# HG changeset patch
# User Giulio Moro <giuliomoro@yahoo.it>
# Date 1442084755 -3600
# Node ID e77e2e712fbc55e4a10be502d4a959a3a512c33d
# Parent  04b1678614c95fac0d01af8fcb1b35b2a91f901b
To work with the ClockSync plugin

diff -r 04b1678614c9 -r e77e2e712fbc .cproject
--- a/.cproject	Thu Aug 27 03:33:32 2015 +0100
+++ b/.cproject	Sat Sep 12 20:05:55 2015 +0100
@@ -108,13 +108,13 @@
 				</extensions>
 			</storageModule>
 			<storageModule moduleId="cdtBuildSystem" version="4.0.0">
-				<configuration artifactName="${ProjName}" buildArtefactType="org.eclipse.cdt.build.core.buildArtefactType.exe" buildProperties="org.eclipse.cdt.build.core.buildType=org.eclipse.cdt.build.core.buildType.release,org.eclipse.cdt.build.core.buildArtefactType=org.eclipse.cdt.build.core.buildArtefactType.exe" cleanCommand="rm -rf" description="" id="cdt.managedbuild.config.gnu.exe.release.1521194538" name="Release" parent="cdt.managedbuild.config.gnu.exe.release" postannouncebuildStep="Stopping process on BBB and copying new binary" postbuildStep="ssh root@192.168.7.2 &quot;kill -s 9 \`pidof ${BuildArtifactFileName}\` 2&gt;/dev/null; sleep 0.5; &quot;; scp ${PWD}/${BuildArtifactFileName} root@192.168.7.2:~/beaglert/ &amp;&amp; echo 'done copying\n' | wall || echo 'error'|wall">
+				<configuration artifactName="${ProjName}" buildArtefactType="org.eclipse.cdt.build.core.buildArtefactType.exe" buildProperties="org.eclipse.cdt.build.core.buildType=org.eclipse.cdt.build.core.buildType.release,org.eclipse.cdt.build.core.buildArtefactType=org.eclipse.cdt.build.core.buildArtefactType.exe" cleanCommand="rm -rf" description="" id="cdt.managedbuild.config.gnu.exe.release.1521194538" name="Release" parent="cdt.managedbuild.config.gnu.exe.release" postannouncebuildStep="Stopping process on BBB and copying new binary" postbuildStep="scp ${PWD}/${BuildArtifactFileName} root@192.168.7.2:~/beaglert/ &amp;&amp; echo 'done copying\n' | wall || echo 'error'|wall">
 					<folderInfo id="cdt.managedbuild.config.gnu.exe.release.1521194538." name="/" resourcePath="">
 						<toolChain id="cdt.managedbuild.toolchain.gnu.exe.release.1612059942" name="Linux GCC" superClass="cdt.managedbuild.toolchain.gnu.exe.release">
 							<targetPlatform id="cdt.managedbuild.target.gnu.platform.exe.release.908983575" name="Debug Platform" superClass="cdt.managedbuild.target.gnu.platform.exe.release"/>
 							<builder buildPath="${workspace_loc:/BBB_audio+input/Release}" id="cdt.managedbuild.target.gnu.builder.exe.release.511190290" keepEnvironmentInBuildfile="false" managedBuildOn="true" name="Gnu Make Builder" superClass="cdt.managedbuild.target.gnu.builder.exe.release"/>
 							<tool command="arm-linux-gnueabihf-g++&#10;" id="cdt.managedbuild.tool.gnu.archiver.base.810674388" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.base"/>
-							<tool command="arm-linux-gnueabihf-g++&#10;" commandLinePattern="${COMMAND} ${FLAGS} ${OUTPUT_FLAG} ${OUTPUT_PREFIX}${OUTPUT} ${INPUTS}" id="cdt.managedbuild.tool.gnu.cpp.compiler.exe.release.163790048" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.exe.release">
+							<tool command="arm-linux-gnueabihf-g++" commandLinePattern="${COMMAND} ${FLAGS} ${OUTPUT_FLAG} ${OUTPUT_PREFIX}${OUTPUT} ${INPUTS}" id="cdt.managedbuild.tool.gnu.cpp.compiler.exe.release.163790048" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.exe.release">
 								<option id="gnu.cpp.compiler.exe.release.option.optimization.level.2031085570" name="Optimization Level" superClass="gnu.cpp.compiler.exe.release.option.optimization.level" value="gnu.cpp.compiler.optimization.level.more" valueType="enumerated"/>
 								<option id="gnu.cpp.compiler.exe.release.option.debugging.level.701035863" name="Debug Level" superClass="gnu.cpp.compiler.exe.release.option.debugging.level" value="gnu.cpp.compiler.debugging.level.none" valueType="enumerated"/>
 								<option id="gnu.cpp.compiler.option.include.paths.823255770" name="Include paths (-I)" superClass="gnu.cpp.compiler.option.include.paths" valueType="includePath">
diff -r 04b1678614c9 -r e77e2e712fbc core/Clock.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/Clock.cpp	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,18 @@
+#include "Clock.h"
+
+namespace Clock
+{
+  myClock_t getTimeUs(){
+    struct timeval tv;
+    struct timezone tz;
+    int ret=gettimeofday(&tv, &tz);
+    if(ret == -1){
+       printf("Error while getting time of the day\n");
+      return -1;
+    }
+    myClock_t time=tv.tv_usec + tv.tv_sec*1e6;
+    //   printf("Time is: %.6f\n", time/1000000.0);
+    //   printf("Time is: %lld\n", time);
+    return time;
+  }
+};
\ No newline at end of file
diff -r 04b1678614c9 -r e77e2e712fbc core/ClockSync.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/ClockSync.cpp	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,250 @@
+#include "ClockSync.h"
+
+void ClockSync::setVirtualClock(VirtualClock &aVirtualClock){
+	virtualClock=&aVirtualClock;
+}
+void ClockSync::init(bool thisIsSlave, int aPort, VirtualClock &aVirtualClock){
+	setVirtualClock(aVirtualClock);
+	slave=thisIsSlave;
+	setPort(aPort);
+	//  isSlave() ? client.setServer("127.0.0.1") : client.setServer("127.0.0.1");
+	isSlave() ? client.setServer("192.168.7.1") : client.setServer("192.168.7.2");
+	bufferLength=kSyncMessageLength;
+	T1=-1;
+	T1p=-1;
+	T2=-1;
+	T2p=-1;
+	receiveLoopSleepUs=10;
+	receiveLoopTimeout=1e5;
+	movingAverage.setLength(201);
+	expectedClockSyncType=isSlave() ? kSync : kNone;
+}
+ClockSync::ClockSync(bool thisIsSlave, int aPort, VirtualClock &aVirtualClock){
+	init(thisIsSlave, aPort, aVirtualClock);
+}
+void* ClockSync::getBuffer(){
+	return buffer;
+}
+bool ClockSync::isSlave(){
+	return slave;
+}
+bool ClockSync::isMaster(){
+	return !slave;
+}
+int ClockSync::getType(){
+	return ((int*)buffer)[0];
+}
+myClock_t ClockSync::getTimestamp(){
+	return *((myClock_t*)((char*)buffer+sizeof(int)));
+}
+void ClockSync::setType(int clockSyncType){
+	((int*)buffer)[0]=clockSyncType;
+}
+void ClockSync::setTimestamp(myClock_t timestamp){
+	((myClock_t*)((char*)buffer+sizeof(int)))[0]=timestamp;
+}
+void ClockSync::print(){
+	 //printf("type: %d, timestamp: %lld\n",*((int*)buffer),*((myClock_t*)(((int*)buffer)+1)));
+}
+void ClockSync::setPort(int aPort){
+	if(aPort>0){
+		int inPort=isSlave() ? aPort : aPort+1;
+		int outPort=isSlave() ? aPort+1: aPort;
+		server.bindToPort(inPort);
+		client.setPort(outPort);
+		//printf("Receiving on port %d\n", inPort);
+		//printf("Sending to port %d\n", outPort);
+	}
+}
+/** 
+ * sends a clockSync without blocking, checks results and returns the timestamp
+ * immediately after the clockSync has been sent or -1 if there was an error or timeout expired.
+*/
+myClock_t ClockSync::send(){
+	//  print();
+	int ret;
+	ret=client.waitUntilReady(false, 0);
+	if(ret<=0){ //don't retry
+		return -1;
+	}
+	ret=client.send(buffer, bufferLength);
+	myClock_t timestamp=(myClock_t)virtualClock->getNow();
+	if(ret<0){
+	//if there was an error while sending, don't retry
+		return -1;
+	}
+	return timestamp; //get the accurate time *after* you sent the sync clockSync
+}
+/** 
+ * receives a clockSync without blocking, checks results and returns the timestamp
+ * immediately after the clockSync has been received, or -1 if there was an error 
+ * or 0 if timeout expired.
+*/
+myClock_t ClockSync::receive(){
+	int ret;
+	ret=server.waitUntilReady(true, 0);
+	if(ret<=0){ //don't retry
+		return 0;
+	}
+	ret=server.read(buffer, bufferLength, false);
+	myClock_t timestamp=(myClock_t)virtualClock->getNow();
+	if(timestamp==0){
+		//printf("The virtualClock period is <=0\n");
+		return -3;
+	}
+	if(ret==-1){
+		//if there was an error while receiving, don't retry
+		return -1;
+	}
+	if(ret!=bufferLength){
+		//printf("Received a clockSync of the wrong size: %d\n", ret);
+		return -2;
+	}
+	//  print();
+	return timestamp; //get the accurate time *after* you sent the sync clockSync
+}
+
+int ClockSync::masterSendSync(){
+	//let's send a sync clockSync!
+	//printf("Sending a sync clockSync\n");
+	setType(kSync);
+	setTimestamp(-1);//do not care about sending the timestamp, a more accurate one will be sent in the follow up
+	localTimestamp=send();
+	if(localTimestamp<0){
+		//printf("Could not send sync clockSync\n");
+		return -1; //error, don't retry, start over
+	}
+	//let's send a followUp
+	//printf("sent a sync clockSync\n");
+	setType(kFollowUp);
+	setTimestamp(localTimestamp);
+	if(localTimestamp<0){
+		//printf("Could not send followup clockSync\n");
+		return -2; //error, don't retry, start over
+	}
+	int ret=send();
+	if(ret<0){
+		//printf("Error while sending followup\n");
+		return -3;
+	}
+	//printf("sent a followUp clockSync\n");
+	expectedClockSyncType=kDelayReq;
+	return 1;
+}
+#ifdef USE_JUCE
+#define NOTGSHOULDSTOP 1
+#else
+extern bool gShouldStop;
+#define NOTGSHOULDSTOP (!gShouldStop)
+#endif /* USE_JUCE */
+int ClockSync::receiveLoop(){
+	int receiveLoopElapsed=0;
+	while( NOTGSHOULDSTOP && (isSlave() || (receiveLoopElapsed<receiveLoopTimeout))){ //when slave, does not timeout!
+		receiveLoopElapsed+=receiveLoopSleepUs;
+		usleep(receiveLoopSleepUs); //how often to check for new clockSyncs;
+		//   //printf("waiting for clockSyncs\n");
+		localTimestamp=receive();
+		if(localTimestamp<=0){
+			if(localTimestamp==0){
+				//  //printf("Socket not ready to be read: %lld\n", localTimestamp);
+			}
+			else if(localTimestamp==-1){
+				//printf("Error while receiving: %lld\n", localTimestamp);
+			}
+			else if(localTimestamp==-2){
+				//  //printf("Wrong size of the received clockSync: %lld\n", localTimestamp);
+			}
+			continue ; //keep waiting
+		}
+		clockSyncType=getType();
+		clockSyncTimestamp=getTimestamp();
+		if(clockSyncType!=expectedClockSyncType){
+			//printf("Wrong clockSync type: %d, expected: %d\n",clockSyncType, expectedClockSyncType);
+			return -2; //start over
+		}
+		//printf("Received clockSync type: %d, clockSyncTimestamp: %lld\n", clockSyncType, clockSyncTimestamp);
+		if(isSlave()==true){
+			int ret=slaveHandleMessage();
+			if(ret==1 && clockSyncType==kDelayResp){ //we are done, end of a cycle!
+				return 1;
+			} else if (ret!=1) {
+				return -1; //
+			} else {
+				continue;
+			}
+		}
+		if(isMaster()==true){ //this is master
+			int ret=masterHandleMessage();
+			if(ret==1 && clockSyncType==kDelayReq){ //we are done, end of a cycle!
+				return 1;
+			} else {
+				return -2; //we are done but something was wrong
+			}
+		}
+	}
+	//printf("Receive loop timeout\n");
+	return -1;
+}
+
+int ClockSync::slaveHandleMessage(){
+	switch(clockSyncType){
+		case kSync: //the clockSync timestamp is meaningless, the localTimestamp is when kSync was received
+			T1p=localTimestamp;
+			expectedClockSyncType=kFollowUp;
+			break;
+		case kFollowUp: //the clockSyncTimestamp is the time when kSync was sent, the localTimestamp is meaningless
+			T1=clockSyncTimestamp;
+			//send delayReq
+			setType(kDelayReq);
+			setTimestamp(-1);
+			T2=send();
+			if(T2<0){
+				//printf("Error while sending delayReq\n");
+				return -1;
+			}
+			expectedClockSyncType=kDelayResp;
+			break;
+		case kDelayResp: {//the clockSyncTimestamp is the instant when the master received the kDelayResp clockSync, the localTimestamp is meaningless
+			T2p=clockSyncTimestamp;
+			//TODO: evaluate things
+			double offset=(T1p-T1-T2p+T2)/2.0d;
+			printf("-----------OFFSET IS : %04.1f, average: %04.2f\n", offset, movingAverage.add(offset));
+			expectedClockSyncType=kSync; //end of the cycle, wait for next sync.
+			break;
+		}
+		default:
+			//printf("Unexpected message type\n"); // we should never get here
+			return -1;
+	}
+	return 1;
+}
+
+int ClockSync::masterHandleMessage(){
+	switch(clockSyncType){
+		case kDelayReq:
+			//TODO: do something with it
+			//send kDelayResp
+			setType(kDelayResp);
+			setTimestamp(localTimestamp);
+			send();
+			expectedClockSyncType=kNone;
+		break;
+	}
+}
+
+int ClockSync::sendReceiveLoop(){
+	if(isSlave()==true){
+		 //printf("Waiting for a sync clockSync\n");
+	} else { //if this is master
+		usleep(100000); //this times (roughly) how often sync clockSyncs are being sent.
+		int ret=masterSendSync();
+		if(ret<=0)
+			return -1;
+	}
+	int ret=receiveLoop();
+	if(ret<=0)
+		return -2;
+	return 1;
+}
+
+
diff -r 04b1678614c9 -r e77e2e712fbc core/ClockSyncThread.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/ClockSyncThread.cpp	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,67 @@
+#include "ClockSyncThread.h"
+#ifdef USE_JUCE
+#else //declare static members TODO: rather refactor this similar to other threads so that only run and clockSyncTask are static
+	myClock_t ClockSyncThread::lastTime; // Used for clock synchronization
+	bool ClockSyncThread::listening;
+	ClockSync ClockSyncThread::clockSync;
+	VirtualClock* ClockSyncThread::virtualClock;
+	bool ClockSyncThread::threadIsExiting;
+	AuxiliaryTask ClockSyncThread::clockSyncTask;
+#endif
+#ifdef USE_JUCE
+ClockSyncThread::ClockSyncThread(const String &threadName) :
+			Thread(threadName)
+#else
+ClockSyncThread::ClockSyncThread()
+#endif /* USE_JUCE */
+{
+};
+ClockSyncThread::~ClockSyncThread(){
+#ifdef USE_JUCE
+	stopThread(1000);
+#else
+	stopThread();
+#endif /* USE_JUCE */
+}
+void ClockSyncThread::init(bool isSlave, int aPort, VirtualClock &aVirtualClock){
+	setVirtualClock(aVirtualClock);
+	listening=false;
+	clockSync.init(isSlave, aPort, *virtualClock);
+#ifdef USE_JUCE
+	startThread(5);
+#else
+	threadIsExiting=false;
+	clockSyncTask=BeagleRT_createAuxiliaryTask(&ClockSyncThread::run,98, "clockSyncTask");
+	//TODO: the thread cannot be started here at the moment because init() is called in setup(), where tasks cannot be scheduled
+#endif /* USE_JUCE */
+}
+
+#ifdef USE_JUCE
+#else
+void ClockSyncThread::startThread(){
+	printf("starting\n");
+	BeagleRT_scheduleAuxiliaryTask(clockSyncTask);
+	printf("started\n");
+}
+void ClockSyncThread::stopThread(){
+	threadIsExiting=true;
+}
+bool ClockSyncThread::threadShouldExit(){
+	return(gShouldStop || threadIsExiting );
+}
+#endif /* USE_JUCE */
+
+void ClockSyncThread::setVirtualClock(VirtualClock &aVirtualClock){
+	virtualClock=&aVirtualClock;
+};
+
+void ClockSyncThread::run(){
+	while(!threadShouldExit()){
+		clockSync.sendReceiveLoop();
+		usleep(5000);
+//		double now=virtualClock->getNow();
+//		printf("th(end+1)=%f;\n", now/44100.0f);
+//		printf("act(end+1)=%lld;\n", Clock::getTimeUs());
+	}
+	printf("Thread is not running \n");
+}
diff -r 04b1678614c9 -r e77e2e712fbc core/ReceiveAudioThread.cpp
--- a/core/ReceiveAudioThread.cpp	Thu Aug 27 03:33:32 2015 +0100
+++ b/core/ReceiveAudioThread.cpp	Sat Sep 12 20:05:55 2015 +0100
@@ -203,7 +203,7 @@
     if(isListening()==false)
         return -1;
     static int numCalls=0;
-    if(writePointer<0 || (numCalls&16383)==0){ //if writePointer has not been initalized yet ...
+    if(writePointer<0 /*|| (numCalls&16383)==0*/){ //if writePointer has not been initalized yet ...
 #ifdef USE_JUCE
 #else //debug
     	rt_printf("reinit the writePointer, readPointer: %f;\n",readPointer);
diff -r 04b1678614c9 -r e77e2e712fbc core/UdpClient.cpp
--- a/core/UdpClient.cpp	Thu Aug 27 03:33:32 2015 +0100
+++ b/core/UdpClient.cpp	Sat Sep 12 20:05:55 2015 +0100
@@ -1,62 +1,77 @@
-/*
- * udpClient.cpp
- *
- *  Created on: 19 May 2015
- *      Author: giulio moro
- */
-#include "../include/UdpClient.h"
-
-	UdpClient::UdpClient(){
-		outSocket=socket(AF_INET, SOCK_DGRAM, 0);
-		isSetPort=false;
-		isSetServer=false;
-		enabled=false;
-	}
-	UdpClient::UdpClient(int aPort, const char* aServerName){
-		outSocket=socket(AF_INET, SOCK_DGRAM, 0);
-		if(outSocket<0){
-			enabled=false;
-			return;
-		}
-		setPort(aPort);
-		setServer(aServerName);
-		isSetPort=true;
-		isSetServer=true;
-		enabled=true;
-	}
-	UdpClient::~UdpClient(){
-	   close(outSocket);
-	}
-	void UdpClient::setPort(int aPort){
-		port=aPort;
-		destinationServer.sin_port = htons(port);
-		destinationServer.sin_family = AF_INET;
-		isSetPort=true;
-		if(isSetServer){
-			enabled=true;
-		}
-	};
-	void UdpClient::setServer(const char* aServerName){
-		inet_pton(AF_INET,aServerName,&destinationServer.sin_addr);
-		isSetServer=true;
-		if(isSetPort){
-			enabled=true;
-		}
-	};
-	int UdpClient::send(void * message, int size){
-		if(!enabled)
-			return -1;
-		unsigned int length;
-		length=sizeof(struct sockaddr_in);
-		int n=sendto(outSocket,message,size,0,(const struct sockaddr *)&destinationServer,length);
-		if (n < 0){
-			return n;
-		}
-		return 1;
-	};
-	int UdpClient::write(const char* remoteHostname, int remotePortNumber, void* sourceBuffer, int numBytesToWrite){
-		setServer(remoteHostname);
-		setPort(remotePortNumber);
-		send(sourceBuffer, numBytesToWrite);
-	}
-
+/*
+ * udpClient.cpp
+ *
+ *  Created on: 19 May 2015
+ *      Author: giulio moro
+ */
+#include "UdpClient.h"
+
+	UdpClient::UdpClient(){
+		outSocket=socket(AF_INET, SOCK_DGRAM, 0);
+		isSetPort=false;
+		isSetServer=false;
+		enabled=false;
+	}
+	UdpClient::UdpClient(int aPort, const char* aServerName){
+		outSocket=socket(AF_INET, SOCK_DGRAM, 0);
+		if(outSocket<0){
+			enabled=false;
+			return;
+		}
+		setPort(aPort);
+		setServer(aServerName);
+		isSetPort=true;
+		isSetServer=true;
+		enabled=true;
+    memset(&stTimeOut, 0, sizeof(struct timeval));
+	}
+	UdpClient::~UdpClient(){
+	   close(outSocket);
+	}
+	void UdpClient::setPort(int aPort){
+		port=aPort;
+		destinationServer.sin_port = htons(port);
+		destinationServer.sin_family = AF_INET;
+		isSetPort=true;
+		if(isSetServer){
+			enabled=true;
+		}
+	};
+	void UdpClient::setServer(const char* aServerName){
+		inet_pton(AF_INET,aServerName,&destinationServer.sin_addr);
+		isSetServer=true;
+		if(isSetPort){
+			enabled=true;
+		}
+	};
+	int UdpClient::send(void * message, int size){
+		if(!enabled)
+			return -1;
+		unsigned int length;
+		length=sizeof(struct sockaddr_in);
+		int n=sendto(outSocket,message,size,0,(const struct sockaddr *)&destinationServer,length);
+		if (n < 0){
+			return n;
+		}
+		return 1;
+	};
+	int UdpClient::write(const char* remoteHostname, int remotePortNumber, void* sourceBuffer, int numBytesToWrite){
+		setServer(remoteHostname);
+		setPort(remotePortNumber);
+		send(sourceBuffer, numBytesToWrite);
+	}
+  int UdpClient::waitUntilReady(bool readyForReading, int timeoutMsecs){
+//	If the socket is ready on return, this returns 1. If it times-out before the socket becomes ready, it returns 0. If an error occurs, it returns -1.
+    if(enabled==false)
+		return -1;
+    if(timeoutMsecs<0)
+		return select(outSocket+1, NULL, &stWriteFDS, NULL, NULL); //calling this with a NULL timeout will block indefinitely
+    FD_ZERO(&stWriteFDS);
+    FD_SET(outSocket, &stWriteFDS);
+	float timeOutSecs=timeoutMsecs*0.001;
+	stTimeOut.tv_sec=(int)timeOutSecs;
+	timeOutSecs-=(int)timeOutSecs;
+	stTimeOut.tv_usec=(int)(timeOutSecs*1000000);
+    int descriptorReady= select(outSocket+1, NULL, &stWriteFDS, NULL, &stTimeOut);
+    return descriptorReady>0? 1 : descriptorReady;
+  }
\ No newline at end of file
diff -r 04b1678614c9 -r e77e2e712fbc core/UdpServer.cpp
--- a/core/UdpServer.cpp	Thu Aug 27 03:33:32 2015 +0100
+++ b/core/UdpServer.cpp	Sat Sep 12 20:05:55 2015 +0100
@@ -4,7 +4,7 @@
  *  Created on: 19 May 2015
  *      Author: giulio moro
  */
-#include "../include/UdpServer.h"
+#include "UdpServer.h"
 
 UdpServer::UdpServer(int aPort){
 	init(aPort);
@@ -29,6 +29,7 @@
 	enabled=bindToPort(aPort);
 	wasteBufferSize=2048;
 	wasteBuffer=malloc(wasteBufferSize);
+  memset(&stTimeOut,0,sizeof(struct timeval));
 	return enabled;
 }
 
diff -r 04b1678614c9 -r e77e2e712fbc core/VirtualClock.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/VirtualClock.cpp	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,40 @@
+#include "VirtualClock.h"
+void VirtualClock::init(){
+	firstRun=true;
+	movingAverage.setLength(31); //TODO: a better filtering algorithm ( Did you say Kalman?)
+	period=-1;
+}
+	
+VirtualClock::VirtualClock(){
+	init();
+}
+void VirtualClock::sync(){
+	sync(1);
+}
+void VirtualClock::sync(double count){
+	myClock_t currentTime=Clock::getTimeUs();
+	if(firstRun==true){
+		firstRun=false;
+		startTime=currentTime;
+	} else {
+		period=movingAverage.add((currentTime-lastSync)/count); //TODO: replace with Kalman filter
+	}
+	lastSync=currentTime;
+}
+
+double VirtualClock::getNow(){
+	myClock_t now=Clock::getTimeUs();
+	if(period<=0){
+		return now;
+	}
+	//  double beginningOfPeriod=lastSync; // TODO: if sync() does not get called every time (but e.g. only every so often),
+													 // then this line (and the class) needs editing
+	myClock_t elapsed=(now-startTime);
+	double frac=elapsed/(double)period;
+	//  printf("now=%lld; beginningOfPeriod=%f; lastSync=%lld; period=%lld; frac=%f\n", now, beginningOfPeriod, lastSync, period, frac);
+	return frac;
+}
+
+double VirtualClock::getPeriod(){
+	return period;
+}
diff -r 04b1678614c9 -r e77e2e712fbc include/Clock.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/Clock.h	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,12 @@
+#ifndef CLOCK_H_INCLUDED
+#define CLOCK_H_INCLUDED
+#include <sys/time.h>
+#include <stdio.h>
+
+typedef long long int myClock_t;
+
+namespace Clock
+{
+  myClock_t getTimeUs();
+}
+#endif /* CLOCK_H_INCLUDED */
\ No newline at end of file
diff -r 04b1678614c9 -r e77e2e712fbc include/ClockSync.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/ClockSync.h	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,81 @@
+#ifndef CLOCK_SYNC_H_INCLUDED
+#define CLOCK_SYNC_H_INCLUDED
+#include "stats.hpp"
+#include "UdpServer.h"
+#include "UdpClient.h"
+#include "Clock.h"
+#include "VirtualClock.h"
+
+enum ptpMessageConsts{
+	kSyncMessageLength=sizeof(myClock_t)+sizeof(int)
+};
+enum ptpMessageType{
+	kSync=0,
+	kFollowUp=1,
+	kDelayReq=2,
+	kDelayResp=3,
+	kNone=4
+};
+
+enum ptpStatus{
+	kSyncSent,
+	kFollowUpSent,
+	kDelayReqSent,
+	kDelayRespSent
+};
+
+class ClockSync{
+private:
+	MovingAverage<double> movingAverage;
+	UdpServer server;
+	UdpClient client;
+	bool slave;
+	int bufferLength;
+	int clockSyncType;
+	int expectedClockSyncType;
+	myClock_t clockSyncTimestamp;
+	myClock_t localTimestamp;
+	myClock_t T1;
+	myClock_t T1p;
+	myClock_t T2;
+	myClock_t T2p;
+	int receiveLoopSleepUs;
+	int receiveLoopTimeout;
+	char buffer[kSyncMessageLength];
+	VirtualClock *virtualClock;
+public:
+	ClockSync(){};
+	ClockSync(bool thisIsSlave, int aPort, VirtualClock &aVirtualClock);
+	void init(bool thisIsSlave, int aPort, VirtualClock &aVirtualClock);
+	void* getBuffer();
+	bool isSlave();
+	bool isMaster();
+	int getType();
+	myClock_t getTimestamp();
+	void setVirtualClock(VirtualClock &aVirtualClock);
+	void setPort(int aPort);
+	void setType(int clockSyncType);
+	void setTimestamp(myClock_t timestamp);
+	void print();
+	/** 
+	 * sends a clockSync without blocking, checks results and returns the timestamp
+	 * immediately after the clockSync has been sent or -1 if there was an error or timeout expired.
+	*/
+	myClock_t send();
+	/** 
+	 * receives a clockSync without blocking, checks results and returns the timestamp
+	 * immediately after the clockSync has been received, or -1 if there was an error 
+	 * or 0 if timeout expired.
+	*/
+	myClock_t receive();
+	int masterSendSync();
+	int receiveLoop();
+	int slaveHandleMessage();
+	int masterHandleMessage();
+	int sendReceiveLoop();
+	operator void*(){
+	return getBuffer();
+	}
+};
+
+#endif /* CLOCK_SYNC_H_INCLUDED */
\ No newline at end of file
diff -r 04b1678614c9 -r e77e2e712fbc include/ClockSyncThread.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/ClockSyncThread.h	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,48 @@
+#ifndef CLOCK_SYNC_THREAD_H_INCLUDED
+#define CLOCK_SYNC_THREAD_H_INCLUDED
+
+#ifdef USE_JUCE
+#include <JuceHeader.h>
+#define IS_STATIC
+#else
+#define IS_STATIC static
+#include <BeagleRT.h>
+#endif /*USE_JUCE*/
+
+#include "ClockSync.h"
+
+#ifdef USE_JUCE
+class ClockSyncThread : public Thread {
+#else
+class ClockSyncThread {
+#endif /* USE_JUCE */
+private:
+	IS_STATIC myClock_t lastTime; // Used for clock synchronization
+	IS_STATIC bool listening;
+	IS_STATIC ClockSync clockSync;
+	IS_STATIC VirtualClock *virtualClock;
+#ifdef USE_JUCE
+#else
+	IS_STATIC bool threadIsExiting;
+	IS_STATIC AuxiliaryTask clockSyncTask;
+#endif /* USE_JUCE */
+
+public:
+#ifdef USE_JUCE
+    ClockSyncThread(const String &threadName);
+#else
+    ClockSyncThread();
+#endif /* USE_JUCE */
+    ~ClockSyncThread();
+    IS_STATIC void init(bool isSlave, int aPort, VirtualClock &aVirtualClock);
+    IS_STATIC void setVirtualClock(VirtualClock &aVirtualClock);
+
+    IS_STATIC void run();
+#ifdef USE_JUCE
+#else
+    IS_STATIC void startThread();
+    IS_STATIC void stopThread();
+    IS_STATIC bool threadShouldExit();
+#endif // USE_JUCE
+};
+#endif  // CLOCK_SYNC_THREAD_H_INCLUDED
diff -r 04b1678614c9 -r e77e2e712fbc include/UdpClient.h
--- a/include/UdpClient.h	Thu Aug 27 03:33:32 2015 +0100
+++ b/include/UdpClient.h	Sat Sep 12 20:05:55 2015 +0100
@@ -23,6 +23,8 @@
 		int port;
 		int enabled;
 		int outSocket;
+    struct timeval stTimeOut;
+    fd_set stWriteFDS;
 		bool isSetPort;
 		bool isSetServer;
 		struct sockaddr_in destinationServer;
@@ -34,6 +36,7 @@
 		void setServer(const char* aServerName);
 		int send(void* message, int size);
 		int write(const char* remoteHostname, int remotePortNumber, void* sourceBuffer, int numBytesToWrite);
+    int waitUntilReady(bool readyForReading, int timeoutMsecs);
 };
 
 
diff -r 04b1678614c9 -r e77e2e712fbc include/VirtualClock.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/VirtualClock.h	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,39 @@
+#ifndef VIRTUAL_CLOCK_H_INCLUDED
+#define VIRTUAL_CLOCK_H_INCLUDED
+
+#include "stats.hpp"
+#include "Clock.h"
+
+class VirtualClock{
+private:
+	myClock_t startTime;
+	myClock_t lastSync;
+	bool firstRun;
+	double period;
+	MovingAverage<double> movingAverage;
+public:
+	void init();
+	VirtualClock();
+/**
+	Call this method at regular intervals to sync che virtual clock
+*/
+	void sync();
+/**
+	Call this method asynchronously, passing a number of equally spaced events that have elapsed since the last call.
+*/
+	void sync(double count);
+/**
+	Get the current time according to the VirtualClock.
+	
+	@return Time elapsed since the first call to sync(), in period units. 
+*/
+	double getNow();
+/** 
+	Get the length of the period.
+	
+	Get the length of the period (difference between calls to sync() after various filtering operations)
+*/
+	double getPeriod();
+};
+
+#endif /* VIRTUAL_CLOCK_H_INCLUDED */
diff -r 04b1678614c9 -r e77e2e712fbc include/stats.hpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/stats.hpp	Sat Sep 12 20:05:55 2015 +0100
@@ -0,0 +1,64 @@
+#ifndef STATS_HPP_INCLUDED
+#define STATS_HPP_INCLUDED
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+
+template<class TYPE> 
+class MovingAverage{
+private:
+  TYPE* array;
+  int length;
+  int pointer;
+  TYPE sum;
+  double scale;
+  double average;
+  void dealloc(){
+    free(array);
+    //  delete array;
+  }
+   
+  void init(int aLength){
+    length=aLength;
+    scale=1.0/length;
+    //  array= new TYPE(length); // for some reason this causes memory corruption, so I am using malloc() instead...
+    array=(TYPE*)malloc(sizeof(TYPE)*length);
+    sum=0;
+    if(array==NULL)
+      printf("Error while allocating array\n");
+    memset(array, 0, sizeof(TYPE)*length);
+    pointer=0;
+  }
+public:
+  MovingAverage(){
+    init(0);
+  }
+  MovingAverage(int aLength){
+    init(aLength);
+  }
+  ~MovingAverage(){
+    dealloc();
+  }
+  int getLength(){
+    return length;
+  }
+  void setLength(int aLength){
+    dealloc();
+    init(aLength);
+  }
+  double add(TYPE newElement){
+    sum-=array[pointer];
+    array[pointer]=newElement;
+    sum+=newElement;
+    average=sum*scale;
+    pointer++;
+    if(pointer==length)
+      pointer=0;
+    return average;
+  }
+  double getAverage(){
+    return average;
+  }
+};
+
+#endif /* STATS_HPP_INCLUDED */
\ No newline at end of file
diff -r 04b1678614c9 -r e77e2e712fbc projects/scope/render.cpp
--- a/projects/scope/render.cpp	Thu Aug 27 03:33:32 2015 +0100
+++ b/projects/scope/render.cpp	Sat Sep 12 20:05:55 2015 +0100
@@ -3,13 +3,14 @@
 #include <ReceiveAudioThread.h>
 #include <ClockSynchronizer.h>
 #include <cmath>
+#include <ClockSyncThread.h>
 
 float gPhase1, gPhase2;
 float gFrequency1, gFrequency2;
 float gInverseSampleRate;
 
 //Scope scope(2);   //create a scope object with 2 channels
-NetworkSend networkSend;
+//NetworkSend networkSend;
 
 // initialise_render() is called once before the audio rendering starts.
 // Use it to perform any initialisation and allocation which is dependent
@@ -19,20 +20,24 @@
 // in from the call to initAudio().
 //
 // Return true on success; returning false halts the program.
-ReceiveAudioThread receiveAudio0;
+//ReceiveAudioThread receiveAudio0;
 //ReceiveAudioThread receiveAudio1;
 ClockSynchronizer clockSynchronizer;
 extern I2c_Codec* gAudioCodec;
+VirtualClock virtualClock;
+ClockSyncThread clockSyncThread;
 bool setup(BeagleRTContext *context, void *userData)
 {
-	receiveAudio0.init(10000, context->audioFrames, 0);
+//	receiveAudio0.init(10000, context->audioFrames, 0);
 //	receiveAudio1.init(10000, context->audioFrames, 1);
 
 //	scope.setup();  //call this once in setup to initialise the scope
 //	scope.setPort(0, 9999);
 //	scope.setPort(1, 10000);
-	networkSend.setup(context->audioSampleRate, context->audioFrames, 0, 9999, "192.168.7.1");
+//	networkSend.setup(context->audioSampleRate, context->audioFrames, 0, 9999, "192.168.7.1");
 	clockSynchronizer.setup();
+	virtualClock.init();
+	clockSyncThread.init(true, 5000, virtualClock); //start as slave
 	gInverseSampleRate = 1.0/context->audioSampleRate;
 	
 	gPhase1 = 0.0;
@@ -51,10 +56,26 @@
 
 void render(BeagleRTContext *context, void *userData)
 {
+	virtualClock.sync(context->audioFrames);
 	static int count=0;
+	if(count==0)
+		clockSyncThread.startThread();
+	static float phase=0;
+	float phaseInc=200.0/44100.0*2*M_PI;
+//	rt_printf("phaseInc: %f, phase: %f\n",phaseInc,phase);
+	for(unsigned int n=0; n<context->audioFrames; n++){
+		context->audioOut[n*2]=sinf(phaseInc);//context->audioIn[n*2];
+		context->audioOut[n*2+1]=sinf(phaseInc);//context->audioIn[n*2];
+		phase+=200.0/44100.0*2*M_PI;
+		if(phase>=2*M_PI)
+			phase-=2*M_PI;
+//		context->audioOut[n*2+1]=rand()/(float)RAND_MAX;context->audioIn[n*2];
+	}
+	count++;
+	/*
 //	if((count&262143)==0){
 //	static int nextCall=160000;
-	if( ((count&(2047-1))==0 /*&& count>200000*/)){
+	if( ((count&(2047))==0)){
 //		rt_printf("b %d\n", count);
 		clockSynchronizer.update(networkSend.getTimestamp(), receiveAudio0.getTimestamp(), receiveAudio0.getLastTime());
 //		nextCall=count+100000;
@@ -64,7 +85,7 @@
 //		clockSynchronizer.update(networkSend.getTimestamp(), receiveAudio0.getTimestamp(), receiveAudio0.getLastTime());
 //	}
 	if(count==0){
-		gAudioCodec->setAudioSamplingRate( 44101);
+		gAudioCodec->setAudioSamplingRate( 44100);
 		rt_printf("startHread\n");
 		ReceiveAudioThread::startThread();
 	}
@@ -100,12 +121,15 @@
 			gPhase1 -= 2.0 * M_PI;
 		if(gPhase2 > 2.0 * M_PI)
 			gPhase2 -= 2.0 * M_PI;
+		int value=count%1000;
+		context->audioOut[n*2]=value>=500 ? 1 : -1;
+		context->audioOut[n*2+1]=context->audioOut[n*2];
 		count++;
 	}
 	if(count>0){
 		float samplingRateRatio=1;
 		int channelsInDestinationBuffer=2;
-		int channelToWriteTo=0;
+		int channelToWriteTo=1;
 		int length=receiveAudio0.getSamplesSrc(context->audioOut, context->audioFrames,
 				samplingRateRatio, channelsInDestinationBuffer, channelToWriteTo);
 		if((unsigned int)length!=context->audioFrames){
@@ -114,8 +138,10 @@
 //		int readPointer1=receiveAudio1.getSamplesSrc(context->audioOut, context->audioFrames, 1, 2, 1);
 	}
 	for(unsigned int n=0; n<context->audioFrames; n++){
-		context->audioOut[n*2+1]=context->audioOut[n*2];
+//		context->audioOut[n*2+1]=context->audioOut[n*2];
 	}
+	*/
+
 }
 
 // cleanup_render() is called once at the end, after the audio has stopped.