransformerFactoryConfigurationError;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
-import javax.xml.validation.Schema;
-import javax.xml.validation.SchemaFactory;
-
-import org.xml.sax.SAXException;
-import org.xml.sax.SAXParseException;
-
-import ch.psi.fda.model.v1.Configuration;
-import ch.psi.fda.model.v1.Data;
-
-/**
- * Manage the serialization and deserialization of the model
- * @author ebner
- *
- */
-public class ModelManager {
-
-	/**
-	 * Deserialize an instance of a data model of the type Configuration
-	 * Before creating the object model variables will be replaced
-	 * 
-	 * @param file				Scan file
-	 * @param variables			Scan variables
-	 * @throws JAXBException	Something went wrong while unmarshalling
-	 * @throws SAXException		Cannot read model schema file
-	 * @throws ParserConfigurationException 
-	 * @throws IOException 
-	 * @throws TransformerFactoryConfigurationError 
-	 * @throws TransformerException 
-	 */
-	public static Configuration unmarshall(File file, HashMap<String, String> variables) throws JAXBException, SAXException, IOException,
-			ParserConfigurationException, TransformerFactoryConfigurationError, TransformerException {
-
-		// Load template file
-		Transformer xformer = TransformerFactory.newInstance().newTransformer(new StreamSource(file));
-		// Overwrite parameters
-		for(String key: variables.keySet()){
-			xformer.setParameter(key, variables.get(key));
-		}
-
-		
-		// Workaround for complex parameters (parameter including xml fragments)
-		// How the workaround works:
-		// Because we want to set complex parameters we first have to apply the xslt transformation to the input 
-		// stream and create an other output stream. In the template file the complex parameter must be referenced as follows
-		// <xsl:value-of select="$var.regions" disable-output-escaping="yes" />
-		// If it is not done this way the < and > of the tags will be replaced by &lt; and &gt;
-		// Also if we directly transform to a DOMResult the dom tree would not include the 
-		// nodes added by the parameter but just a text object. Therefor we do the workaround via the StreamResult ...
-		ByteArrayOutputStream bstream = new ByteArrayOutputStream();
-		StreamResult sresult = new StreamResult(bstream);
-		
-
-		// Perform transformation (using template file also as input source)
-		xformer.transform(new StreamSource(file), sresult );
-		
-		
-		// Workaround for complex parameters
-		ByteArrayInputStream bistream = new ByteArrayInputStream(bstream.toByteArray());
-		StreamSource bsource = new StreamSource(bistream);
-
-		
-		JAXBContext context = JAXBContext.newInstance(Configuration.class);
-		Unmarshaller u = context.createUnmarshaller();
-
-		// Validation
-		SchemaFactory sf = SchemaFactory.newInstance(javax.xml.XMLConstants.W3C_XML_SCHEMA_NS_URI);
-		Source s = new StreamSource(Configuration.class.getResourceAsStream("/model-v1.xsd"));
-		Schema schema = sf.newSchema(new Source[]{s}); // Use schema reference provided in XML
-		u.setSchema(schema);
-		
-		try{
-			Configuration model = (Configuration) u.unmarshal(bsource, Configuration.class).getValue();
-
-			// Ensure that the filename inside the xml file is always the file name
-			Data d = model.getData();
-			if(d==null){
-				d = new Data();
-				model.setData(d);
-			}
-			d.setFileName(file.getName().replaceAll("\\.xml$", ""));
-			
-			return (model);
-		}
-		catch(UnmarshalException e){
-			// Check 
-			if(e.getLinkedException() instanceof SAXParseException){
-				throw new RuntimeException("Configuration file does not comply to required model specification\nCause: "+e.getLinkedException().getMessage(), e);
-			}
-			throw e;
-		}
-	}
-	
-	
-	/**
-	 * Deserialize an instance of a data model of the type Configuration
-	 * @param file
-	 * @throws JAXBException	Something went wrong while unmarshalling
-	 * @throws SAXException		Cannot read model schema file
-	 */
-	public static Configuration unmarshall(File file) throws JAXBException, SAXException {
-
-		JAXBContext context = JAXBContext.newInstance(Configuration.class);
-		Unmarshaller u = context.createUnmarshaller();
-
-		// Validation
-		SchemaFactory sf = SchemaFactory.newInstance(javax.xml.XMLConstants.W3C_XML_SCHEMA_NS_URI);
-		Source s = new StreamSource(Configuration.class.getResourceAsStream("/model-v1.xsd"));
-		Schema schema = sf.newSchema(new Source[]{s}); // Use schema reference provided in XML
-		u.setSchema(schema);
-		
-		try{
-			Configuration model = (Configuration) u.unmarshal(new StreamSource(file), Configuration.class).getValue();
-			
-			// Ensure that the filename inside the xml file is always the file name
-			Data d = model.getData();
-			if(d==null){
-				d = new Data();
-				model.setData(d);
-			}
-			d.setFileName(file.getName().replaceAll("\\.xml$", ""));
-			
-			return (model);
-		}
-		catch(UnmarshalException e){
-			// Check 
-			if(e.getLinkedException() instanceof SAXParseException){
-				throw new RuntimeException("Configuration file does not comply to required model specification\nCause: "+e.getLinkedException().getMessage(), e);
-			}
-			throw e;
-		}
-	}
-	
-	/**
-	 * Serialize an instance of a data model of the type Configuration
-	 * @param model				Model datastructure
-	 * @param file				File to write the model data into
-	 * @throws JAXBException	Something went wrong while marshalling model
-	 * @throws SAXException		Cannot read model schema files
-	 */
-	public static void marshall(Configuration model, File file) throws JAXBException, SAXException{
-		QName qname = new QName("http://www.psi.ch/~ebner/models/scan/1.0", "configuration");
-		
-		JAXBContext context = JAXBContext.newInstance(Configuration.class);
-		Marshaller m = context.createMarshaller();
-		m.setProperty("jaxb.formatted.output", true);
-		
-		// Validation
-		SchemaFactory sf = SchemaFactory.newInstance(javax.xml.XMLConstants.W3C_XML_SCHEMA_NS_URI);
-		Source s = new StreamSource(Configuration.class.getResourceAsStream("/model-v1.xsd"));
-		Schema schema = sf.newSchema(new Source[]{s}); // Use schema reference provided in XML
-		m.setSchema(schema);
-		
-		// Set scan name equal to file name
-		Data d = model.getData();
-		if(d==null){
-			d = new Data();
-			model.setData(d);
-		}
-		d.setFileName(file.getName().replaceAll("\\.xml$", ""));
-		
-		m.marshal( new JAXBElement<Configuration>(qname, Configuration.class, model ), file);
-	}
-}

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

@@ -1,179 +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.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import com.jmatio.io.MatFileWriter;
-import com.jmatio.types.MLArray;
-import com.jmatio.types.MLDouble;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Serialize data received by a DataQueue into a Matlab file
- * @author ebner
- *
- */
-public class DataSerializerMAT implements DataSerializer{
-	
-	private DataQueue queue;
-	private File file;
-	
-	private boolean appendSuffix = false;
-	
-	/**
-	 * Construtor
-	 * @param queue	Data queue holding the data to serialize
-	 * @param file	Name of the Matlab file to serialize the data to
-	 */
-	public DataSerializerMAT(DataQueue queue, File file){
-		this.queue = queue;
-		this.file = file;
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-			
-			// WORKAROUND BEGIN
-			File outfile;
-			if(appendSuffix){
-				// Append a count suffix to the file. If there is already a file with 
-				// this suffix increase the counter for the suffix
-				int cnt = 0;
-				String fname = this.file.getAbsolutePath(); // Determine file name
-				String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
-				fname = fname.replaceAll("\\."+extension+"$", "");
-				
-				outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-				
-				while(outfile.exists()){
-					cnt++;
-					outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-				}
-			}
-			else{
-				outfile = this.file;
-			}
-			// WORKAROUND END
-
-			
-			// Transposed data list
-			List<List<Object>> dlist = new ArrayList<List<Object>>();
-			List<Class<?>> clist = new ArrayList<Class<?>>();
-			
-			boolean firstF = true;
-			
-			// Write data
-			// Read Message
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				if(message instanceof DataMessage){
-					DataMessage m = (DataMessage) message;
-					
-					// Initialize list
-					if(firstF){
-						for(Object o: m.getData()){
-							dlist.add(new ArrayList<Object>());
-							clist.add(o.getClass());
-						}
-						firstF=false;
-					}
-					
-					// Put data into data list
-					for(int i=0;i< m.getData().size();i++){
-						Object object = m.getData().get(i);
-						dlist.get(i).add(object);
-					}
-				}
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			// Create Matlab vectors
-			ArrayList<MLArray> matlablist = new ArrayList<MLArray>();
-			for(int t=0; t<dlist.size(); t++ ){
-				// Get component metadata
-				ComponentMetadata c = queue.getDataMessageMetadata().getComponents().get(t);
-				c.getId();
-				
-				List<Object> list = dlist.get(t);
-				
-				
-				
-				if(clist.get(t).isArray()){
-					// Array Handling
-				}
-				else if(clist.get(t).equals(Double.class)){
-					// Data is of type Double
-					MLDouble darray = new MLDouble(escapeString(c.getId()),(Double[])list.toArray(new Double[list.size()]),1);
-					matlablist.add(darray);
-				}
-				
-				
-			}
-			
-			// Write Matlab file
-			MatFileWriter writerr = new MatFileWriter();
-			writerr.write(outfile, matlablist);
-			
-			
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data serializer was interrupted while writing data to file",e);
-		} catch (IOException e) {
-			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
-		}
-		
-	}
-	
-	/**
-	 * Escape string to be Matlab key conform
-	 * @param value
-	 * @return	Escaped string value
-	 */
-	private String escapeString(String value){
-		
-		String evalue = value.replaceAll("-", "_");
-		evalue = evalue.replaceAll(":", "_");
-		evalue = evalue.replaceAll("\\.", "_");
-		evalue = evalue.replaceAll(" ", "_");
-		evalue = evalue.replaceAll("\\(", "_");
-		evalue = evalue.replaceAll("\\)", "_");
-		evalue = evalue.replaceAll("\\[", "_");
-		evalue = evalue.replaceAll("\\]", "_");
-		
-		return(evalue);
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/serializer/DataSerializerMAT2D.java

@@ -1,254 +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.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-
-import com.jmatio.io.MatFileWriter;
-import com.jmatio.types.MLArray;
-import com.jmatio.types.MLDouble;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Serialize data received by a DataQueue into a Matlab file
- * @author ebner
- *
- */
-public class DataSerializerMAT2D implements DataSerializer{
-
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(DataSerializerMAT2D.class.getName());
-	
-	private DataQueue queue;
-	private File file;
-	private boolean appendSuffix = false;
-	
-	/**
-	 * Construtor
-	 * @param queue	Data queue holding the data to serialize
-	 * @param file	Name of the Matlab file to serialize the data to
-	 */
-	public DataSerializerMAT2D(DataQueue queue, File file){
-		this.queue = queue;
-		this.file = file;
-		
-		// Check if input queue does only hold 2D data
-		int maxdim=0;
-		for(ComponentMetadata m: queue.getDataMessageMetadata().getComponents()){
-			if(m.getDimension()>maxdim){
-				maxdim=m.getDimension();
-			}
-			
-			if(m.getDimension()>1){
-				throw new RuntimeException("Serializer does only support 2D data (XD data found)");
-			}
-		}
-		
-		if(maxdim<1){
-			throw new RuntimeException("Serializer does only support 2D data ("+maxdim+"D data found)");
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-			
-			// WORKAROUND BEGIN
-			File outfile;
-			if(appendSuffix){
-				// Append a count suffix to the file. If there is already a file with 
-				// this suffix increase the counter for the suffix
-				int cnt = 0;
-				String fname = this.file.getAbsolutePath(); // Determine file name
-				String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
-				fname = fname.replaceAll("\\."+extension+"$", "");
-				
-				outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-				
-				while(outfile.exists()){
-					cnt++;
-					outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-				}
-			}
-			else{
-				outfile = this.file;
-			}
-			// WORKAROUND END
-
-			
-			// Transposed data list
-			List<List<List<Object>>> dlist = new ArrayList<List<List<Object>>>();
-			List<Class<?>> clist = new ArrayList<Class<?>>();
-			int dsize = 0; // Size of the dimension
-			int dcount = 0;
-			Integer mindsize = null;
-			
-			boolean firstF = true;
-			
-			// Write data
-			// Read Message
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				if(message instanceof DataMessage){
-					DataMessage m = (DataMessage) message;
-					
-					// Initialize list
-					if(firstF){
-						for(Object o: m.getData()){
-							// TODO Create list of lists (for each line one list - to
-							// be able to fill up empty data points if there are some)
-							List<List<Object>> l = new ArrayList<List<Object>>();
-							l.add(new ArrayList<Object>());
-							dlist.add(l);
-							
-							clist.add(o.getClass());
-						}
-						firstF=false;
-					}
-					
-					// Put data into data list
-					for(int i=0;i< m.getData().size();i++){
-						Object object = m.getData().get(i);
-						List<List<Object>> lo = dlist.get(i);
-						lo.get(lo.size()-1).add(object); // add data to latest list
-					}
-					
-					dcount++;
-				}
-				else if(message instanceof StreamDelimiterMessage){
-					StreamDelimiterMessage m = (StreamDelimiterMessage) message;
-					if(m.getNumber()==0){
-						// Determine minimum dimension size
-						if(dsize<dcount){
-							dsize=dcount;
-						}
-						
-						// Determine maximum dimension size
-						if(mindsize == null){
-							mindsize=dcount;
-						}
-						if(mindsize>dcount){
-							mindsize=dcount;
-						}
-						
-						// Add a new list for all component to the dlist
-						for(List<List<Object>> lo:dlist){
-							lo.add(new ArrayList<Object>());
-						}
-						
-						dcount=0;
-					}
-				}
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			logger.info("dsize: "+dsize + " mindsize:"+mindsize);
-			
-			// Create Matlab vectors
-			ArrayList<MLArray> matlablist = new ArrayList<MLArray>();
-			logger.info("dlist size: "+dlist.size());
-			for(int t=0; t<dlist.size(); t++ ){
-				
-				// Get component metadata
-				ComponentMetadata c = queue.getDataMessageMetadata().getComponents().get(t);
-				
-				// Combine all lists to one big list (pad if there are data points missing)
-				List<Object> list = new ArrayList<Object>();
-				List<List<Object>> ol = dlist.get(t);
-				
-				// Remove last array list as it is empty
-				ol.remove(ol.size()-1);
-				
-				for(List<Object> li: ol){
-					list.addAll(li);
-					// Pad list if there are missing data points for some lines
-					for(int i=li.size();i<dsize;i++){
-						logger.info("Pad data point: "+i);
-						list.add(Double.NaN);
-					}
-				}
-				
-				
-//				List<Object> list = dlist.get(t);
-				logger.info("List: "+list.size());
-				
-				
-				if(clist.get(t).isArray()){
-					// Array Handling
-				}
-				else if(clist.get(t).equals(Double.class)){
-					// Data is of type Double
-					MLDouble darray = new MLDouble(escapeString(c.getId()),(Double[])list.toArray(new Double[list.size()]), dsize);
-					matlablist.add(darray);
-				}
-				
-				
-			}
-			
-			// Write Matlab file
-			MatFileWriter writerr = new MatFileWriter();
-			writerr.write(outfile, matlablist);
-			
-			
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data serializer was interrupted while writing data to file",e);
-		} catch (IOException e) {
-			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
-		}
-		
-	}
-	
-	/**
-	 * Escape string to be Matlab key conform
-	 * @param value
-	 * @return	Escaped string value
-	 */
-	private String escapeString(String value){
-		
-		String evalue = value.replaceAll("-", "_");
-		evalue = evalue.replaceAll(":", "_");
-		evalue = evalue.replaceAll("\\.", "_");
-		evalue = evalue.replaceAll(" ", "_");
-		evalue = evalue.replaceAll("\\(", "_");
-		evalue = evalue.replaceAll("\\)", "_");
-		evalue = evalue.replaceAll("\\[", "_");
-		evalue = evalue.replaceAll("\\]", "_");
-		
-		return(evalue);
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/serializer/DataSerializerMAT2DZigZag.java

@@ -1,235 +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.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.logging.Logger;
-
-import com.jmatio.io.MatFileWriter;
-import com.jmatio.types.MLArray;
-import com.jmatio.types.MLDouble;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Serialize data received by a DataQueue into a Matlab file
- * @author ebner
- *
- */
-public class DataSerializerMAT2DZigZag implements DataSerializer{
-	
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(DataSerializerMAT2DZigZag.class.getName());
-	
-	private DataQueue queue;
-	private File file;
-	private boolean appendSuffix = false;
-	
-	/**
-	 * Construtor
-	 * @param queue	Data queue holding the data to serialize
-	 * @param file	Name of the Matlab file to serialize the data to
-	 */
-	public DataSerializerMAT2DZigZag(DataQueue queue, File file){
-		this.queue = queue;
-		this.file = file;
-		
-		// Check if input queue does only hold 2D data
-		int maxdim=0;
-		for(ComponentMetadata m: queue.getDataMessageMetadata().getComponents()){
-			if(m.getDimension()>maxdim){
-				maxdim=m.getDimension();
-			}
-			
-			if(m.getDimension()>1){
-				throw new RuntimeException("Serializer does only support 2D data (XD data found)");
-			}
-		}
-		
-		if(maxdim<1){
-			throw new RuntimeException("Serializer does only support 2D data ("+maxdim+"D data found)");
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-			
-			// WORKAROUND BEGIN
-			File outfile;
-			if(appendSuffix){
-				// Append a count suffix to the file. If there is already a file with 
-				// this suffix increase the counter for the suffix
-				int cnt = 0;
-				String fname = this.file.getAbsolutePath(); // Determine file name
-				String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
-				fname = fname.replaceAll("\\."+extension+"$", "");
-				
-				outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-				
-				while(outfile.exists()){
-					cnt++;
-					outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-				}
-			}
-			else{
-				outfile = this.file;
-			}
-			// WORKAROUND END
-
-			
-			// Transposed data list
-			List<List<Object>> dlist = new ArrayList<List<Object>>();
-			List<List<Object>> dlistTmp = new ArrayList<List<Object>>();
-			List<Class<?>> clist = new ArrayList<Class<?>>();
-			int dsize = 0; // Size of the dimension
-			int dcount = 0;
-			
-			int delimiterCount = 0;
-			
-			boolean firstF = true;
-			boolean firstC = true;
-			
-			// Write data
-			// Read Message
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				if(message instanceof DataMessage){
-					DataMessage m = (DataMessage) message;
-					
-					if(firstC){
-						for(Object o: m.getData()){
-							dlist.add(new ArrayList<Object>());
-							clist.add(o.getClass());
-							firstC=false;
-						}
-					}
-					
-					// Initialize list
-					if(firstF){
-						for(int i=0;i<m.getData().size();i++){
-							dlistTmp.add(new ArrayList<Object>());
-						}
-						firstF=false;
-					}
-					
-					// Put data into data list
-					for(int i=0;i< m.getData().size();i++){
-						Object object = m.getData().get(i);
-						dlistTmp.get(i).add(object);
-					}
-					
-					dcount++;
-				}
-				else if(message instanceof StreamDelimiterMessage){
-					StreamDelimiterMessage m = (StreamDelimiterMessage) message;
-					if(m.getNumber()==0){
-						if(dsize<dcount){
-							dsize=dcount;
-						}
-						dcount=0;
-						
-						// Add temporary list to final list
-						for(int i=0;i<dlist.size();i++){
-							if(delimiterCount%2==1){
-								Collections.reverse(dlistTmp.get(i));
-							}
-							dlist.get(i).addAll(dlistTmp.get(i));
-						}
-						
-						dlistTmp.clear();
-						
-						firstF=true;
-						delimiterCount++;
-					}
-				}
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			// Create Matlab vectors
-			ArrayList<MLArray> matlablist = new ArrayList<MLArray>();
-			logger.info("dlist size: "+dlist.size());
-			for(int t=0; t<dlist.size(); t++ ){
-				// Get component metadata
-				ComponentMetadata c = queue.getDataMessageMetadata().getComponents().get(t);
-				
-				List<Object> list = dlist.get(t);
-				
-				if(clist.get(t).isArray()){
-					// Array Handling
-				}
-				else if(clist.get(t).equals(Double.class)){
-					// Data is of type Double
-					MLDouble darray = new MLDouble(escapeString(c.getId()),(Double[])list.toArray(new Double[list.size()]), dsize);
-					matlablist.add(darray);
-				}
-				
-				
-			}
-			
-			// Write Matlab file
-			MatFileWriter writerr = new MatFileWriter();
-			writerr.write(outfile, matlablist);
-			
-			
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data serializer was interrupted while writing data to file",e);
-		} catch (IOException e) {
-			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
-		}
-		
-	}
-	
-	/**
-	 * Escape string to be Matlab key conform
-	 * @param value
-	 * @return	Escaped string value
-	 */
-	private String escapeString(String value){
-		
-		String evalue = value.replaceAll("-", "_");
-		evalue = evalue.replaceAll(":", "_");
-		evalue = evalue.replaceAll("\\.", "_");
-		evalue = evalue.replaceAll(" ", "_");
-		evalue = evalue.replaceAll("\\(", "_");
-		evalue = evalue.replaceAll("\\)", "_");
-		evalue = evalue.replaceAll("\\[", "_");
-		evalue = evalue.replaceAll("\\]", "_");
-		
-		return(evalue);
-	}
-	
-}

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

@@ -1,235 +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 ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-
-/**
- * Serialize data received by a DataQueue
- * @author ebner
- *
- */
-public class DataSerializerTXT implements DataSerializer{
-	
-	
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(DataSerializerTXT.class.getName());
-	
-	private DataQueue queue;
-	private File file;
-	
-	private boolean appendSuffix = true;
-
-	/**
-	 * 
-	 * @param queue
-	 * @param file
-	 * @param appendSuffix	Flag whether to append a _0000 suffix after the original file name
-	 */
-	public DataSerializerTXT(DataQueue queue, File file, boolean appendSuffix){
-		this.queue = queue;
-		this.file = file;
-		this.appendSuffix = appendSuffix;
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-			
-			// WORKAROUND BEGIN
-			File outfile;
-//			if(appendSuffix){
-//				// Append a count suffix to the file. If there is already a file with 
-//				// this suffix increase the counter for the suffix
-//				int cnt = 0;
-//				String fname = this.file.getAbsolutePath(); // Determine file name
-//				String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
-//				fname = fname.replaceAll("\\."+extension+"$", "");
-//				
-//				outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-//				
-//				while(outfile.exists()){
-//					cnt++;
-//					outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-//				}
-//			}
-//			else{
-//				outfile = this.file;
-//			}
-			// WORKAROUND END
-			
-			
-			
-			
-			
-			// Write header
-			StringBuffer b = new StringBuffer();
-			StringBuffer b1 = new StringBuffer();
-			b.append("#");
-			b1.append("#");
-			for(ComponentMetadata c: queue.getDataMessageMetadata().getComponents()){
-
-				b.append(c.getId());
-				b.append("\t");
-				
-				b1.append(c.getDimension());
-				b1.append("\t");
-			}
-			b.setCharAt(b.length()-1, '\n');
-			b1.setCharAt(b1.length()-1, '\n');
-			
-			
-			int icount = 0;
-			boolean newfile = true;
-			boolean dataInBetween = false;
-			BufferedWriter writer = null;
-			
-			// Get basename of the file
-			String basename = this.file.getAbsolutePath(); // Determine file name
-			String extension = basename.replaceAll("^.*\\.", ""); // Determine extension
-			basename = basename.replaceAll("\\."+extension+"$", "");
-			
-			// Write data
-			// Read Message
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				if(message instanceof DataMessage){
-					dataInBetween = true;
-					if(newfile){
-						// 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();
-					}
-				}
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			if(writer!=null){
-				// Close file
-				writer.close(); //If the stream was closed previously this has no effect
-			}
-			// Writer can be null if a scan is defined without a dimension
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data serializer was interrupted while writing data to file",e);
-		} catch (IOException e) {
-			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
-		}
-		
-	}
-	
-	
-//	/**
-//	 * Enable/disable the generation of the _0000 suffix in front of the extension of the out file
-//	 * @param appendSuffix the appendSuffix to set
-//	 */
-//	public void setAppendSuffix(boolean appendSuffix) {
-//		this.appendSuffix = appendSuffix;
-//	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/serializer/DataSerializerTXT2D.java

@@ -1,205 +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.ArrayList;
-import java.util.List;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Serialize data received by a DataQueue into a Matlab file
- * @author ebner
- *
- */
-public class DataSerializerTXT2D implements DataSerializer{
-	
-	private DataQueue queue;
-	private File file;
-	private boolean appendSuffix = false;
-	
-	/**
-	 * Construtor
-	 * @param queue	Data queue holding the data to serialize
-	 * @param file	Name of the Matlab file to serialize the data to
-	 */
-	public DataSerializerTXT2D(DataQueue queue, File file){
-		this.queue = queue;
-		this.file = file;
-		
-		// Check if input queue does only hold 2D data
-		int maxdim=0;
-		for(ComponentMetadata m: queue.getDataMessageMetadata().getComponents()){
-			if(m.getDimension()>maxdim){
-				maxdim=m.getDimension();
-			}
-			
-			if(m.getDimension()>1){
-				throw new RuntimeException("Serializer does only support 2D data (XD data found)");
-			}
-		}
-		
-		if(maxdim<1){
-			throw new RuntimeException("Serializer does only support 2D data ("+maxdim+"D data found)");
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-			
-			// WORKAROUND BEGIN
-			File outfile;
-			if(appendSuffix){
-				// Append a count suffix to the file. If there is already a file with 
-				// this suffix increase the counter for the suffix
-				int cnt = 0;
-				String fname = this.file.getAbsolutePath(); // Determine file name
-				String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
-	//			fname = fname.replaceAll("(_[0-9]+)?\\."+extension+"$", "");
-				fname = fname.replaceAll("\\."+extension+"$", "");
-				
-				outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-				
-				while(outfile.exists()){
-					cnt++;
-					outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-				}
-			}
-			else{
-				outfile = this.file;
-			}
-			// WORKAROUND END
-
-			
-			// Transposed data list
-			List<List<Object>> dlist = new ArrayList<List<Object>>();
-			List<Class<?>> clist = new ArrayList<Class<?>>();
-			int dsize = 0; // Size of the dimension
-			int dcount = 0;
-			
-			boolean firstF = true;
-			
-			// Write data
-			// Read Message
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				if(message instanceof DataMessage){
-					DataMessage m = (DataMessage) message;
-					
-					// Initialize list
-					if(firstF){
-						for(Object o: m.getData()){
-							dlist.add(new ArrayList<Object>());
-							clist.add(o.getClass());
-						}
-						firstF=false;
-					}
-					
-					// Put data into data list
-					for(int i=0;i< m.getData().size();i++){
-						Object object = m.getData().get(i);
-						dlist.get(i).add(object);
-					}
-					
-					dcount++;
-				}
-				else if(message instanceof StreamDelimiterMessage){
-					StreamDelimiterMessage m = (StreamDelimiterMessage) message;
-					if(m.getNumber()==0){
-						if(dsize<dcount){
-							dsize=dcount;
-						}
-						dcount=0;
-					}
-				}
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			// Open file
-			BufferedWriter writer = new BufferedWriter(new FileWriter(outfile));
-			
-			// Create text images
-			for(int t=0; t<dlist.size(); t++ ){
-				// Get component metadata
-				ComponentMetadata c = queue.getDataMessageMetadata().getComponents().get(t);
-				
-				writer.write(c.getId()+"\n");
-				
-				List<Object> list = dlist.get(t);
-				
-				
-				
-				if(clist.get(t).isArray()){
-					// Array Handling
-				}
-				else if(clist.get(t).equals(Double.class)){
-					// Data is of type Double
-					
-					StringBuffer b = new StringBuffer();
-					int counter = 0;
-					for(Object o: list){
-						b.append(o);
-						counter++;
-						if(counter==dsize){
-							b.append("\n");
-							counter=0;
-						}
-						else{
-							b.append(" ");
-						}
-					}
-					
-					writer.write(b.toString());
-				}
-				
-				writer.write("\n");
-				
-			}
-			
-			// Close file
-			writer.close();
-			
-			
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data serializer was interrupted while writing data to file",e);
-		} 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/serializer/DataSerializerTXTSplit.java

@@ -1,240 +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.ArrayList;
-import java.util.List;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Serialize data received by a DataQueue
- * @author ebner
- *
- */
-public class DataSerializerTXTSplit implements DataSerializer{
-	
-	private DataQueue queue;
-	private File file;
-	
-	private int maxdim = 0;
-	
-//	private boolean appendSuffix = false;
-
-	public DataSerializerTXTSplit(DataQueue queue, File file){
-		this.queue = queue;
-		this.file = file;
-		
-		
-		// Determine maximum dimension
-		for(ComponentMetadata m: queue.getDataMessageMetadata().getComponents()){
-			if(m.getDimension()>maxdim){
-				maxdim=m.getDimension();
-			}
-		}
-		
-		if(maxdim<1){
-			throw new RuntimeException("Split serializer only supports data > 1 dimension");
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-			
-			// WORKAROUND BEGIN
-//			File outfile;
-//			if(appendSuffix){
-//				// Append a count suffix to the file. If there is already a file with 
-//				// this suffix increase the counter for the suffix
-//				int cnt = 0;
-//				String fname = this.file.getAbsolutePath(); // Determine file name
-//				String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
-//				fname = fname.replaceAll("\\."+extension+"$", "");
-//				
-//				outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-//				
-//				while(outfile.exists()){
-//					cnt++;
-//					outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-//				}
-//			}
-//			else{
-//				outfile = this.file;
-//			}
-			// WORKAROUND END
-			
-			
-			
-			List<String> header = new ArrayList<String>();
-			
-			// Write header
-			StringBuffer b = new StringBuffer();
-			StringBuffer b1 = new StringBuffer();
-			b.append("#");
-			b1.append("#");
-			for(ComponentMetadata c: queue.getDataMessageMetadata().getComponents()){
-
-				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');
-			header.add(b.toString());
-			header.add(b1.toString());
-			
-			List<String> data = new ArrayList<String>();
-			// Write data
-			// Read Message
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				if(message instanceof DataMessage){
-					
-					// Write message to file - each message will result in one line
-					DataMessage m = (DataMessage) message;
-					StringBuffer buffer = new StringBuffer();
-					for(Object o: m.getData()){
-						if(o.getClass().isArray()){
-							// If the array object is of type double[] display its content
-							if(o instanceof double[]){
-								double[] oa = (double[]) o;
-								for(double o1 : oa){
-									buffer.append(o1);
-									buffer.append(" "); // Use space instead of tab
-								}
-								buffer.replace(buffer.length()-1,buffer.length()-1 , "\t"); // Replace last space with tab
-							}
-							else if(o instanceof Object[]){
-								// TODO need to be recursive ...
-								Object[] oa = (Object[])o;
-								for(Object o1 : oa){
-									buffer.append(o1);
-									buffer.append(" "); // Use space instead of tab
-								}
-								buffer.replace(buffer.length()-1,buffer.length()-1 , "\t"); // Replace last space with tab
-							}
-							else{
-								buffer.append("-"); // Not supported
-							}
-						}
-						else{
-							buffer.append(o);
-							buffer.append("\t");
-						}
-					}
-					
-					buffer.deleteCharAt(buffer.length()-1); // Remove last character (i.e. \t)
-					buffer.append("\n"); // Append newline
-					data.add(buffer.toString());
-				}
-				else if(message instanceof StreamDelimiterMessage){
-					StreamDelimiterMessage m = (StreamDelimiterMessage) message;
-					if(m.getNumber()==maxdim-1){
-						writeData(header, data);
-						// Clear data
-						data.clear();
-					}
-				}
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-//			// Open file
-//			BufferedWriter writer = new BufferedWriter(new FileWriter(outfile));
-//			
-//			// Close file
-//			writer.close();
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data serializer was interrupted while writing data to file",e);
-		} catch (IOException e) {
-			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
-		}
-		
-	}
-	
-	private void writeData(List<String> header, List<String> data) throws IOException{
-		
-		// WORKAROUND BEGIN
-		File outfile;
-//		if(appendSuffix){
-			// Append a count suffix to the file. If there is already a file with 
-			// this suffix increase the counter for the suffix
-			int cnt = 0;
-			String fname = this.file.getAbsolutePath(); // Determine file name
-			String extension = fname.replaceAll("^.*\\.", ""); // Determine extension
-			fname = fname.replaceAll("\\."+extension+"$", "");
-			
-			outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-			
-			while(outfile.exists()){
-				cnt++;
-				outfile = new File(String.format("%s_%04d.%s", fname, cnt, extension));
-			}
-//		}
-//		else{
-//			outfile = this.file;
-//		}
-		// WORKAROUND END
-		
-		// Open file
-		BufferedWriter writer = new BufferedWriter(new FileWriter(outfile));
-		
-		// Write header
-		for(String s: header){
-			writer.write(s);
-		}
-		
-		// Write data
-		for(String s: data){
-			writer.write(s);
-		}
-		
-		
-		// Close file
-		writer.close();
-	}
-	
-	
-	/**
-	 * Enable/disable the generation of the _0000 suffix in front of the extension of the out file
-	 * @param appendSuffix the appendSuffix to set
-	 */
-	public void setAppendSuffix(boolean appendSuffix) {
-//		this.appendSuffix = appendSuffix;
-	}
-}

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

@@ -1,74 +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 ch.psi.fda.core.messages.DataQueue;
-
-/**
- * @author ebner
- *
- */
-public class FilterSet {
-
-	private  DataQueue queue;
-	private List<SeriesDataFilter> filters = new ArrayList<SeriesDataFilter>();
-	private String name;
-	
-	public FilterSet(DataQueue queue){
-		this("", queue);
-	}
-	
-	public FilterSet(String name, DataQueue queue){
-		this.queue = queue;
-	}
-
-	/**
-	 * @return the queue
-	 */
-	public DataQueue getQueue() {
-		return queue;
-	}
-
-	/**
-	 * @return the filters
-	 */
-	public List<SeriesDataFilter> getFilters() {
-		return filters;
-	}
-
-	/**
-	 * @return the name
-	 */
-	public String getName() {
-		return name;
-	}
-
-	/**
-	 * @param name the name to set
-	 */
-	public void setName(String name) {
-		this.name = name;
-	}
-	
-	
-}

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

@@ -1,676 +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 org.jfree.data.xy.XYSeries;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataQueue;
-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.model.v1.ArrayDetector;
-import ch.psi.fda.model.v1.ContinuousPositioner;
-import ch.psi.fda.model.v1.Detector;
-import ch.psi.fda.model.v1.LinearPositioner;
-import ch.psi.fda.model.v1.Positioner;
-import ch.psi.fda.model.v1.PseudoPositioner;
-import ch.psi.fda.model.v1.Visualization;
-import ch.psi.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.JFreeMatrixPlot;
-//import ch.psi.plot.xyz.JFreeMatrixPlotData;
-//import ch.psi.plot.xyz.JFreeMatrixPlotMetadata;
-import ch.psi.plot.xyz.MatrixPlot;
-import ch.psi.plot.xyz.MatrixPlotData;
-
-/**
- * Serialize data received by a DataQueue
- * @author ebner
- *
- */
-public class Visualizer {
-	
-	// Logger
-	private static Logger logger = Logger.getLogger(Visualizer.class.getName());
-	
-	private FilterSet filterSet = null;
-	private List<Plot> plots = new ArrayList<Plot>();
-	
-	private Thread visualizationThread = null;
-	
-	/**
-	 * Terminate at end of stream
-	 */
-	private boolean terminateAtEOS = false;
-	private volatile boolean terminate = false;
-	
-	
-	private boolean updateAtStreamElement = true;
-	private boolean updateAtStreamDelimiter = true;
-	private boolean updateAtEndOfStream = false;
-	
-	public Visualizer(DataQueue queue, List<Visualization> vl){
-		addFilterSet(queue, vl);
-	}
-	
-	private void addFilterSet(DataQueue queue, List<Visualization> vl){
-		filterSet = mapVisualizations(queue, vl);
-	}
-
-
-	/**
-	 * Visualize data
-	 * Method blocks until visualization is done
-	 */
-	public void visualize() {
-		if(filterSet != null ){
-			DataQueue queue = filterSet.getQueue();
-			List<SeriesDataFilter> filters = filterSet.getFilters();
-			
-			int ecount = 0;
-			boolean clearPlot = false;
-			terminate = false;
-	
-			// Read Messages
-			Message message = null;
-			try {
-				message = queue.getQueue().take();
-			} catch (InterruptedException e) {
-				terminate = true;
-				// Reset interrupted status
-				Thread.currentThread().interrupt();
-				
-			}
-	
-			while ( (!Thread.currentThread().isInterrupted()) && (!terminate) ) {
-	
-				if (message instanceof DataMessage) {
-					final DataMessage m = (DataMessage) message;
-					
-					// 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 (Plot plot: plots) {
-							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 = ((LinePlot) xyfilter.getPlot()).getData().getSeries(xyfilter.getCount()); // TODO Does not work with multiple series filter per plot !!!!
-							XYSeriesP series = xyfilter.getActualSeries(); // TODO Does not work with multiple series filter per plot !!!!
-	//						series.add((Double) m.getData().get(xyfilter.getIndexX()), (Double) m.getData().get(xyfilter.getIndexY()));
-							
-							
-							// There might be other values than double in the data, therefore we have to check for it
-							Object dX = m.getData().get(xyfilter.getIndexX());
-							Object dY = m.getData().get(xyfilter.getIndexY());
-							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 = (double[]) m.getData().get(xyfilter.getIndexY());
-									// 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) m.getData().get(xyzfilter.getIndexX()),(Double) m.getData().get(xyzfilter.getIndexY()), (Double) m.getData().get(xyzfilter.getIndexZ()));
-							}
-							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[]) m.getData().get(xyzfilter.getIndexZ());
-								double y = (Double) m.getData().get(xyzfilter.getIndexY());
-								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);
-							}
-						}
-					}
-					
-				} else if (message instanceof StreamDelimiterMessage) {
-					StreamDelimiterMessage ddm = (StreamDelimiterMessage) message;
-	
-					for(SeriesDataFilter filter: filters){
-						if(filter instanceof XYSeriesDataFilter){
-							// Create new series
-							XYSeriesDataFilter xyfilter = (XYSeriesDataFilter) filter;
-							if (ddm.getNumber() == xyfilter.getDimensionX()) {
-								// Indicate to create new series at the next message
-								xyfilter.setCount(xyfilter.getCount()+1); // Increment count of the filter
-								xyfilter.setNewseries(true);
-							}
-						}
-					}
-	
-					// Update matrix plot at the end of each line
-					if(updateAtStreamDelimiter){
-						for (Plot plot: 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 (ddm.isIflag()) {
-						clearPlot = true;
-					}
-				} else if (message instanceof EndOfStreamMessage) {
-					ecount++;
-					if(terminateAtEOS){
-						terminate = true;
-					}
-					
-					
-					// Update plots if updateAtEndOfStream flag is set
-					if(updateAtEndOfStream){
-						// Update matrix plots
-						for (Plot plot: plots) {
-							if(plot instanceof MatrixPlot){
-								((MatrixPlot)plot).update();
-								((MatrixPlot)plot).adaptColorMapScale(); // Update color scale at the end
-							}
-							else if(plot instanceof LinePlot){
-								((LinePlot) plot).update();
-							}
-						}
-					}
-				}
-	
-				// End loop if terminate flag is true
-				if(terminate){
-					break;
-				}
-				
-				// Read next message
-				try {
-					message = queue.getQueue().take();
-				} catch (InterruptedException e) {
-					terminate = true;
-					// Reset interrupted status
-					Thread.currentThread().interrupt();
-				}
-			}
-		}
-		logger.info("End visualization");
-	}
-	
-	/**
-	 * Starts a visualization thread for this visualizer
-	 */
-	public void startVisualization(){
-		// Throw an exception if visualization is already running
-		if(visualizationThread!=null){
-			throw new IllegalStateException("Visualization already running");
-		}
-		
-		visualizationThread = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				visualize();
-			}
-		});
-		// Start thread
-		visualizationThread.start();
-	}
-	
-	/**
-	 * Stop visualization thread of this visualizer
-	 * Waits until the visualiztion thread is stopped
-	 * @throws InterruptedException 
-	 */
-	public void stopVisualization() throws InterruptedException{
-		// Wait until visualiztion thread is stopped
-		visualizationThread.interrupt();
-		visualizationThread.join(10000); // Wait 10 seconds to have the visualization Thread to come to an end
-		
-		visualizationThread = null;
-	}
-	
-	
-	/**
-	 * Retrieve id string of the passed object
-	 * @param object
-	 * @return	Id string of object
-	 */
-	private 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;
-	}
-	
-	/**
-	 * Get configured visualizations
-	 * Note: This method is public because it is also used by the VisualizationEngine
-	 * @param vl	List of configured visualizations
-	 * @return	List of visualization configuration
-	 */
-	private FilterSet mapVisualizations(DataQueue queue, List<Visualization> vl){
-		FilterSet fset = new FilterSet(queue);
-		List<SeriesDataFilter> filters = fset.getFilters();
-		
-		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());
-				plots.add(plot);
-				
-				// Create data filter for visualization
-				String idX = getId(lp.getX());
-				int indexX = queue.getDataMessageMetadata().getIndex(idX);
-				int dimX = queue.getDataMessageMetadata().getComponents().get(indexX).getDimension();
-				
-				List<Object> l = lp.getY();
-				for(Object o: l){
-					String idY = getId(o);
-					int indexY = queue.getDataMessageMetadata().getIndex(idY);
-					int dimY = queue.getDataMessageMetadata().getComponents().get(indexY).getDimension();
-					
-					XYSeriesDataFilter filter = new XYSeriesDataFilter(idX, idY, indexX, indexY, plot);
-					filter.setDimensionX(dimX);
-					filter.setDimensionY(dimY);
-					filter.setSeriesName(idY);
-					filters.add(filter);
-				}
-			}
-			else if(v instanceof ch.psi.fda.model.v1.LinePlotArray){
-				// Array visualization
-				ch.psi.fda.model.v1.LinePlotArray lp = (ch.psi.fda.model.v1.LinePlotArray) v;
-				
-				// Create plot for visualization
-				ch.psi.plot.xy.LinePlot plot = new ch.psi.plot.xy.LinePlot(lp.getTitle());
-				plots.add(plot);
-				
-				// Create data filter for visualization
-				List<Object> l = lp.getY();
-				for(Object o: l){
-					String idY = getId(o);
-					int indexY = queue.getDataMessageMetadata().getIndex(idY);
-					int dimY = queue.getDataMessageMetadata().getComponents().get(indexY).getDimension();
-					
-					XYSeriesArrayDataFilter filter = new XYSeriesArrayDataFilter(idY, indexY, plot);
-					filter.setDimensionY(dimY);
-					filter.setMaxSeries(lp.getMaxSeries()*lp.getY().size()); // Workaround - keep for each array max series
-					filter.setOffset(lp.getOffset());
-					filter.setSize(lp.getSize());
-					filter.setSeriesName(idY);
-					filters.add(filter);
-				}
-			}
-			else if(v instanceof ch.psi.fda.model.v1.MatrixPlot){
-				
-				// MatrixPlot does currently not support RegionPositioners because of the
-				// plotting problems this would cause. If regions of the positioner have different
-				// step sizes it is not easily possible (without (specialized) rasterization) to plot the data.
-				
-				ch.psi.fda.model.v1.MatrixPlot mp = (ch.psi.fda.model.v1.MatrixPlot) v;
-				
-
-				double minX, maxX;
-				int nX;
-				double minY, maxY;
-				int nY;
-				
-				String idX, idY, idZ;
-				
-				// X Axis
-				if(mp.getX() instanceof LinearPositioner){
-					LinearPositioner linp = ((LinearPositioner)mp.getX());
-					idX = linp.getId();
-					
-					minX = (Math.min(linp.getStart(), linp.getEnd()));
-					maxX = (Math.max(linp.getStart(), linp.getEnd()));
-					nX = ((int) Math.floor((Math.abs(maxX-minX))/linp.getStepSize()) + 1);
-				}
-				else if(mp.getX() instanceof PseudoPositioner){
-					PseudoPositioner pp = ((PseudoPositioner)mp.getX());
-					idX = pp.getId();
-					minX = (1); // Count starts at 1
-					maxX = (pp.getCounts());
-					nX = (pp.getCounts());
-				}
-				else if(mp.getX() instanceof ContinuousPositioner){
-					ContinuousPositioner conp = ((ContinuousPositioner)mp.getX());
-					idX = conp.getId();
-					
-					minX = (Math.min(conp.getStart(), conp.getEnd()));
-					maxX = (Math.max(conp.getStart(), conp.getEnd()));
-					nX = ((int) Math.floor((Math.abs(maxX-minX))/conp.getStepSize()) + 1);
-				}
-				else{
-					// Fail as we cannot determine the min, max and number of steps
-					throw new RuntimeException(mp.getX().getClass().getName()+" is not supported as x-axis of a MatrixPlot");
-				}
-				
-				// Y Axis
-				if(mp.getY() instanceof LinearPositioner){
-					LinearPositioner linp = ((LinearPositioner)mp.getY());
-					idY = linp.getId();
-					minY = (Math.min(linp.getStart(), linp.getEnd()));
-					maxY = (Math.max(linp.getStart(), linp.getEnd()));
-					nY = ((int) Math.floor((Math.abs(maxY-minY))/linp.getStepSize()) + 1);
-				}
-				else if(mp.getY() instanceof PseudoPositioner){
-					PseudoPositioner pp = ((PseudoPositioner)mp.getY());
-					idY = pp.getId();
-					minY = (1); // Count starts at 1
-					maxY = (pp.getCounts());
-					nY = (pp.getCounts());
-				}
-				else{
-					// Fail as we cannot determine the min, max and number of steps
-					throw new RuntimeException(mp.getY().getClass().getName()+" is not supported as y-axis of a MatrixPlot");
-				}
-				
-				// Z Dimension
-				idZ = getId(mp.getZ());
-
-				// Create plot for visualization
-				MatrixPlotData data = new MatrixPlotData(minX, maxX, nX, minY, maxY, nY);
-				MatrixPlot plot = new MatrixPlot(mp.getTitle(), data);
-				plots.add(plot);
-				
-				// Create data filter for visualization
-				int indexX = queue.getDataMessageMetadata().getIndex(idX);
-				int indexY = queue.getDataMessageMetadata().getIndex(idY);
-				int indexZ = queue.getDataMessageMetadata().getIndex(idZ);
-
-				int dimX = queue.getDataMessageMetadata().getComponents().get(indexX).getDimension();
-				int dimY = queue.getDataMessageMetadata().getComponents().get(indexY).getDimension();
-				int dimZ = queue.getDataMessageMetadata().getComponents().get(indexZ).getDimension();
-				
-				XYZSeriesDataFilter filter = new XYZSeriesDataFilter(idX, idY, idZ, indexX, indexY, indexZ, plot);
-				filter.setDimensionX(dimX);
-				filter.setDimensionY(dimY);
-				filter.setDimensionZ(dimZ);
-				filters.add(filter);
-			}
-			else if(v instanceof ch.psi.fda.model.v1.MatrixPlotArray){
-				// Support for 2D waveform plots
-				ch.psi.fda.model.v1.MatrixPlotArray mp = (ch.psi.fda.model.v1.MatrixPlotArray) v;
-				
-				// Get size of the array detector
-				int arraySize = 0;
-				Object o = mp.getZ();
-				if(o instanceof ArrayDetector){
-					ArrayDetector ad = (ArrayDetector) o;
-					arraySize = ad.getArraySize();
-				}
-				else{
-					// Workaround
-					arraySize = mp.getSize(); // of array is from a manipulation the size is not known. Then the size will indicate the size of the array to display
-				}
-				
-				int offset = mp.getOffset();
-				// Determine size for array
-				int size = mp.getSize();
-				if(size>0 && offset+size<arraySize){
-					size = mp.getSize();
-				}
-				else{
-					size=arraySize-offset;
-				}
-				
-				
-				double minY, maxY;
-				int nY;
-				
-				double minX = offset;
-				double maxX = offset+size-1;
-				int nX = size;
-				
-				String idY, idZ;
-				
-				// Y Axis
-				if(mp.getY() instanceof LinearPositioner){
-					LinearPositioner linp = ((LinearPositioner)mp.getY());
-					idY = linp.getId();
-					
-					minY = (Math.min(linp.getStart(), linp.getEnd()));
-					maxY = (Math.max(linp.getStart(), linp.getEnd()));
-					nY = ((int) Math.floor((Math.abs(maxY-minY))/linp.getStepSize()) + 1);
-				}
-				else if(mp.getY() instanceof PseudoPositioner){
-					PseudoPositioner pp = ((PseudoPositioner)mp.getY());
-					idY = pp.getId();
-					minY = (1); // Count starts at 1
-					maxY = (pp.getCounts());
-					nY = (pp.getCounts());
-				}
-				else if(mp.getY() instanceof ContinuousPositioner){
-					ContinuousPositioner conp = ((ContinuousPositioner)mp.getY());
-					idY = conp.getId();
-					
-					minY = (Math.min(conp.getStart(), conp.getEnd()));
-					maxY = (Math.max(conp.getStart(), conp.getEnd()));
-					nY = ((int) Math.floor((Math.abs(maxY-minY))/conp.getStepSize()) + 1);
-				}
-				else{
-					// Fail as we cannot determine the min, max and number of steps
-					throw new RuntimeException(mp.getY().getClass().getName()+" is not supported as x-axis of a MatrixPlot");
-				}
-				
-				
-				// Z Dimension
-				idZ = getId(mp.getZ());
-
-				// Create plot for visualization
-				MatrixPlotData data = new MatrixPlotData(minX, maxX, nX, minY, maxY, nY);
-				MatrixPlot plot = new MatrixPlot(mp.getTitle(), data);
-				plots.add(plot);
-				
-				// Create data filter for visualization
-				int indexY = queue.getDataMessageMetadata().getIndex(idY);
-				int indexZ = queue.getDataMessageMetadata().getIndex(idZ);
-
-				int dimY = queue.getDataMessageMetadata().getComponents().get(indexY).getDimension();
-				int dimZ = queue.getDataMessageMetadata().getComponents().get(indexZ).getDimension();
-				
-				XYZSeriesArrayDataFilter filter = new XYZSeriesArrayDataFilter(idY, idZ, indexY, indexZ, offset, size, plot);
-				filter.setDimensionY(dimY);
-				filter.setDimensionZ(dimZ);
-				filters.add(filter);
-			}
-			else{
-				// Visualization type (currently) not supported
-				throw new RuntimeException(v.getClass().getName()+" is not supported as visualization type");
-			}
-		}
-		return fset;
-	}
-	
-	/**
-	 * Get the plot panels for the visualizations
-	 * @return	List of configured JPanels
-	 */
-	public List<JPanel> getPlotPanels(){
-		List<JPanel> panels = new ArrayList<JPanel>();
-		for(Plot plot: plots){
-			panels.add(plot.getChartPanel());
-		}
-		
-		return panels;
-	}
-
-	/**
-	 * @param terminateAtEOS the terminateAtEOS to set
-	 */
-	public void setTerminateAtEOS(boolean terminateAtEOS) {
-		this.terminateAtEOS = terminateAtEOS;
-	}
-
-	/**
-	 * @return the terminateAtEOS
-	 */
-	public boolean isTerminateAtEOS() {
-		return terminateAtEOS;
-	}
-
-	/**
-	 * @return the updateAtStreamElement
-	 */
-	public boolean isUpdateAtStreamElement() {
-		return updateAtStreamElement;
-	}
-
-	/**
-	 * @param updateAtStreamElement the updateAtStreamElement to set
-	 */
-	public void setUpdateAtStreamElement(boolean updateAtStreamElement) {
-		this.updateAtStreamElement = updateAtStreamElement;
-	}
-
-	/**
-	 * @return the updateAtStreamDelimiter
-	 */
-	public boolean isUpdateAtStreamDelimiter() {
-		return updateAtStreamDelimiter;
-	}
-
-	/**
-	 * @param updateAtStreamDelimiter the updateAtStreamDelimiter to set
-	 */
-	public void setUpdateAtStreamDelimiter(boolean updateAtStreamDelimiter) {
-		this.updateAtStreamDelimiter = updateAtStreamDelimiter;
-	}
-
-	/**
-	 * @return the updateAtEndOfStream
-	 */
-	public boolean isUpdateAtEndOfStream() {
-		return updateAtEndOfStream;
-	}
-
-	/**
-	 * @param updateAtEndOfStream the updateAtEndOfStream to set
-	 */
-	public void setUpdateAtEndOfStream(boolean updateAtEndOfStream) {
-		this.updateAtEndOfStream = updateAtEndOfStream;
-	}
-	
-}

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

@@ -1,187 +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 ch.psi.plot.Plot;
-import ch.psi.plot.xy.XYSeriesP;
-
-/**
- * Metadata of a group of XYSeries.
- * This metadata holds the information needed by the DataVisualizer
- * to plot series.
- * 
- * @author ebner
- *
- */
-public class XYSeriesDataFilter implements SeriesDataFilter{
-	
-	private final String idX;
-	private final String idY;
-	
-	// Name of the series generated by this filter
-	private String seriesName = "";
-	
-	// Index of stream message components used for x and y
-	private final int indexX;
-	private final int indexY;
-	
-	// Dimension of the x,y value - used to determine whether a new series should be created for this filter
-	private int dimensionX;
-	private int dimensionY;
-	
-	// Number of series generated for this filter 
-	private int count = 0;
-	
-	// Plot the data of this filter goes to
-	private final Plot plot;
-	
-	// TODO WORKAROUND - XYZ filter must not have this property !!!!
-	private XYSeriesP actualSeries = null;
-	private boolean newseries = false;
-	
-	
-	public XYSeriesDataFilter(String idX, String idY, int indexX, int indexY, Plot plot){
-		this.idX = idX;
-		this.idY = idY;
-		this.indexX = indexX;
-		this.indexY = indexY;
-		this.plot = plot;
-	}
-	
-	/**
-	 * @return the xId
-	 */
-	public String getIdX() {
-		return idX;
-	}
-	
-	/**
-	 * @return the yId
-	 */
-	public String getIdY() {
-		return idY;
-	}
-
-	/**
-	 * @return the seriesName
-	 */
-	public String getSeriesName() {
-		return seriesName;
-	}
-
-	/**
-	 * @param seriesName the seriesName to set
-	 */
-	public void setSeriesName(String seriesName) {
-		this.seriesName = seriesName;
-	}
-
-	/**
-	 * @return the indexX
-	 */
-	public int getIndexX() {
-		return indexX;
-	}
-
-	/**
-	 * @return the indexY
-	 */
-	public int getIndexY() {
-		return indexY;
-	}
-
-	/**
-	 * @return the dimensionX
-	 */
-	public int getDimensionX() {
-		return dimensionX;
-	}
-
-	/**
-	 * @return the dimensionY
-	 */
-	public int getDimensionY() {
-		return dimensionY;
-	}
-
-	/**
-	 * @param dimensionY the dimensionY to set
-	 */
-	public void setDimensionY(int dimensionY) {
-		this.dimensionY = dimensionY;
-	}
-
-	/**
-	 * @param dimensionX the dimensionX to set
-	 */
-	public void setDimensionX(int dimensionX) {
-		this.dimensionX = dimensionX;
-	}
-
-	/**
-	 * @return the count
-	 */
-	public int getCount() {
-		return count;
-	}
-
-	/**
-	 * @param count the count to set
-	 */
-	public void setCount(int count) {
-		this.count = count;
-	}
-
-	/**
-	 * @return the plot
-	 */
-	public Plot getPlot() {
-		return plot;
-	}
-
-	/**
-	 * @return the actualSeries
-	 */
-	public XYSeriesP getActualSeries() {
-		return actualSeries;
-	}
-
-	/**
-	 * @param actualSeries the actualSeries to set
-	 */
-	public void setActualSeries(XYSeriesP actualSeries) {
-		this.actualSeries = actualSeries;
-	}
-
-	/**
-	 * @return the newseries
-	 */
-	public boolean isNewseries() {
-		return newseries;
-	}
-
-	/**
-	 * @param newseries the newseries to set
-	 */
-	public void setNewseries(boolean newseries) {
-		this.newseries = newseries;
-	}
-	
-}

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/actions/JythonActionTest.java

@@ -1,103 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.actions;
-
-import gov.aps.jca.CAException;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.TestChannels;
-import ch.psi.fda.core.actions.JythonAction;
-import ch.psi.fda.core.scripting.JythonParameterMappingChannel;
-
-/**
- * @author ebner
- *
- */
-public class JythonActionTest {
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.actions.JythonAction#execute()}.
-	 * @throws CAException 
-	 */
-	@Test
-	public void testExecute() throws CAException {
-		String script = "import math\ndef process(o):\n    print o.getValue()\n    o.setValue(-1.0)\n    print o.getValue()\n    val=math.cos(10.0) + math.sin(o.getValue())\n    print val\n    o.setValue(val)";
-		List<JythonParameterMappingChannel> mapping = new ArrayList<JythonParameterMappingChannel>();
-		mapping.add(new JythonParameterMappingChannel("o", TestChannels.ANALOG_OUT, Double.class));
-		JythonAction action = new JythonAction(script, mapping);
-		
-		// Execute action
-		action.execute();
-	}
-	
-	/**
-	 * Check whether too much mappings are detected
-	 * Test method for {@link ch.psi.fda.core.actions.JythonAction#execute()}.
-	 * @throws CAException 
-	 */
-	@Test(expected=IllegalArgumentException.class)
-	public void testWrongMapping1() throws CAException {
-		String script = "import math\ndef process(o):\n    print o.getValue()\n    o.setValue(-1.0)\n    print o.getValue()\n    val=math.cos(10.0) + math.sin(o.getValue())\n    print val\n    o.setValue(val)";
-		List<JythonParameterMappingChannel> mapping = new ArrayList<JythonParameterMappingChannel>();
-		mapping.add(new JythonParameterMappingChannel("o", TestChannels.ANALOG_OUT, Double.class));
-		mapping.add(new JythonParameterMappingChannel("b", TestChannels.ANALOG_OUT, Double.class));
-		JythonAction action = new JythonAction(script, mapping);
-		
-		// Execute action
-		action.execute();
-	}
-	
-	/**
-	 * Check whether a mapping to a wrong variable is detected
-	 * Test method for {@link ch.psi.fda.core.actions.JythonAction#execute()}.
-	 * @throws CAException 
-	 */
-	@Test(expected=IllegalArgumentException.class)
-	public void testWrongMapping2() throws CAException {
-		String script = "import math\ndef process(o):\n    print o.getValue()\n    o.setValue(-1.0)\n    print o.getValue()\n    val=math.cos(10.0) + math.sin(o.getValue())\n    print val\n    o.setValue(val)";
-		List<JythonParameterMappingChannel> mapping = new ArrayList<JythonParameterMappingChannel>();
-		mapping.add(new JythonParameterMappingChannel("ooo", TestChannels.ANALOG_OUT, Double.class));
-		JythonAction action = new JythonAction(script, mapping);
-		
-		// Execute action
-		action.execute();
-	}
-
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/collector/CollectorTest.java

@@ -1,236 +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.collector;
-
-import static org.junit.Assert.*;
-
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.core.collector.Collector;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.ControlMessage;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * @author ebner
- *
- */
-public class CollectorTest {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(CollectorTest.class.getName());
-	
-	class TestCollector implements Runnable{
-
-		private final DataQueue queue;
-		public TestCollector(DataQueue queue){
-			this.queue = queue;
-		}
-		/* (non-Javadoc)
-		 * @see java.lang.Runnable#run()
-		 */
-		@Override
-		public void run() {
-			try {
-				while(true){
-					Message m = queue.getQueue().take();
-					if(m instanceof DataMessage){
-						DataMessage x = (DataMessage) m;
-						logger.fine( x.toString() );
-					}
-					else if(m instanceof ControlMessage){
-						logger.fine("---- "+m.toString()+" ----");
-					}
-				}
-			} catch (InterruptedException e) {
-				logger.log(Level.SEVERE, "An Exception occured while reading data from the data queue", e);
-			}
-		}
-		
-	}
-	
-	private BlockingQueue<Message> q1;
-	private BlockingQueue<Message> q2;
-	private BlockingQueue<Message> q3;
-	
-	private DataMessageMetadata m1;
-	private DataMessageMetadata m2;
-	private DataMessageMetadata m3;
-	
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-		// Create blocking queues
-		q1 = new LinkedBlockingQueue<Message>();
-		q2 = new LinkedBlockingQueue<Message>();
-		q3 = new LinkedBlockingQueue<Message>();
-		
-		m1 = new DataMessageMetadata();
-		m1.getComponents().add(new ComponentMetadata("id2-0"));
-		m2 = new DataMessageMetadata();
-		m2.getComponents().add(new ComponentMetadata("id1-0"));
-		m3 = new DataMessageMetadata();
-		m3.getComponents().add(new ComponentMetadata("id0-0"));
-		
-		// Dimension y 1,2,3
-		DataMessage m = new DataMessage();
-		m.getData().add(1d);
-		q1.put(m);
-		m = new DataMessage();
-		m.getData().add(2d);
-		q1.put(m);
-		m = new DataMessage();
-		m.getData().add(3d);
-		q1.put(m);
-		q1.put(new EndOfStreamMessage());
-		
-		// Dimension x 0.1,0.2
-		m = new DataMessage();
-		m.getData().add(0.1);
-		q2.put(m);
-		m = new DataMessage();
-		m.getData().add(0.2);
-		q2.put(m);
-		q2.put(new EndOfStreamMessage());
-		
-		m = new DataMessage();
-		m.getData().add(0.1);
-		q2.put(m);
-		m = new DataMessage();
-		m.getData().add(0.2);
-		q2.put(m);
-		q2.put(new EndOfStreamMessage());
-		
-		m = new DataMessage();
-		m.getData().add(0.1);
-		q2.put(m);
-		m = new DataMessage();
-		m.getData().add(0.2);
-		q2.put(m);
-		q2.put(new EndOfStreamMessage());
-		
-		// Dimension
-		m = new DataMessage();
-		m.getData().add(0.01);
-		q3.put(m);
-		m = new DataMessage();
-		m.getData().add(0.02);
-		q3.put(m);
-		q3.put(new EndOfStreamMessage());
-		
-		m = new DataMessage();
-		m.getData().add(0.01);
-		q3.put(m);
-		m = new DataMessage();
-		m.getData().add(0.02);
-		q3.put(m);
-		q3.put(new EndOfStreamMessage());
-		
-		m = new DataMessage();
-		m.getData().add(0.01);
-		q3.put(m);
-		m = new DataMessage();
-		m.getData().add(0.02);
-		q3.put(m);
-		q3.put(new EndOfStreamMessage());
-		
-		m = new DataMessage();
-		m.getData().add(0.01);
-		q3.put(m);
-		m = new DataMessage();
-		m.getData().add(0.02);
-		q3.put(m);
-		q3.put(new EndOfStreamMessage());
-		
-		m = new DataMessage();
-		m.getData().add(0.01);
-		q3.put(m);
-		m = new DataMessage();
-		m.getData().add(0.02);
-		q3.put(m);
-		q3.put(new EndOfStreamMessage());
-		
-		m = new DataMessage();
-		m.getData().add(0.01);
-		q3.put(m);
-		m = new DataMessage();
-		m.getData().add(0.02);
-		q3.put(m);
-		q3.put(new EndOfStreamMessage());
-		
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.collector.Collector#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRun() throws InterruptedException {
-		Collector collector = new Collector();
-		collector.getQueues().add(new DataQueue(q1, m1));
-		collector.getQueues().add(new DataQueue(q2, m2));
-		collector.getQueues().add(new DataQueue(q3, m3));
-		
-		Thread t = new Thread(new TestCollector(collector.getOutQueue()));
-		t.start();
-		
-		// Check component metadata of output queue
-		int c=2;
-		for(ComponentMetadata cm: collector.getOutQueue().getDataMessageMetadata().getComponents()){
-			logger.info(cm.toString());
-			if(cm.getDimension() != c){
-				fail("Dimension number does not match required dimension number");
-			}
-			if(! cm.getId().equals("id"+c+"-0")){
-				fail("Id does not match required id");
-			}
-			c--;
-		}
-		
-		collector.run();
-		
-		// Wait some time to ensure that collector was able to finish processing
-		Thread.sleep(2000);
-		// Execute collector via the ExecutorService framework
-//		ExecutorService executor = Executors.newCachedThreadPool();
-//		executor.execute(collector);
-	}
-
-}

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

@@ -1,145 +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;
-
-/**
- * @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.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.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.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.DistributedFile#listFiles()}.
-	 */
-	@Test
-	public void testListFiles() {
-//		fail("Not yet implemented");
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.DistributedFile#getName()}.
-	 */
-	@Test
-	public void testGetName() {
-		logger.info(file.getName());
-		logger.info(smbfile.getName());
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.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.DistributedFile#delete()}.
-	 */
-	@Test
-	public void testDelete() {
-//		fail("Not yet implemented");
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.DistributedFile#getInputStream()}.
-	 */
-	@Test
-	public void testGetInputStream() {
-//		fail("Not yet implemented");
-	}
-
-}

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

@@ -1,242 +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 gov.aps.jca.CAException;
-
-import java.util.concurrent.BlockingQueue;
-import java.util.logging.Level;
-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.actors.OTFActuator;
-import ch.psi.fda.core.loops.OTFLoop;
-import ch.psi.fda.core.messages.ControlMessage;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.MillisecondTimestampSensor;
-import ch.psi.fda.core.sensors.OTFNamedChannelSensor;
-import ch.psi.fda.core.sensors.OTFReadbackSensor;
-import ch.psi.fda.core.sensors.OTFScalerChannelSensor;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * @author ebner
- *
- */
-public class OTFLoopTest {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(OTFLoopTest.class.getName());
-	
-	class TestCollector implements Runnable{
-
-		private final BlockingQueue<Message> queue;
-		public TestCollector(BlockingQueue<Message> queue){
-			this.queue = queue;
-		}
-		/* (non-Javadoc)
-		 * @see java.lang.Runnable#run()
-		 */
-		@Override
-		public void run() {
-			try {
-				while(true){
-					Message m = queue.take();
-					if(m instanceof DataMessage){
-						DataMessage x = (DataMessage) m;
-						logger.fine( x.toString() );
-					}
-					else if(m instanceof ControlMessage){
-						logger.fine("---- "+m.toString()+" ----");
-					}
-				}
-			} catch (InterruptedException e) {
-				logger.log(Level.SEVERE, "An Exception occured while reading data from the data queue", e);
-			}
-		}
-		
-	}
-	
-	private static final TestConfiguration configuration = TestConfiguration.getInstance();
-	
-	
-	private OTFLoop loopZigZag;
-	private OTFLoop loop;
-	private ChannelBean<Integer> statusChannel;
-	
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-		
-		statusChannel = ChannelBeanFactory.getFactory().createChannelBean(Integer.class, configuration.getOtfPrefix()+":USTAT", false);
-		
-		OTFActuator actor = new OTFActuator("id", configuration.getMotor1(), null, 0, 8, 0.5, 0.5, 0);
-		OTFReadbackSensor s1 = new OTFReadbackSensor("id0");
-		OTFScalerChannelSensor s2 = new OTFScalerChannelSensor("id1", 0);
-		OTFScalerChannelSensor s3 = new OTFScalerChannelSensor("id2", 1);
-		MillisecondTimestampSensor s4 = new MillisecondTimestampSensor("id3");
-		OTFNamedChannelSensor s5 = new OTFNamedChannelSensor("id4", configuration.getAnalogIn1());
-		
-		
-		// ZigZag loop
-		loopZigZag = new OTFLoop(configuration.getOtfPrefix(), configuration.getServer(), configuration.getShare(), configuration.getSmbShare(), true);
-		loopZigZag.setActor(actor);
-		loopZigZag.getSensors().add(s1);
-		loopZigZag.getSensors().add(s2);
-		loopZigZag.getSensors().add(s3);
-		loopZigZag.getSensors().add(s4);
-		loopZigZag.getSensors().add(s5);
-		
-		
-		// Normal loop
-		loop = new OTFLoop(configuration.getOtfPrefix(), configuration.getServer(), configuration.getShare(), configuration.getSmbShare(), false);
-		loop.setActor(actor);		
-		loop.getSensors().add(s1);
-		loop.getSensors().add(s2);
-		loop.getSensors().add(s3);
-		loop.getSensors().add(s4);
-		loop.getSensors().add(s5);
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.OTFLoop#execute()}.
-	 * Test ordinary 1D OTF scan
-	 * @throws CAException 
-	 */
-	@Test
-	public void testExecute() throws CAException, InterruptedException {
-		
-		Thread t = new Thread(new TestCollector(loop.getDataQueue().getQueue()));
-		t.start();
-		
-		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.OTFLoop#execute()}.
-	 * Test OTF ZigZag mode
-	 * @throws CAException 
-	 */
-	@Test
-	public void testExecuteZigZag() throws CAException, InterruptedException {
-		
-		Thread t = new Thread(new TestCollector(loopZigZag.getDataQueue().getQueue()));
-		t.start();
-		
-		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.OTFLoop#execute()}.
-	 * Test abort functionality while executing an OTF scan
-	 * @throws CAException 
-	 */
-	@Test
-	public void testExecuteAbort() throws CAException, InterruptedException {
-		
-		// Data collector thread
-		Thread t = new Thread(new TestCollector(loop.getDataQueue().getQueue()));
-		t.start();
-		
-		// 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");
-		}
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.ActorSensorLoop#getDataMessageMetadata()}.
-	 */
-	@Test
-	public void testGetDataMessageMetadata(){
-		DataMessageMetadata m = loop.getDataQueue().getDataMessageMetadata();
-		
-		int numberOfSensors = 5;
-		if(m.getComponents().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.getComponents().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");
-		}
-	}
-	
-}

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

@@ -1,66 +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 java.util.logging.Logger;
-
-import jcifs.smb.SmbFile;
-
-import org.junit.Ignore;
-import org.junit.Test;
-
-/**
- * @author ebner
- *
- */
-public class SambaTest {
-	
-	private static final Logger logger = Logger.getLogger(SambaTest.class.getName());
-
-	@Test
-	public void testSamba() throws Exception{
-//		 System.setProperty("jcifs.smb.client.dfs.disabled", "true");
-//		System.setProperty("jcifs.smb.client.ssnLimit", "1");
-		
-//		System.setProperty("jcifs.smb.client.domain", "x05la.psi.ch");
-//		System.setProperty("jcifs.smb.client.username", "x05laop");
-//		System.setProperty("jcifs.smb.client.password", "mXAS");
-//		
-//		System.setProperty("jcifs.util.loglevel", "6");
-		
-//		System.setProperty("jcifs.smb.lmCompatibility", "0");
-		
-//		jcifs.smb.client.{domain,username,password
-		
-		String smbShare = "";
-//		smbShare = "smb://x05laop:mXAS@x05la/x05laop/Data1/otfTmp/";
-//		smbShare = "smb://x05la.psi.ch/x05laop/Data1/otfTmp/";
-//		smbShare = "smb://x05laop:mXAS@x05la/x05laop/Data1/otfTmp/000000.txt.lock";
-		smbShare = "smb://:@yoke.psi.ch/nfs/";
-//		NtlmPasswordAuthentication auth = new NtlmPasswordAuthentication("x05laop:mXAS");
-//		SmbFile tmpDir = new SmbFile(smbShare,auth);
-//		SmbFile tmpDir = new SmbFile(smbShare);
-		
-//		tmpDir.createNewFile();
-//		logger.info(""+tmpDir.exists());
-//		logger.info(""+tmpDir.isDirectory());
-//		SmbFile tmpFile = new SmbFile(tmpDir, "000000.txt.lock");
-//		tmpFile.exists();
-	}
-}

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

@@ -1,136 +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.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * @author ebner
- *
- */
-public class ParallelCrlogicStreamMergeTest {
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.loops.cr.ParallelCrlogicStreamMerge#merge()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testMerge() throws InterruptedException {
-	
-		BlockingQueue<Message> dataQueue = new LinkedBlockingQueue<Message>();
-		DataMessage dm = new DataMessage();
-		dm.getData().add(0.0035d);
-		dm.getData().add(10.000000123);
-		dataQueue.add(dm);
-		
-		dm = new DataMessage();
-		dm.getData().add(0.015);
-		dm.getData().add(10.000000143);
-		dataQueue.add(dm);
-		
-		dm = new DataMessage();
-		dm.getData().add(0.026);
-		dm.getData().add(10.000000163);
-		dataQueue.add(dm);
-		
-		dataQueue.add(new EndOfStreamMessage());
-
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		dmm.getComponents().add(new ComponentMetadata("cractuator"));
-		dmm.getComponents().add(new ComponentMetadata("tstamp"));
-		DataQueue dqueue = new DataQueue(dataQueue, dmm);
-		
-		
-		BlockingQueue<Message> dataQueue2 = new LinkedBlockingQueue<Message>();
-		DataMessage dm2 = new DataMessage();
-		dm2.getData().add(9000d);
-		dm2.getData().add(122d);
-		dm2.getData().add(0.1d);
-		dataQueue2.add(dm2);
-		
-		dm2 = new DataMessage();
-		dm2.getData().add(10000d);
-		dm2.getData().add(122d);
-		dm2.getData().add(1d);
-		dataQueue2.add(dm2);
-		
-		dm2 = new DataMessage();
-		dm2.getData().add(10000d);
-		dm2.getData().add(153d);
-		dm2.getData().add(2d);
-		dataQueue2.add(dm2);
-		
-		dm2 = new DataMessage();
-		dm2.getData().add(10000d);
-		dm2.getData().add(162d);
-		dm2.getData().add(3d);
-		dataQueue2.add(dm2);
-		
-		dataQueue2.add(new EndOfStreamMessage());
-
-		DataMessageMetadata dmm2 = new DataMessageMetadata();
-		dmm2.getComponents().add(new ComponentMetadata("milli"));
-		dmm2.getComponents().add(new ComponentMetadata("nano"));
-		dmm2.getComponents().add(new ComponentMetadata("sensor1"));
-		
-		DataQueue dqueue2 = new DataQueue(dataQueue2, dmm2);
-		
-		
-		
-		ParallelCrlogicStreamMerge streamMerge = new ParallelCrlogicStreamMerge(dqueue, dqueue2);
-		streamMerge.merge();
-		
-		// Print merged queue
-		BlockingQueue<Message> queue = streamMerge.getDataQueue().getQueue();
-		Message m = queue.take();
-		while(! (m instanceof EndOfStreamMessage)){
-			System.out.println(m.toString());
-			m = queue.take();
-		}
-		
-	}
-
-}

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

@@ -1,153 +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 gov.aps.jca.CAException;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.logging.Logger;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import ch.psi.fda.TestConfiguration;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.actors.OTFActuator;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.ChannelAccessDoubleSensor;
-import ch.psi.fda.core.sensors.MillisecondTimestampSensor;
-import ch.psi.fda.core.sensors.OTFNamedChannelSensor;
-import ch.psi.fda.core.sensors.OTFScalerChannelSensor;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * @author ebner
- *
- */
-public class ParallelCrlogicTest {
-	
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(ParallelCrlogicTest.class.getName());
-	
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-	
-//	@Ignore
-	@Test(timeout=60000)
-	public void testExecute() throws InterruptedException, CAException{
-		
-		TestConfiguration c = TestConfiguration.getInstance();
-		
-		boolean zigZag = false;
-		
-		String readback = null;
-		double start = 0;
-		double end = 2;
-		double stepSize = 0.01;
-		double integrationTime = 0.01;
-		double additionalBacklash = 0;
-		
-		List<Sensor> sensors = new ArrayList<Sensor>();
-		ChannelAccessDoubleSensor s2 = new ChannelAccessDoubleSensor("mot1", c.getMotor1()+".RVAL");
-		ChannelAccessDoubleSensor s1 = new ChannelAccessDoubleSensor("mot2", c.getMotor1()+".RBV");
-		ChannelAccessDoubleSensor s3 = new ChannelAccessDoubleSensor("mot2", "ARIDI-PCT:CURRENT");
-		
-		sensors.add(s1);
-		sensors.add(s2);
-		sensors.add(s3);
-		
-		ScrlogicLoop scrlogic = new ScrlogicLoop(sensors);
-		
-		
-		CrlogicLoop crlogic = new CrlogicLoop(c.getCrlogicPrefix(), c.getServer(), c.getShare(), c.getSmbShare(), zigZag);
-		crlogic.setActor(new OTFActuator("cmot", c.getMotor1(), readback, start, end, stepSize, integrationTime, additionalBacklash));
-		crlogic.getSensors().add(new OTFNamedChannelSensor("trigger", "TRIGGER0"));
-		crlogic.getSensors().add(new OTFScalerChannelSensor("scaler0", 0));
-		crlogic.getSensors().add(new OTFScalerChannelSensor("scaler1", 1));
-		crlogic.getSensors().add(new MillisecondTimestampSensor("timestamp"));
-		
-		
-		// Initialize scaler template
-		VSC16ScalerChannelsTemplate scalertemplate = new VSC16ScalerChannelsTemplate();
-		ChannelBeanFactory.getFactory().createChannelBeans(scalertemplate, c.getPrefixScaler());
-		
-		
-		ParallelCrlogic pcrlogic = new ParallelCrlogic(crlogic, scrlogic);
-		
-		logger.info("Start scaler");
-		scalertemplate.getCommand().setValueNoWait(VSC16ScalerChannelsTemplate.Command.Count.ordinal());
-		
-		pcrlogic.prepare();
-		pcrlogic.execute();
-		pcrlogic.cleanup();
-		
-		logger.info("Stop scaler");
-		scalertemplate.getCommand().setValue(VSC16ScalerChannelsTemplate.Command.Done.ordinal());
-		
-		System.out.println("PARALLEL CRLOGIC data:");
-		BlockingQueue<Message> queue = pcrlogic.getDataQueue().getQueue();
-		Message m = queue.take();
-		while(! (m instanceof EndOfStreamMessage)){
-			System.out.println(m.toString());
-			m = queue.take();
-		}
-		
-		// Destroy scaler template
-		ChannelBeanFactory.getFactory().destroyChannelBeans(scalertemplate);
-		
-		pcrlogic.destroy();
-		
-		
-//		System.out.println("CRLOGIC data:");
-//		BlockingQueue<Message> queue = crlogic.getDataQueue().getQueue();
-//		Message m = queue.take();
-//		while(! (m instanceof EndOfStreamMessage)){
-//			System.out.println(m.toString());
-//			m = queue.take();
-//		}
-//		
-//		
-//		System.out.println("SCRLOGIC data:");
-//		queue = scrlogic.getDataQueue().getQueue();
-//		m = queue.take();
-//		while(! (m instanceof EndOfStreamMessage)){
-//			System.out.println(m.toString());
-//			m = queue.take();
-//		}
-	}
-
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/manipulator/ManipulatorTest.java

@@ -1,547 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.manipulator;
-
-import static org.junit.Assert.*;
-
-import gov.aps.jca.CAException;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Logger;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import ch.psi.fda.TestChannels;
-import ch.psi.fda.core.manipulator.JythonManipulation;
-import ch.psi.fda.core.manipulator.Manipulation;
-import ch.psi.fda.core.manipulator.Manipulator;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.scripting.JythonParameterMapping;
-import ch.psi.fda.core.scripting.JythonParameterMappingChannel;
-import ch.psi.fda.core.scripting.JythonParameterMappingID;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * @author ebner
- *
- */
-public class ManipulatorTest {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ManipulatorTest.class.getName());
-	
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-		
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.manipulator.Manipulator#Manipulator()}.
-	 */
-	@Test(expected=IllegalArgumentException.class)
-	public void testConstructor() {
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(), dmm);
-		
-		String id="computedId";
-		String script = "import math\ndef process(o):\n    return math.cos(10.0) + math.sin(o)";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-		
-		// This constructor need to throw an IllegalArgumentException as there is no component
-		// id "myid" which is expected in the mapping
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		new Manipulator(inQueue, manipulations);
-		
-	}
-	
-	@Test
-	public void testConstructorNoMappingNoParam() {
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(), dmm);
-
-		DataMessage m = new DataMessage();
-		m.getData().add(10d);
-		m.getData().add(0.2d);
-		inQueue.getQueue().add(m);
-		inQueue.getQueue().add(new EndOfStreamMessage());
-		
-		String id="cid";
-		String script = "import math\ndef process():\n    return 0.0";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-		
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		new Manipulator(inQueue, manipulations);
-		// Expect IllegalArgument Exception as there is no mapping for the parameter c
-	}
-	
-	@Test
-	public void testConstructorMappingNoParam() {
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		dmm.getComponents().add(new ComponentMetadata("myid"));
-		dmm.getComponents().add(new ComponentMetadata("myid2"));
-		DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(), dmm);
-
-		DataMessage m = new DataMessage();
-		m.getData().add(10d);
-		m.getData().add(0.2d);
-		inQueue.getQueue().add(m);
-		inQueue.getQueue().add(new EndOfStreamMessage());
-		
-		String id="cid";
-		String script = "import math\ndef process():\n    return 0.0";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-		
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		new Manipulator(inQueue, manipulations);
-		// Expect IllegalArgument Exception as there is no mapping for the parameter c
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.core.manipulator.Manipulator#Manipulator()}.
-	 */
-	@Test(expected=IllegalArgumentException.class)
-	public void testConstructorNoMapping() {
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		dmm.getComponents().add(new ComponentMetadata("myid"));
-		dmm.getComponents().add(new ComponentMetadata("myid2"));
-		DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(), dmm);
-
-		DataMessage m = new DataMessage();
-		m.getData().add(10d);
-		m.getData().add(0.2d);
-		inQueue.getQueue().add(m);
-		inQueue.getQueue().add(new EndOfStreamMessage());
-		
-		String id="cid";
-		String script = "import math\ndef process(o ,c):\n    return math.cos(c) + math.sin(o)";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-		
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		new Manipulator(inQueue, manipulations);
-		// Expect IllegalArgument Exception as there is no mapping for the parameter c
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.core.manipulator.Manipulator#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRun() throws InterruptedException {
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		dmm.getComponents().add(new ComponentMetadata("myid"));
-		DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(), dmm);
-
-		DataMessage m = new DataMessage();
-		m.getData().add(10d);
-		inQueue.getQueue().add(m);
-		inQueue.getQueue().add(new EndOfStreamMessage());
-		
-		String id="cid";
-		String script = "import math\ndef process(o):\n    return math.cos(10.0) + math.sin(o)";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		Manipulator manipulator = new Manipulator(inQueue, manipulations);
-		
-		// Check whether output queue message structur complies to expected one
-		DataMessageMetadata outMeta = manipulator.getOutQueue().getDataMessageMetadata();
-		
-		// Test whether only the expected components are within the outgoing queue
-		if(outMeta.getComponents().size()!=2){
-			fail("There are more than the expected components in the outgoing message");
-		}
-		
-		// Test whether the id of the first component matches the expected id
-		if(!outMeta.getComponents().get(0).getId().equals("myid")){
-			fail("Id of the first component does not match the expected id 'myid'");
-		}
-		
-		// Test whether the id of the second component (which was computed) matches the expected id
-		if(!outMeta.getComponents().get(1).getId().equals("cid")){
-			fail("Id of the second component does not match the expected id 'cid'");
-		}
-		
-		
-		manipulator.run();
-		
-		Message message = manipulator.getOutQueue().getQueue().take();
-		while(!(message instanceof EndOfStreamMessage)){
-			
-			logger.info(message.toString());
-			
-			if(message instanceof DataMessage){
-				DataMessage dm = (DataMessage) message;
-				dm.getData().get(0);
-				double res = ((Double)dm.getData().get(1)) - (Math.cos(10.0)+Math.sin(((Double)dm.getData().get(0))));
-				if( Math.abs(res) > 0.000000001){
-					fail("Calculation failed");
-				}
-			}
-			
-			message = manipulator.getOutQueue().getQueue().take();
-		}
-		
-		logger.info(""+(Math.cos(10.0)+Math.sin(10)));
-	}
-	
-	/**
-	 * Test run that returns an integer
-	 * @throws InterruptedException
-	 */
-	@Test
-	public void testRunIntegerReturn() throws InterruptedException {
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		dmm.getComponents().add(new ComponentMetadata("myid"));
-		DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(), dmm);
-
-		DataMessage m = new DataMessage();
-		m.getData().add(10d);
-		inQueue.getQueue().add(m);
-		inQueue.getQueue().add(new EndOfStreamMessage());
-		
-		String id="cid";
-		String script = "import math\ndef process(o):\n    return 1";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		Manipulator manipulator = new Manipulator(inQueue, manipulations);
-		
-		// Check whether output queue message structur complies to expected one
-		DataMessageMetadata outMeta = manipulator.getOutQueue().getDataMessageMetadata();
-		
-		// Test whether only the expected components are within the outgoing queue
-		if(outMeta.getComponents().size()!=2){
-			fail("There are more than the expected components in the outgoing message");
-		}
-		
-		// Test whether the id of the first component matches the expected id
-		if(!outMeta.getComponents().get(0).getId().equals("myid")){
-			fail("Id of the first component does not match the expected id 'myid'");
-		}
-		
-		// Test whether the id of the second component (which was computed) matches the expected id
-		if(!outMeta.getComponents().get(1).getId().equals("cid")){
-			fail("Id of the second component does not match the expected id 'cid'");
-		}
-		
-		
-		manipulator.run();
-		
-		Message message = manipulator.getOutQueue().getQueue().take();
-		while(!(message instanceof EndOfStreamMessage)){
-			
-			logger.info(message.toString());
-			
-			if(message instanceof DataMessage){
-				DataMessage dm = (DataMessage) message;
-				dm.getData().get(0);
-			}
-			
-			message = manipulator.getOutQueue().getQueue().take();
-		}
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.core.manipulator.Manipulator#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Ignore
-	@Test
-	public void testRunLongTimeTest() throws InterruptedException {
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		dmm.getComponents().add(new ComponentMetadata("myid"));
-		final DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(1000), dmm);
-
-		Thread tf = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				try{
-					for(Double i=0d;i<1000000;i++){
-						DataMessage m = new DataMessage();
-						m.getData().add(i);
-						inQueue.getQueue().put(m);
-	//					try {
-	//						Thread.sleep(1);
-	//					} catch (InterruptedException e) {
-	//					}
-					}
-					inQueue.getQueue().put(new EndOfStreamMessage());
-				}
-				catch(InterruptedException e){
-					e.printStackTrace();
-				}
-			}
-		});
-		
-		
-		String id="cid";
-		String script = "import math\ndef process(o):\n    return math.cos(10.0) + math.sin(o)";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		Manipulator manipulator = new Manipulator(inQueue, manipulations);
-		
-
-		
-		Thread t = new Thread(manipulator);
-		
-		final DataQueue outQueue = manipulator.getOutQueue();
-		
-		Thread tp = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				try{
-					int count=0;
-					Message message;
-					while((message = outQueue.getQueue().take()) != null){
-						if(!(message instanceof EndOfStreamMessage)){
-							logger.info(count+" - "+message.toString());
-						}
-						else{
-							break;
-						}
-						count++;
-					}
-				}
-				catch (Exception e) {
-					e.printStackTrace();
-				}
-			}
-		});
-		
-		tf.start();
-		t.start();
-		tp.start();
-		
-		tf.join();
-		t.join();
-		tp.join();
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.core.manipulator.Manipulator#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRunMultipleParameter() throws InterruptedException {
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		dmm.getComponents().add(new ComponentMetadata("myid"));
-		dmm.getComponents().add(new ComponentMetadata("myid2"));
-		DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(), dmm);
-
-		DataMessage m = new DataMessage();
-		m.getData().add(10d);
-		m.getData().add(0.2d);
-		inQueue.getQueue().add(m);
-		inQueue.getQueue().add(new EndOfStreamMessage());
-		
-		String id="cid";
-		String script = "import math\ndef process(o ,c):\n    return math.cos(c) + math.sin(o)";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		mapping.add(new JythonParameterMappingID("c", "myid2"));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-		
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		Manipulator manipulator = new Manipulator(inQueue, manipulations);
-		
-		// Check whether output queue message structur complies to expected one
-		DataMessageMetadata outMeta = manipulator.getOutQueue().getDataMessageMetadata();
-		
-		// Test whether only the expected components are within the outgoing queue
-		if(outMeta.getComponents().size()!=3){
-			fail("There are more than the expected components in the outgoing message");
-		}
-		
-		// Test whether the id of the first component matches the expected id
-		if(!outMeta.getComponents().get(0).getId().equals("myid")){
-			fail("Id of the first component does not match the expected id 'myid'");
-		}
-		
-		if(!outMeta.getComponents().get(1).getId().equals("myid2")){
-			fail("Id of the first component does not match the expected id 'myid'");
-		}
-		
-		// Test whether the id of the second component (which was computed) matches the expected id
-		if(!outMeta.getComponents().get(2).getId().equals("cid")){
-			fail("Id of the second component does not match the expected id 'cid'");
-		}
-		
-		
-		manipulator.run();
-		
-		Message message = manipulator.getOutQueue().getQueue().take();
-		while(!(message instanceof EndOfStreamMessage)){
-			
-			logger.info(message.toString());
-			
-			if(message instanceof DataMessage){
-				DataMessage dm = (DataMessage) message;
-				dm.getData().get(0);
-				double res = ((Double)dm.getData().get(2)) - (Math.cos(((Double)dm.getData().get(1)))+Math.sin(((Double)dm.getData().get(0))));
-				if( Math.abs(res) > 0.000000001){
-					fail("Calculation failed");
-				}
-			}
-			
-			
-			message = manipulator.getOutQueue().getQueue().take();
-		}
-		
-		logger.info(""+(Math.cos(0.2)+Math.sin(10)));
-		
-	}
-	
-	
-	/**
-	 * Test method for {@link ch.psi.fda.core.manipulator.Manipulator#run()}.
-	 * @throws InterruptedException 
-	 * @throws CAException 
-	 */
-	@Test
-	public void testRunMultipleParameterAndChannel() throws InterruptedException, CAException {
-		
-		Double setValue = 12.22;
-		
-		ChannelBean<Double> cbean = ChannelBeanFactory.getFactory().createChannelBean(Double.class, TestChannels.ANALOG_OUT, false);
-		
-		DataMessageMetadata dmm = new DataMessageMetadata();
-		dmm.getComponents().add(new ComponentMetadata("myid"));
-		dmm.getComponents().add(new ComponentMetadata("myid2"));
-		DataQueue inQueue = new DataQueue(new LinkedBlockingQueue<Message>(), dmm);
-
-		DataMessage m = new DataMessage();
-		m.getData().add(10d);
-		m.getData().add(0.2d);
-		inQueue.getQueue().add(m);
-		inQueue.getQueue().add(new EndOfStreamMessage());
-		
-		String id="cid";
-		String script = "import math\ndef process(o ,c,d):\n    d.setValue("+setValue+")\n    print d.getValue()\n    return math.cos(c) + math.sin(o)";
-		List<JythonParameterMapping> mapping = new ArrayList<JythonParameterMapping>();
-		mapping.add(new JythonParameterMappingID("o", "myid"));
-		mapping.add(new JythonParameterMappingID("c", "myid2"));
-		mapping.add(new JythonParameterMappingChannel("d", TestChannels.ANALOG_OUT, Double.class));
-		JythonManipulation manipulation = new JythonManipulation(id, script, mapping);
-		
-		List<Manipulation> manipulations = new ArrayList<Manipulation>();
-		manipulations.add(manipulation);
-		Manipulator manipulator = new Manipulator(inQueue, manipulations);
-		
-		// Check whether output queue message structur complies to expected one
-		DataMessageMetadata outMeta = manipulator.getOutQueue().getDataMessageMetadata();
-		
-		// Test whether only the expected components are within the outgoing queue
-		if(outMeta.getComponents().size()!=3){
-			fail("There are more than the expected components in the outgoing message");
-		}
-		
-		// Test whether the id of the first component matches the expected id
-		if(!outMeta.getComponents().get(0).getId().equals("myid")){
-			fail("Id of the first component does not match the expected id 'myid'");
-		}
-		
-		if(!outMeta.getComponents().get(1).getId().equals("myid2")){
-			fail("Id of the first component does not match the expected id 'myid'");
-		}
-		
-		// Test whether the id of the second component (which was computed) matches the expected id
-		if(!outMeta.getComponents().get(2).getId().equals("cid")){
-			fail("Id of the second component does not match the expected id 'cid'");
-		}
-		
-		// Change something different on the channel than the value that will be set in the manipulator script
-		cbean.setValue(setValue+1);
-		
-		manipulator.run();
-		
-		Message message = manipulator.getOutQueue().getQueue().take();
-		while(!(message instanceof EndOfStreamMessage)){
-			
-			logger.info(message.toString());
-			
-			if(message instanceof DataMessage){
-				DataMessage dm = (DataMessage) message;
-				dm.getData().get(0);
-				double res = ((Double)dm.getData().get(2)) - (Math.cos(((Double)dm.getData().get(1)))+Math.sin(((Double)dm.getData().get(0))));
-				if( Math.abs(res) > 0.000000001){
-					fail("Calculation failed");
-				}
-			}
-			
-			
-			message = manipulator.getOutQueue().getQueue().take();
-		}
-		
-		logger.info(""+(Math.cos(0.2)+Math.sin(10)));
-		
-		// Check whether the channel was set correctly by the manipulator script
-		if(Math.abs(cbean.getValue()-setValue)>0.00000001){
-			fail("Channel was not set correctly in the manipulator script");
-		}
-		
-	}
-
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/sensors/ChannelAccessDoubleArraySensorTest.java

@@ -1,86 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import static org.junit.Assert.*;
-
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.TestChannels;
-import ch.psi.fda.core.sensors.ChannelAccessDoubleArraySensor;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * Test class for the ScalarDoubleSensorChannelAccess class.
- * @author ebner
- *
- */
-public class ChannelAccessDoubleArraySensorTest {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessDoubleArraySensorTest.class.getName());
-
-	private static final String channelName = TestChannels.DOUBLE_WAVEFORM;
-	private static final int numberOfPoints = 10;
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.sensors.ChannelAccessDoubleSensor#read()}.
-	 * @throws CAException 
-	 */
-	@Test
-	public void testRead() throws CAException, InterruptedException {
-		ChannelAccessDoubleArraySensor sensor = new ChannelAccessDoubleArraySensor("id0", channelName, numberOfPoints);
-		ChannelBean<double[]> channel = ChannelBeanFactory.getFactory().createChannelBean(double[].class, channelName, false);
-		
-		// Prepare sensor channel
-		double[] setValue = new double[] { 0.1,0.2,0.3,4,5,6,77,88,99,10.2};
-		channel.setValue(setValue);
-		
-		// Get sensor readout value
-		double[] value = (double[]) sensor.read();
-		for(int i=0;i<setValue.length;i++){
-			logger.finest("Sensor value["+i+"]: "+value[i]);
-			if(Math.abs(value[i] - setValue[i])>0.0000001){ // The precision of the channel is 6
-				fail("Sensor readout value does not match actual value");
-			}
-		}
-	}
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/sensors/ChannelAccessDoubleSensorTest.java

@@ -1,84 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import static org.junit.Assert.*;
-
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.TestChannels;
-import ch.psi.fda.core.sensors.ChannelAccessDoubleSensor;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * Test class for the ScalarDoubleSensorChannelAccess class.
- * @author ebner
- *
- */
-public class ChannelAccessDoubleSensorTest {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessDoubleSensorTest.class.getName());
-
-	private static final String channelName = TestChannels.ANALOG_OUT;
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.sensors.ChannelAccessDoubleSensor#read()}.
-	 * @throws CAException 
-	 */
-	@Test
-	public void testRead() throws CAException, InterruptedException {
-		ChannelAccessDoubleSensor sensor = new ChannelAccessDoubleSensor("id0", channelName);
-		ChannelBean<Double> channel = ChannelBeanFactory.getFactory().createChannelBean(Double.class, channelName, false);
-		
-		// Prepare sensor channel
-		Double setValue = 0.1d;
-		channel.setValue(setValue);
-		
-		// Get sensor readout value
-		Double value = (Double) sensor.read();
-		logger.finest("Sensor value: "+value);
-		if(!value.equals(setValue)){
-			fail("Sensor readout value does not match actual value");
-		}
-	}
-
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/sensors/ChannelAccessStringSensorTest.java

@@ -1,77 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import static org.junit.Assert.*;
-
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.TestChannels;
-
-/**
- * Test class for the ScalarDoubleSensorChannelAccess class.
- * @author ebner
- *
- */
-public class ChannelAccessStringSensorTest {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessStringSensorTest.class.getName());
-
-	private static final String channelName = TestChannels.ANALOG_OUT+".NAME";
-	private static final String actualValue = TestChannels.ANALOG_OUT;
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.sensors.ChannelAccessDoubleSensor#read()}.
-	 * @throws CAException 
-	 */
-	@Test
-	public void testRead() throws CAException, InterruptedException {
-		ChannelAccessStringSensor sensor = new ChannelAccessStringSensor("id0", channelName);
-
-		// Get sensor readout value
-		String value = (String) sensor.read();
-		logger.info("Sensor value: "+value);
-		if(!value.equals(actualValue)){
-			fail("Sensor readout "+value+" value does not match actual value "+actualValue);
-		}
-	}
-
-}

ch.psi.fda/src/test/java/ch/psi/fda/core/sensors/ComplexSensorTest.java

@@ -1,133 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.sensors;
-
-import static org.junit.Assert.*;
-
-import java.util.HashMap;
-import java.util.logging.Logger;
-
-import gov.aps.jca.CAException;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.TestChannels;
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.sensors.ChannelAccessDoubleSensor;
-import ch.psi.fda.core.sensors.ComplexSensor;
-import ch.psi.jcae.ChannelBean;
-import ch.psi.jcae.ChannelBeanFactory;
-
-/**
- * Test class for the ScalarDoubleSensorChannelAccess class.
- * @author ebner
- *
- */
-public class ComplexSensorTest {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ComplexSensorTest.class.getName());
-
-	private static final String channelName = TestChannels.ANALOG_OUT;
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.core.sensors.ChannelAccessDoubleSensor#read()}.
-	 * @throws CAException 
-	 */
-	@Test
-	public void testRead() throws CAException, InterruptedException {
-		
-		final HashMap<String, Long> timestamps = new HashMap<String,Long>();
-		
-		ChannelAccessDoubleSensor s1 = new ChannelAccessDoubleSensor("id0", channelName);
-		ComplexSensor sensor = new ComplexSensor("id2", s1);
-		
-		// Add pre action
-		sensor.getPreActions().add(new Action() {
-			
-			@Override
-			public void execute() {
-				logger.info("PreAction");
-				timestamps.put("pre", System.currentTimeMillis());
-			}
-			
-			@Override
-			public void destroy() {
-			}
-			
-			@Override
-			public void abort() {
-			}
-		});
-		
-		// Add post action
-		sensor.getPostActions().add(new Action() {
-			
-			@Override
-			public void execute() {
-				logger.info("PostAction");
-				timestamps.put("post", System.currentTimeMillis());
-			}
-			
-			@Override
-			public void destroy() {
-			}
-			
-			@Override
-			public void abort() {
-			}
-		});
-		
-		// Create channel bean for test sensor channel
-		ChannelBean<Double> channel = ChannelBeanFactory.getFactory().createChannelBean(Double.class, channelName, false);
-		
-		// Prepare sensor channel
-		Double setValue = 0.1d;
-		channel.setValue(setValue);
-		
-		// Get sensor readout value
-		Double value = (Double) sensor.read();
-		
-		logger.finest("Sensor value: "+value);
-		if(!value.equals(setValue)){
-			fail("Sensor readout value does not match actual value");
-		}
-		
-		if(timestamps.get("post")<timestamps.get("pre")){
-			fail("Post got executed before pre");
-		}
-	}
-}

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

@@ -1,127 +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.deserializer;
-
-import java.io.File;
-import java.net.URI;
-import java.net.URL;
-import java.util.concurrent.BlockingQueue;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.ControlMessage;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * @author ebner
- *
- * For testing whether the created MDA file is correct use following 
- * program on a SLS SL5 beamline console (or slslc05/06)
- */
-public class DataDeserializerMDATest {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(DataDeserializerMDATest.class.getName());
-	
-	private DataDeserializerMDA deserializer;
-	
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-		URL url = this.getClass().getClassLoader().getResource("testdata/mda/mdadata7.mda");
-		deserializer = new DataDeserializerMDA(new File(new URI(url.toString())));
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.deserializer.DataDeserializerTXT#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRun() throws InterruptedException {
-		
-		Thread t = new Thread(new Runnable() {
-			@Override
-			public void run() {
-				try {
-					BlockingQueue<Message> q = deserializer.getQueue().getQueue();
-					
-					while(true){
-						Message m = q.take();
-						if(m instanceof DataMessage){
-							DataMessage x = (DataMessage) m;
-							logger.info( x.toString() );
-						}
-						else if(m instanceof ControlMessage){
-							if(m instanceof EndOfStreamMessage){
-								break;
-							}
-							logger.info("---- "+m.toString()+" ----");
-						}
-					}
-					
-					StringBuilder b = new StringBuilder();
-					b.append("[");
-					StringBuilder b1 = new StringBuilder();
-					b1.append("[");
-					for(ComponentMetadata cm : deserializer.getQueue().getDataMessageMetadata().getComponents()){
-						b.append(" ");
-						b.append(cm.getId());
-						b1.append(" ");
-						b1.append(cm.getDimension());
-					}
-					b.append(" ]");
-					b1.append(" ]");
-					
-					logger.info("Metadata "+b.toString());
-					logger.info("Metadata "+b1.toString());
-				} catch (InterruptedException e) {
-					logger.log(Level.SEVERE, "An Exception occured while reading data from the data queue", e);
-				}
-			}
-		});
-		
-		Thread tt = new Thread(deserializer);
-		
-		tt.start();
-		t.start();
-		
-		tt.join();
-		t.join();
-		
-
-	}
-
-}

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

@@ -1,235 +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.File;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-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.serializer.DataSerializer;
-import ch.psi.fda.serializer.DataSerializerMAT;
-import ch.psi.fda.serializer.DataSerializerMAT2D;
-import ch.psi.fda.serializer.DataSerializerTXT;
-import ch.psi.fda.serializer.DataSerializerTXT2D;
-import ch.psi.fda.serializer.DataSerializerTXTSplit;
-
-/**
- * @author ebner
- *
- */
-public class DataSerializerTest {
-
-	private static final String tmpDirectory = "target/tmp";
-	
-	
-	private DataQueue queue;
-	
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-		new File(tmpDirectory).mkdirs();
-		BlockingQueue<Message> q3 = new LinkedBlockingQueue<Message>();
-		DataMessageMetadata m3 = new DataMessageMetadata();
-		
-		this.queue = new DataQueue(q3, m3);
-
-	}
-	
-	/**
-	 * Generate 1D data
-	 * @throws InterruptedException
-	 */
-	private void generate1DData() throws InterruptedException{
-		
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id0", 0));
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id1", 0));
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id2", 0));
-		
-		// Dimension
-		DataMessage m = new DataMessage();
-		m.getData().add(0.000000000000000001);
-		m.getData().add(0.1);
-		m.getData().add(1d); // have this value as double
-		queue.getQueue().put(m);
-		
-		m = new DataMessage();
-		m.getData().add(0.02);
-		m.getData().add(0.2);
-		m.getData().add(2d); // have this value as double
-		queue.getQueue().put(m);
-		queue.getQueue().put(new EndOfStreamMessage());
-	}
-	
-	/**
-	 * Generate 2D test data
-	 * @throws InterruptedException
-	 */
-	private void generate2DData() throws InterruptedException{
-		
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id0", 1));
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id1", 0));
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id2", 0));
-		
-		for(double i=0;i<5;i++){
-			for(double t=0.1; t<10; t=t+0.1){
-				// Dimension
-				DataMessage m = new DataMessage();
-				m.getData().add(i);
-				m.getData().add(t);
-				m.getData().add(Math.log(t)); // have this value as double
-				queue.getQueue().put(m);
-			}
-			queue.getQueue().put(new StreamDelimiterMessage(0));
-		}
-		queue.getQueue().put(new StreamDelimiterMessage(1));
-		
-		
-		queue.getQueue().put(new EndOfStreamMessage());
-	}
-	
-	/**
-	 * Generate 3d test data
-	 * @throws InterruptedException
-	 */
-	private void generate3DData() throws InterruptedException{
-		
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id0", 2));
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id1", 1));
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id2", 0));
-		queue.getDataMessageMetadata().getComponents().add(new ComponentMetadata("id3", 0));
-		
-		for(double z=30;z<36;z++){
-			for(double i=0;i<6;i++){
-				for(double t=0.1; t<1.1; t=t+0.1){
-					// Dimension
-					DataMessage m = new DataMessage();
-					m.getData().add(z);
-					m.getData().add(i);
-					m.getData().add(t);
-					m.getData().add(Math.log(t)); // have this value as double
-					queue.getQueue().put(m);
-				}
-				queue.getQueue().put(new StreamDelimiterMessage(0));
-			}
-			queue.getQueue().put(new StreamDelimiterMessage(1));
-		}
-		queue.getQueue().put(new StreamDelimiterMessage(2));
-		
-		
-		queue.getQueue().put(new EndOfStreamMessage());
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRunTXT() throws InterruptedException {
-		generate1DData();
-		DataSerializer serializer = new DataSerializerTXT(queue, new File(tmpDirectory+"/test.txt"), true);
-		serializer.run();
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRunMAT() throws InterruptedException {
-		generate1DData();
-		DataSerializer serializer = new DataSerializerMAT(queue, new File(tmpDirectory+"/test.mat"));
-		serializer.run();
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRunMAT2D() throws InterruptedException {
-		generate2DData();
-		DataSerializer serializer = new DataSerializerMAT2D(queue, new File(tmpDirectory+"/test-2d.mat"));
-		serializer.run();
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRunTXT2D() throws InterruptedException {
-		generate2DData();
-		DataSerializer serializer = new DataSerializerTXT2D(queue, new File(tmpDirectory+"/test-2d.txt"));
-		serializer.run();
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRunSplitTXT() throws InterruptedException {
-		generate2DData();
-		DataSerializer serializer = new DataSerializerTXTSplit(queue, new File(tmpDirectory+"/test-2d-split.txt"));
-		serializer.run();
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerMDA#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRun2D() throws InterruptedException {
-		generate2DData();
-		DataSerializer serializer = new DataSerializerMDA(queue, new File(tmpDirectory+"/test-2d.mda"));
-		serializer.run();
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerMDA#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Test
-	public void testRun3D() throws InterruptedException {
-		generate3DData();
-		DataSerializer serializer = new DataSerializerMDA(queue, new File(tmpDirectory+"/test-3d.mda"));
-		serializer.run();
-	}
-}

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

@@ -1,303 +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.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import javax.swing.JFrame;
-import javax.swing.JPanel;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-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.model.v1.MatrixPlot;
-import ch.psi.fda.model.v1.PseudoPositioner;
-import ch.psi.fda.model.v1.Visualization;
-import ch.psi.fda.visualizer.Visualizer;
-
-/**
- * All test cases in this test class are meant to be executed manually
- * Remove @Ignore in front of the test function to be able to run it.
- * 
- * @author ebner
- *
- */
-public class DataVisualizerTest {
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test method for {@link ch.psi.fda.visualizer.Visualizer#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Ignore
-	@Test
-	public void testRun() throws InterruptedException {
-		final BlockingQueue<Message> q = new LinkedBlockingQueue<Message>();
-		DataMessageMetadata dm = new DataMessageMetadata();
-		dm.getComponents().add(new ComponentMetadata("id1", 0));
-		dm.getComponents().add(new ComponentMetadata("id2", 0));
-		dm.getComponents().add(new ComponentMetadata("id3", 0));
-		DataQueue queue = new DataQueue(q,dm);
-
-		// Create visualization
-		List<Visualization> vlist = new ArrayList<Visualization>();
-		ch.psi.fda.model.v1.LinePlot p = new ch.psi.fda.model.v1.LinePlot();
-		p.setX("id1");
-		p.getY().add("id2");
-		vlist.add(p);
-		p = new ch.psi.fda.model.v1.LinePlot();
-		p.setX("id1");
-		p.getY().add("id3");
-		vlist.add(p);
-		
-		// Create visualizer
-		Visualizer visualizer = new Visualizer(queue, vlist);
-		
-		JFrame f = new JFrame();
-		f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-		f.setSize(600, 400);
-		JPanel pan = new JPanel();
-		for(JPanel pp: visualizer.getPlotPanels()){
-			pan.add(pp);
-		}
-		f.add(pan);
-		f.setVisible(true);
-		
-		
-		// Thread creating data
-		Thread t = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				DataMessage m;
-				for(double t=0;t<4;t++){
-					for(double i =0;i<100;i=i+0.1){
-						m = new DataMessage();
-						m.getData().add(i);
-						m.getData().add(t+Math.sin(i));
-						m.getData().add(t+Math.cos(i));
-						q.add(m);
-						try {
-							Thread.sleep(10);
-						} catch (InterruptedException e) {
-							throw new RuntimeException("Sleep interrupted",e);
-						}
-					}
-					q.add(new StreamDelimiterMessage(0));
-				}
-				
-				q.add(new EndOfStreamMessage());
-				
-			}
-		});
-		// Start data thread
-		t.start();
-		
-		
-		visualizer.visualize();
-		
-		t.join();
-		
-		Thread.sleep(10000);
-	}
-	
-	@Ignore
-	@Test
-	public void testRunArray() throws InterruptedException {
-		final BlockingQueue<Message> q = new LinkedBlockingQueue<Message>();
-		DataMessageMetadata dm = new DataMessageMetadata();
-		dm.getComponents().add(new ComponentMetadata("id1", 0));
-		DataQueue queue = new DataQueue(q,dm);
-
-		// Create visualization
-		List<Visualization> vlist = new ArrayList<Visualization>();
-		ch.psi.fda.model.v1.LinePlotArray p = new ch.psi.fda.model.v1.LinePlotArray();
-		p.getY().add("id1");
-		p.setMaxSeries(10);
-		vlist.add(p);
-		
-		// Create visualizer
-		Visualizer visualizer = new Visualizer(queue, vlist);
-		
-		JFrame f = new JFrame();
-		f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-		f.setSize(600, 400);
-		JPanel pan = new JPanel();
-		for(JPanel pp: visualizer.getPlotPanels()){
-			pan.add(pp);
-		}
-		f.add(pan);
-		f.setVisible(true);
-		
-		
-		// Thread creating data
-		Thread t = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				DataMessage m;
-				int npoints = 10000;
-				for(double t=0;t<10;t++){
-					double[] values = new double[npoints];
-					
-					for(int i=0;i<npoints;i++){
-						values[i]= Math.sin(i*0.01)+Math.cos(t);
-					}
-					
-					m = new DataMessage();
-					m.getData().add(values);
-					q.add(m);
-					
-					try {
-						Thread.sleep(1000);
-					} catch (InterruptedException e) {
-						throw new RuntimeException("Sleep interrupted",e);
-					}
-				}
-				q.add(new StreamDelimiterMessage(0));
-				q.add(new EndOfStreamMessage());
-				
-			}
-		});
-		// Start data thread
-		t.start();
-		
-		
-		visualizer.visualize();
-		
-		t.join();
-		
-		Thread.sleep(10000);
-	}
-	
-	/**
-	 * Test method for {@link ch.psi.fda.visualizer.Visualizer#run()}.
-	 * @throws InterruptedException 
-	 */
-	@Ignore
-	@Test
-	public void testRun2D() throws InterruptedException {
-		final BlockingQueue<Message> q = new LinkedBlockingQueue<Message>();
-		DataMessageMetadata dm = new DataMessageMetadata();
-		dm.getComponents().add(new ComponentMetadata("id1", 1));
-		dm.getComponents().add(new ComponentMetadata("id2", 0));
-		dm.getComponents().add(new ComponentMetadata("id3", 0));
-		DataQueue queue = new DataQueue(q,dm);
-		
-		List<Visualization> vlist = new ArrayList<Visualization>();
-		ch.psi.fda.model.v1.LinePlot p = new ch.psi.fda.model.v1.LinePlot();
-		p.setX("id2");
-		p.getY().add("id3");
-		vlist.add(p);
-		
-//		0d,4d,5,0d,100d,1001
-		
-		PseudoPositioner pos = new PseudoPositioner();
-		pos.setId("id1");
-		pos.setCounts(5);
-		
-		PseudoPositioner pos1 = new PseudoPositioner();
-		pos1.setId("id2");
-		pos1.setCounts(1000);
-		
-		MatrixPlot mp = new MatrixPlot();
-		mp.setX(pos);
-		mp.setY(pos1);
-		mp.setZ("id3");
-		vlist.add(mp);
-		
-		// Create visualizer
-		Visualizer visualizer = new Visualizer(queue, vlist);
-		
-		JFrame f = new JFrame();
-		f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-		f.setSize(600, 400);
-//		f.add(plot.getPlotPanel());
-		JPanel pan = new JPanel();
-		for(JPanel pp: visualizer.getPlotPanels()){
-			pan.add(pp);
-		}
-		f.add(pan);
-		f.setVisible(true);
-		
-		
-		// Thread creating data
-		Thread t = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				DataMessage m;
-				for(double t=1;t<=5;t++){
-					for(double i=1;i<=1000;i++){
-						m = new DataMessage();
-						m.getData().add(t);
-						m.getData().add(i);
-						m.getData().add(t+Math.cos(i));
-						q.add(m);
-						try {
-							Thread.sleep(10);
-						} catch (InterruptedException e) {
-							throw new RuntimeException("Sleep interrupted",e);
-						}
-					}
-					q.add(new StreamDelimiterMessage(0));
-				}
-				
-				q.add(new EndOfStreamMessage());
-				
-			}
-		});
-		// Start data thread
-		t.start();
-		
-		
-		visualizer.visualize();
-		
-		t.join();
-		
-		Thread.sleep(10000);
-	}
-	
-}

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
+   ========================================================================== */
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+