Renamed serializer classes (removed Data prefix)

Moved SerializerTXT to core project

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

@@ -38,13 +38,13 @@ import com.google.common.eventbus.EventBus;
 import ch.psi.fda.deserializer.DataDeserializer;
 import ch.psi.fda.deserializer.DataDeserializerMDA;
 import ch.psi.fda.deserializer.DataDeserializerTXT;
-import ch.psi.fda.serializer.DataSerializerMAT;
-import ch.psi.fda.serializer.DataSerializerMAT2D;
-import ch.psi.fda.serializer.DataSerializerMAT2DZigZag;
-import ch.psi.fda.serializer.DataSerializerMDA;
-import ch.psi.fda.serializer.DataSerializerTXT;
-import ch.psi.fda.serializer.DataSerializerTXT2D;
-import ch.psi.fda.serializer.DataSerializerTXTSplit;
+import ch.psi.fda.serializer.SerializerMAT;
+import ch.psi.fda.serializer.SerializerMAT2D;
+import ch.psi.fda.serializer.SerializerMAT2DZigZag;
+import ch.psi.fda.serializer.SerializerMDA;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT2D;
+import ch.psi.fda.serializer.SerializerTXTSplit;
 
 /**
  * Converter to convert the format of datafiles
@@ -98,25 +98,25 @@ public class ConversionMain {
 		}
 
 		if(writer.equals(Writer.MAT)){
-			bus.register(new DataSerializerMAT(output));
+			bus.register(new SerializerMAT(output));
 		}
 		else if(writer.equals(Writer.MAT_2D)){
-			bus.register(new DataSerializerMAT2D(output));
+			bus.register(new SerializerMAT2D(output));
 		}
 		else if(writer.equals(Writer.TXT)){
-			bus.register(new DataSerializerTXT(output, false));
+			bus.register(new SerializerTXT(output, false));
 		}
 		else if(writer.equals(Writer.TXT_2D)){
-			bus.register(new DataSerializerTXT2D(output));
+			bus.register(new SerializerTXT2D(output));
 		}
 		else if(writer.equals(Writer.TXT_SPLIT)){
-			bus.register(new DataSerializerTXTSplit(output));
+			bus.register(new SerializerTXTSplit(output));
 		}
 		else if(writer.equals(Writer.MDA)){
-			bus.register(new DataSerializerMDA(output));
+			bus.register(new SerializerMDA(output));
 		}
 		else if(writer.equals(Writer.MAT_2D_Z)){
-			bus.register(new DataSerializerMAT2DZigZag(output));
+			bus.register(new SerializerMAT2DZigZag(output));
 		}
 		else{
 			throw new IllegalArgumentException("Writer of type "+writer+" not supported.");

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

@@ -106,7 +106,7 @@ import ch.psi.fda.model.v1.SimpleScalarDetector;
 import ch.psi.fda.model.v1.Timestamp;
 import ch.psi.fda.model.v1.Variable;
 import ch.psi.fda.model.v1.VariableParameterMapping;
-import ch.psi.fda.serializer.DataSerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.ChannelDescriptor;
 import ch.psi.jcae.ChannelException;
@@ -130,7 +130,7 @@ public class Acquisition {
 	
 	private ActionLoop actionLoop;
 	private Manipulator manipulator;
-	private DataSerializerTXT serializer;
+	private SerializerTXT serializer;
 	
 	private List<Manipulation> manipulations;
 	private volatile boolean active = false;
@@ -250,7 +250,7 @@ public class Acquisition {
 			b.register(this.manipulator);
 			
 			
-			this.serializer = new DataSerializerTXT(datafile, true);
+			this.serializer = new SerializerTXT(datafile, true);
 			bus.register(serializer);
 		}
 		else{
@@ -259,7 +259,7 @@ public class Acquisition {
 			mapScan(collector, smodel);
 //			col = collector;
 			
-			this.serializer = new DataSerializerTXT(datafile, true);
+			this.serializer = new SerializerTXT(datafile, true);
 			bus.register(serializer);
 		}
 	}

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

@@ -1,197 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.serializer;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.logging.Logger;
-
-import com.google.common.eventbus.Subscribe;
-
-import ch.psi.fda.messages.DataMessage;
-import ch.psi.fda.messages.EndOfStreamMessage;
-import ch.psi.fda.messages.Message;
-import ch.psi.fda.messages.Metadata;
-import ch.psi.fda.messages.StreamDelimiterMessage;
-
-/**
- * Serialize data received by a DataQueue
- */
-public class DataSerializerTXT {
-	
-	private static final Logger logger = Logger.getLogger(DataSerializerTXT.class.getName());
-	
-	private File file;
-	
-	private boolean appendSuffix = true;
-
-	
-	private boolean first = true;
-	private File outfile;
-	
-	private int icount;
-	private String basename;
-	private String extension;
-	private boolean newfile;
-	private boolean dataInBetween;
-	private BufferedWriter writer;
-	private StringBuffer b;
-	private StringBuffer b1;
-	
-	
-	/**
-	 * @param metadata
-	 * @param file
-	 * @param appendSuffix	Flag whether to append a _0000 suffix after the original file name
-	 */
-	public DataSerializerTXT(File file, boolean appendSuffix){
-		this.file = file;
-		this.appendSuffix = appendSuffix;
-	}
-
-	@Subscribe
-	public void onMessage(Message message){
-		try{
-		if(first){
-			first=false;
-			// Write header
-						
-						
-						
-						icount = 0;
-						newfile = true;
-						dataInBetween = false;
-						writer = null;
-						
-						// Get basename of the file
-						basename = this.file.getAbsolutePath(); // Determine file name
-						extension = basename.replaceAll("^.*\\.", ""); // Determine extension
-						basename = basename.replaceAll("\\."+extension+"$", "");
-		}
-		
-		if(message instanceof DataMessage){
-			dataInBetween = true;
-			if(newfile){
-				
-				b = new StringBuffer();
-				b1 = new StringBuffer();
-				b.append("#");
-				b1.append("#");
-				for(Metadata c: ((DataMessage) message).getMetadata()){
-
-					b.append(c.getId());
-					b.append("\t");
-					
-					b1.append(c.getDimension());
-					b1.append("\t");
-				}
-				b.setCharAt(b.length()-1, '\n');
-				b1.setCharAt(b1.length()-1, '\n');
-				
-				// Open new file and write header
-				// Construct file name
-				if(appendSuffix){
-					outfile = new File(String.format("%s_%04d.%s", basename, icount, extension));
-				}
-				else{
-					outfile = new File(String.format("%s.%s", basename, extension));
-				}
-				
-				// Open file
-				logger.fine("Open new data file: "+outfile.getAbsolutePath());
-				writer = new BufferedWriter(new FileWriter(outfile));
-				
-				// Write header
-				writer.write(b.toString());
-				writer.write(b1.toString());
-				
-				newfile=false;
-			}
-			
-			// Write message to file - each message will result in one line
-			DataMessage m = (DataMessage) message;
-			StringBuffer buffer = new StringBuffer();
-			for(Object o: m.getData()){
-				if(o.getClass().isArray()){
-					// If the array object is of type double[] display its content
-					if(o instanceof double[]){
-						double[] oa = (double[]) o;
-						for(double o1 : oa){
-							buffer.append(o1);
-							buffer.append(" "); // Use space instead of tab
-						}
-						buffer.replace(buffer.length()-1,buffer.length()-1 , "\t"); // Replace last space with tab
-					}
-					else if(o instanceof Object[]){
-						// TODO need to be recursive ...
-						Object[] oa = (Object[])o;
-						for(Object o1 : oa){
-							buffer.append(o1);
-							buffer.append(" "); // Use space instead of tab
-						}
-						buffer.replace(buffer.length()-1,buffer.length()-1 , "\t"); // Replace last space with tab
-					}
-					else{
-						buffer.append("-"); // Not supported
-					}
-				}
-				else{
-					buffer.append(o);
-					buffer.append("\t");
-				}
-			}
-			
-			if(buffer.length()>0){
-				buffer.deleteCharAt(buffer.length()-1); // Remove last character (i.e. \t)
-				buffer.append("\n"); // Append newline
-			}
-			writer.write(buffer.toString());
-		}
-		else if(message instanceof StreamDelimiterMessage){
-			StreamDelimiterMessage m = (StreamDelimiterMessage) message;
-			logger.info("Delimiter - number: "+m.getNumber()+" iflag: "+m.isIflag());
-			if(m.isIflag() && appendSuffix){
-				// Only increase iflag counter if there was data in between
-				// subsequent StreamDelimiterMessages.
-				if(dataInBetween){
-					icount++;
-				}
-				dataInBetween = false;
-				
-				// Set flag to open new file
-				newfile = true;
-				
-				// Close file
-				writer.close();
-			}
-		}
-		else if (message instanceof EndOfStreamMessage){
-			if(writer!=null){
-				// Close file
-				writer.close(); //If the stream was closed previously this has no effect
-			}
-		}
-		} catch (IOException e) {
-			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
-		}
-	}
-}

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

@@ -37,7 +37,7 @@ import ch.psi.fda.messages.Metadata;
 /**
  * Serialize data received by a DataQueue into a Matlab file
  */
-public class DataSerializerMAT {
+public class SerializerMAT {
 	
 	private File file;
 	
@@ -49,7 +49,7 @@ public class DataSerializerMAT {
 	 * @param queue	Data queue holding the data to serialize
 	 * @param file	Name of the Matlab file to serialize the data to
 	 */
-	public DataSerializerMAT(File file){
+	public SerializerMAT(File file){
 		this.file = file;
 	}
 

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

@@ -39,9 +39,9 @@ import ch.psi.fda.messages.StreamDelimiterMessage;
 /**
  * Serialize data received by a DataQueue into a Matlab file
  */
-public class DataSerializerMAT2D {
+public class SerializerMAT2D {
 
-	private static final Logger logger = Logger.getLogger(DataSerializerMAT2D.class.getName());
+	private static final Logger logger = Logger.getLogger(SerializerMAT2D.class.getName());
 	
 	private File file;
 	private boolean appendSuffix = false;
@@ -61,7 +61,7 @@ public class DataSerializerMAT2D {
 	 * @param queue	Data queue holding the data to serialize
 	 * @param file	Name of the Matlab file to serialize the data to
 	 */
-	public DataSerializerMAT2D(File file){
+	public SerializerMAT2D(File file){
 		this.file = file;
 		
 		

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

@@ -40,9 +40,9 @@ import ch.psi.fda.messages.StreamDelimiterMessage;
 /**
  * Serialize data received by a DataQueue into a Matlab file
  */
-public class DataSerializerMAT2DZigZag {
+public class SerializerMAT2DZigZag {
 	
-	private static final Logger logger = Logger.getLogger(DataSerializerMAT2DZigZag.class.getName());
+	private static final Logger logger = Logger.getLogger(SerializerMAT2DZigZag.class.getName());
 	
 	private List<Metadata> metadata;
 	private File file;
@@ -66,7 +66,7 @@ public class DataSerializerMAT2DZigZag {
 	 * @param queue	Data queue holding the data to serialize
 	 * @param file	Name of the Matlab file to serialize the data to
 	 */
-	public DataSerializerMAT2DZigZag(File file){
+	public SerializerMAT2DZigZag(File file){
 		this.file = file;
 		
 		

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

@@ -43,9 +43,9 @@ import ch.psi.fda.messages.StreamDelimiterMessage;
  * 
  * http://www.aps.anl.gov/bcda/synApps/sscan/saveData_fileFormat.txt
  */
-public class DataSerializerMDA {
+public class SerializerMDA {
 	
-	private static final Logger logger = Logger.getLogger(DataSerializerMDA.class.getName());
+	private static final Logger logger = Logger.getLogger(SerializerMDA.class.getName());
 	
 	private File file;
 	
@@ -59,7 +59,7 @@ public class DataSerializerMDA {
 	private HashMap<Integer,List<String>> idMap;
 	private int numberOfDimensions;
 	
-	public DataSerializerMDA(File file){
+	public SerializerMDA(File file){
 		this.file = file;
 	}
 

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

@@ -37,7 +37,7 @@ import ch.psi.fda.messages.StreamDelimiterMessage;
 /**
  * Serialize data received by a DataQueue into a Matlab file
  */
-public class DataSerializerTXT2D {
+public class SerializerTXT2D {
 	
 	private File file;
 	private boolean appendSuffix = false;
@@ -56,7 +56,7 @@ public class DataSerializerTXT2D {
 	 * @param queue	Data queue holding the data to serialize
 	 * @param file	Name of the Matlab file to serialize the data to
 	 */
-	public DataSerializerTXT2D(File file){
+	public SerializerTXT2D(File file){
 		this.file = file;
 	}
 

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

@@ -36,7 +36,7 @@ import ch.psi.fda.messages.StreamDelimiterMessage;
 /**
  * Serialize data received by a DataQueue
  */
-public class DataSerializerTXTSplit {
+public class SerializerTXTSplit {
 
 	private File file;
 
@@ -47,7 +47,7 @@ public class DataSerializerTXTSplit {
 	private List<String> header;
 	private List<String> data;
 
-	public DataSerializerTXTSplit(File file) {
+	public SerializerTXTSplit(File file) {
 		this.file = file;
 	}
 

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

@@ -33,11 +33,11 @@ import ch.psi.fda.messages.DataMessage;
 import ch.psi.fda.messages.EndOfStreamMessage;
 import ch.psi.fda.messages.Metadata;
 import ch.psi.fda.messages.StreamDelimiterMessage;
-import ch.psi.fda.serializer.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;
+import ch.psi.fda.serializer.SerializerMAT;
+import ch.psi.fda.serializer.SerializerMAT2D;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT2D;
+import ch.psi.fda.serializer.SerializerTXTSplit;
 
 
 public class SerializerTest {
@@ -146,79 +146,79 @@ public class SerializerTest {
 	}
 
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunTXT() throws InterruptedException {
-		DataSerializerTXT serializer = new DataSerializerTXT(new File(tmpDirectory+"/test.txt"), true);
+		SerializerTXT serializer = new SerializerTXT(new File(tmpDirectory+"/test.txt"), true);
 		bus.register(serializer);
 		generate1DData();
 	}
 
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunMAT() throws InterruptedException {
 		
-		DataSerializerMAT serializer = new DataSerializerMAT(new File(tmpDirectory+"/test.mat"));
+		SerializerMAT serializer = new SerializerMAT(new File(tmpDirectory+"/test.mat"));
 		bus.register(serializer);
 		generate1DData();
 	}
 	
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunMAT2D() throws InterruptedException {
-		DataSerializerMAT2D serializer = new DataSerializerMAT2D(new File(tmpDirectory+"/test-2d.mat"));
+		SerializerMAT2D serializer = new SerializerMAT2D(new File(tmpDirectory+"/test-2d.mat"));
 		bus.register(serializer);
 		generate2DData();
 	}
 	
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunTXT2D() throws InterruptedException {
-		DataSerializerTXT2D serializer = new DataSerializerTXT2D(new File(tmpDirectory+"/test-2d.txt"));
+		SerializerTXT2D serializer = new SerializerTXT2D(new File(tmpDirectory+"/test-2d.txt"));
 		bus.register(serializer);
 		generate2DData();
 	}
 	
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunSplitTXT() throws InterruptedException {
-		DataSerializerTXTSplit serializer = new DataSerializerTXTSplit(new File(tmpDirectory+"/test-2d-split.txt"));
+		SerializerTXTSplit serializer = new SerializerTXTSplit(new File(tmpDirectory+"/test-2d-split.txt"));
 		bus.register(serializer);
 		generate2DData();
 	}
 	
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerMDA#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerMDA#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRun2D() throws InterruptedException {
-		DataSerializerMDA serializer = new DataSerializerMDA(new File(tmpDirectory+"/test-2d.mda"));
+		SerializerMDA serializer = new SerializerMDA(new File(tmpDirectory+"/test-2d.mda"));
 		bus.register(serializer);
 		generate2DData();
 	}
 
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerMDA#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerMDA#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRun3D() throws InterruptedException {
-		DataSerializerMDA serializer = new DataSerializerMDA(new File(tmpDirectory+"/test-3d.mda"));
+		SerializerMDA serializer = new SerializerMDA(new File(tmpDirectory+"/test-3d.mda"));
 		bus.register(serializer);
 		generate3DData();
 	}