Discard first 1028 values

Added file exist check
Configured serializer to not append _0000 to the file name

ch.psi.fda.fdaq/src/main/java/ch/psi/fda/fdaq/FdaqMain.java

@@ -42,6 +42,11 @@ public class FdaqMain {
 		
 		File file = new File(args[0]);
 		
+		if(file.exists()){
+			System.err.println("File "+file.getName()+ " already exists.");
+			System.exit(-1);
+		}
+		
 		FdaqConfiguration configuration = new FdaqConfiguration();
 		String config = System.getProperty(FDAQ_CONFIG);
 		
@@ -65,7 +70,7 @@ public class FdaqMain {
 			}
 		});
 		
-		SerializerTXT serializer = new SerializerTXT(file);
+		SerializerTXT serializer = new SerializerTXT(file, false);
 		serializer.setShowDimensionHeader(false);
 		bus.register(serializer);
 		

ch.psi.fda.fdaq/src/main/java/ch/psi/fda/fdaq/FdaqService.java

@@ -84,7 +84,7 @@ public class FdaqService {
 					bytebuffer.order(ByteOrder.LITTLE_ENDIAN);
 					bytebuffer.putInt(26); // Function number (index of pointer to function)
 					bytebuffer.putInt(numberOfElements);
-					// TODO
+
 					if(first){
 						bytebuffer.putInt(1); // Reset FIFO flag - The first time there need to be a 1 in int to reset the fifo buffer on the box
 						first=false;
@@ -117,6 +117,13 @@ public class FdaqService {
 							logger.info("End of Stream");
 							break;
 						}
+						
+						if(t<1028){
+							// The first 1028 are wrong (not really wrong but there are repeated values/holes)
+							// It has to do with the fact that we asynchronously reset the FIFO.
+							// This is independent of the frequency
+							continue;
+						}
 		
 						int a = buffer.getInt();
 						int b = buffer.getInt();