Mercurial > hg > beaglert

--- a/.cproject	Mon Sep 14 17:31:24 2015 +0100
+++ b/.cproject	Mon Sep 14 17:35:18 2015 +0100
@@ -14,11 +14,11 @@
 				</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.debug,org.eclipse.cdt.build.core.buildArtefactType=org.eclipse.cdt.build.core.buildArtefactType.exe" cleanCommand="rm -rf" description="" id="cdt.managedbuild.config.gnu.exe.debug.528876549" name="Debug" parent="cdt.managedbuild.config.gnu.exe.debug" postannouncebuildStep="Kills the process running on the BeagleBone (if any) and copies the new binary to the BeagleBone in beaglert/" postbuildStep="ssh root@192.168.7.2 &quot;kill -s 2 \`pidof ${BuildArtifactFileName}\` 2&gt;/dev/null; sleep 0.5; scp host:${PWD}/${BuildArtifactFileName} ~/beaglert/ &amp;&amp; echo 'done copying\n' | wall || echo 'error'|wall&quot;">
+				<configuration artifactName="${ProjName}" buildArtefactType="org.eclipse.cdt.build.core.buildArtefactType.exe" buildProperties="org.eclipse.cdt.build.core.buildType=org.eclipse.cdt.build.core.buildType.debug,org.eclipse.cdt.build.core.buildArtefactType=org.eclipse.cdt.build.core.buildArtefactType.exe" cleanCommand="rm -rf" description="" id="cdt.managedbuild.config.gnu.exe.debug.528876549" name="Debug" parent="cdt.managedbuild.config.gnu.exe.debug" postannouncebuildStep="Kills the process running on the BeagleBone (if any) and copies the new binary to the BeagleBone in beaglert/" postbuildStep="ssh root@192.168.7.2 &quot;kill -s 9 \`pidof ${BuildArtifactFileName}\` 2&gt;/dev/null; sleep 0.5; scp host:${PWD}/${BuildArtifactFileName} ~/beaglert/ &amp;&amp; echo 'done copying\n' | wall || echo 'error'|wall&quot;">
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 							<targetPlatform id="cdt.managedbuild.target.gnu.platform.exe.debug.295375065" name="Debug Platform" superClass="cdt.managedbuild.target.gnu.platform.exe.debug"/>
-							<builder buildPath="${workspace_loc:/BBB_audio+input/Debug}" id="cdt.managedbuild.target.gnu.builder.exe.debug.26322421" keepEnvironmentInBuildfile="false" managedBuildOn="true" name="Gnu Make Builder" superClass="cdt.managedbuild.target.gnu.builder.exe.debug">
+							<builder arguments="-j6" buildPath="${workspace_loc:/BBB_audio+input/Debug}" command="make" id="cdt.managedbuild.target.gnu.builder.exe.debug.26322421" keepEnvironmentInBuildfile="false" managedBuildOn="true" name="Gnu Make Builder" superClass="cdt.managedbuild.target.gnu.builder.exe.debug">
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 									<entry flags="VALUE_WORKSPACE_PATH|RESOLVED" kind="outputPath" name="Release"/>
@@ -31,8 +31,6 @@
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 									<listOptionValue builtIn="false" value="/usr/xenomai/include"/>
 									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/include/xenomai/include"/>
-									<listOptionValue builtIn="false" value="/import/teaching/ECS732/arm-gcc/arm-linux-gnueabihf/include"/>
-									<listOptionValue builtIn="false" value="/import/teaching/ECS732/arm-gcc/arm-linux-gnueabihf/include/xenomai/include"/>
 									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/include/ne10"/>
 									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/BeagleRT/include}&quot;"/>
 								</option>
@@ -47,10 +45,8 @@
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 									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/include/xenomai/include"/>
-									<listOptionValue builtIn="false" value="/import/teaching/ECS732/arm-gcc/arm-linux-gnueabihf/include"/>
-									<listOptionValue builtIn="false" value="/import/teaching/ECS732/arm-gcc/arm-linux-gnueabihf/include/xenomai/include"/>
 									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/include/ne10"/>
-									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/BeagleRT/include}&quot;"/>
+									<listOptionValue builtIn="false" value="/BeagleRT/include"/>
 								</option>
 								<option id="gnu.c.compiler.option.misc.other.835792865" name="Other flags" superClass="gnu.c.compiler.option.misc.other" value="-c -fmessage-length=0 -Wpointer-arith -Wunused-result  -D_GNU_SOURCE -D_REENTRANT -D__XENO__ -std=gnu99" valueType="string"/>
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@@ -61,9 +57,10 @@
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 									<listOptionValue builtIn="false" value="/usr/local/linaro/arm-linux-gnueabihf/include/xenomai/lib"/>
-									<listOptionValue builtIn="false" value="/import/teaching/ECS732/arm-gcc/arm-linux-gnueabihf/lib"/>
 									<listOptionValue builtIn="false" value="/usr/lib/arm-linux-gnueabihf"/>
-									<listOptionValue builtIn="false" value="/import/teaching/ECS732/arm-gcc/arm-linux-gnueabihf/lib/xenomai"/>
+									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/lib"/>
+									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/lib/xenomai"/>
+									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/include/xenomai/lib"/>
 								</option>
 								<option id="gnu.cpp.link.option.libs.139390951" name="Libraries (-l)" superClass="gnu.cpp.link.option.libs" valueType="libs">
 									<listOptionValue builtIn="false" value="rt"/>
@@ -82,10 +79,6 @@
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 							<tool command="arm-linux-gnueabihf-as" id="cdt.managedbuild.tool.gnu.assembler.exe.debug.37270610" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.exe.debug">
 								<option id="gnu.both.asm.option.include.paths.1403814918" name="Include paths (-I)" superClass="gnu.both.asm.option.include.paths" valueType="includePath">
-									<listOptionValue builtIn="false" value="/import/teaching/ECS732/arm-gcc/arm-linux-gnueabihf/include/xenomai/include"/>
-									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/include/xenomai/include"/>
-									<listOptionValue builtIn="false" value="/import/teaching/ECS732/arm-gcc/arm-linux-gnueabihf/include"/>
-									<listOptionValue builtIn="false" value="/usr/arm-linux-gnueabihf/include/ne10"/>
 									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/BeagleRT/include}&quot;"/>
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@@ -95,6 +88,7 @@
 					<sourceEntries>
 						<entry excluding="default_main.cpp|audio_routines_old.S" flags="VALUE_WORKSPACE_PATH|RESOLVED" kind="sourcePath" name="core"/>
 						<entry flags="VALUE_WORKSPACE_PATH|RESOLVED" kind="sourcePath" name="include"/>
+						<entry flags="VALUE_WORKSPACE_PATH" kind="sourcePath" name="projects/scope"/>
 						<entry flags="VALUE_WORKSPACE_PATH" kind="sourcePath" name="source"/>
 					</sourceEntries>
 				</configuration>
@@ -114,13 +108,13 @@
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+				<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">
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-							<builder buildPath="${workspace_loc:/BBB_audio+input/Release}" id="cdt.managedbuild.target.gnu.builder.exe.release.511190290" keepEnvironmentInBuildfile="false" managedBuildOn="true" name="Gnu Make Builder" superClass="cdt.managedbuild.target.gnu.builder.exe.release"/>
+							<builder arguments="-j6" buildPath="${workspace_loc:/BBB_audio+input/Release}" command="make" 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"/>
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+							<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">
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/Clock.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,24 @@
+#include "Clock.h"
+
+namespace Clock
+{
+#ifdef USE_JUCE
+	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;
+	}
+#else
+	myClock_t getTimeUs(){
+		return (myClock_t)((rt_timer_read()+500)/1000);
+	}
+#endif /* USE_JUCE */
+};
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/ClockSync.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,337 @@
+#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;
+	resetTs();
+	receiveLoopSleepUs=100;
+	receiveLoopTimeout=1e5;
+	movingAverage.setLength(31);
+	expectedClockSyncType=isSlave() ? kSync : kNone;
+}
+void ClockSync::resetTs(){
+	T1=-1;
+	T1p=-1;
+	T2=-1;
+	T2p=-1;
+}
+bool ClockSync::areTsValid(){
+	return T1>0 && T1p>0 && T2>0 && T2p>0;
+}
+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){
+//	printf("setting timestamp: %lld\n", 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
+			resetTs();
+			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;
+			if(areTsValid()){
+				processOffset(offset);
+
+				/*
+				static int calls=0;
+				static double referenceOffset=0;
+
+				if(calls<100){ // start by averaging everything
+					movingAverage.add(offset);
+				} else { //once we get an estimate, start discarding outliers
+					float maxOffsetDeviation=20;
+					float deviation=fabsf(movingAverage.getAverage()-offset);
+					if(deviation<maxOffsetDeviation){
+						movingAverage.add(offset);
+						printf("w(end+1)=%4.1f;\n", movingAverage.getAverage());
+					} else {
+//						printf("Out of range: %f \n", deviation);
+					}
+				}
+				printf("offset(end+1)=%f;\n", offset);
+				if (calls==100){
+//					printf("Update reference\n");
+					referenceOffset=movingAverage.getAverage();
+				} else 	if (calls==200){
+					calls=99;
+				}
+				calls++;
+*/
+
+//				printf("%lld, %lld, %lld, %lld \n", T1, T1p, T2, T2p);
+//				if(T2-T1p<0){
+//					printf("Negative: %lld, %lld, %lld, %lld \n", T1, T1p, T2, T2p);
+//				}
+			} else {
+				printf("InvalidTs:\n  %lld, %lld, %lld, %lld \n", T1, T1p, T2, T2p);
+			}
+			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;
+}
+#include <I2c_Codec.h>
+extern I2c_Codec* gAudioCodec;
+void ClockSync::processOffset(double offset){
+	static int calls=0;
+	// TODO: change the flow control below so that it can happen multiple times
+	//(base it upon the length of movingAverage rather than the number of calls)
+	if(calls<10) { //get an initial guess
+		movingAverage.add(offset);
+//		printf("-----------OFFSET IS : %04.4f samples, average: %04.4f samples\n",
+//				offset, movingAverage.getAverage());
+	} else if (calls==10){ //then compensate for initial offset
+//		printf("compensating for offset: %f\n", offset);
+		virtualClock->addOffset(movingAverage.getAverage());
+		movingAverage.reset();
+	} else if (calls>=10){ //use IIR filter from now on
+		//filter coefficients obtained from Matlab : [B,A]=butter(2,0.005);
+//		static float B[3]={6.10061787580662e-05, 0.000122012357516132, 6.10061787580662e-05};
+//		static float A[3]={1, -1.97778648377676, 0.978030508491796};
+		static float B[3]={6.10061787580662e-05, 0.000122012357516132, 6.10061787580662e-05};
+		static float A[3]={1, -1.97778648377676, 0.978030508491796};
+		static float pastOut[3]={0,0,0};
+		static float pastIn[3]={0,0,0};
+		float in=offset;
+		float out= -pastOut[1]*A[1] -pastOut[2]*A[2] +in*B[0] +pastIn[1]*B[1] +pastIn[2]*B[2];
+		pastOut[2]=pastOut[1];
+		pastOut[1]=out;
+		pastIn[2]=pastIn[1];
+		pastIn[1]=in;
+		offset=out;
+		static float maxOffset=0;
+		maxOffset=fabsf(offset) > fabsf(maxOffset) ? offset : maxOffset;
+		printf("%10.3f, %10.3f, %10.3f, %10.3f\n", in, offset, offset-pastOut[2], maxOffset); //unfiltered, filtered
+		if(fabsf(offset)>10 && calls>30){
+			calls=11;
+			//TODO: correct for offset
+			float targetSamplingRate=offset>0 ? 44097 : 44103;
+			gAudioCodec->setAudioSamplingRate(targetSamplingRate);
+//			pastOut[1]=pastOut[2]=pastIn[1]=pastIn[2]=offset;
+			printf("------setAudioSmplingRate to %f\n", targetSamplingRate);
+		}
+	}
+	calls++;
+}
+int ClockSync::masterHandleMessage(){
+	switch(clockSyncType){
+		case kDelayReq:
+			//send kDelayResp
+			setType(kDelayResp);
+			setTimestamp(localTimestamp);
+			send();
+			expectedClockSyncType=kNone;
+			return 1;
+		break;
+		default:
+			return -1;
+	}
+}
+
+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;
+}
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/ClockSyncThread.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,66 @@
+#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,60, "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(){
+	BeagleRT_scheduleAuxiliaryTask(clockSyncTask);
+}
+void ClockSyncThread::stopThread(){
+	threadIsExiting=true;
+}
+bool ClockSyncThread::threadShouldExit(){
+	return(gShouldStop || threadIsExiting );
+}
+#endif /* USE_JUCE */
+
+void ClockSyncThread::setVirtualClock(VirtualClock &aVirtualClock){
+	virtualClock=&aVirtualClock;
+};
+
+void ClockSyncThread::run(){
+	printf("var=[");
+	while(!threadShouldExit()){
+		clockSync.sendReceiveLoop();
+//		double now=virtualClock->getNow();
+//		printf("th(end+1)=%f;\n", now);
+//		printf("act(end+1)=%lld;\n", Clock::getTimeUs());
+	}
+	printf("];\n");
+//	printf("Thread is not running \n");
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/ClockSynchronizer.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,136 @@
+/*
+ * ClockSynchronizer.cpp
+ *
+ *  Created on: 26 Aug 2015
+ *      Author: giulio
+ */
+
+#include "ClockSynchronizer.h"
+
+// declare static members
+float ClockSynchronizer::targetSamplingRate;
+float ClockSynchronizer::currentSamplingRate;
+bool ClockSynchronizer::threadRunning;
+int ClockSynchronizer::threadWasRunning;
+bool ClockSynchronizer::staticConstructed=false;
+AuxiliaryTask ClockSynchronizer::setClockTask;
+
+void ClockSynchronizer::staticConstructor(){
+	int priority=90;
+	setClockTask=BeagleRT_createAuxiliaryTask(&ClockSynchronizer::setClock, priority, "setClockTask");
+	threadRunning=false;
+}
+
+void ClockSynchronizer::setClock(){
+//	rt_printf("Setting clock to %f\n",targetSamplingRate);
+	threadRunning=true;
+//I2C magic
+	gAudioCodec->setAudioSamplingRate(targetSamplingRate);
+	threadRunning=false;
+	threadWasRunning=1;
+//	rt_printf("Exiting thread\n");
+};
+
+ClockSynchronizer::ClockSynchronizer() {
+	reset();
+}
+
+ClockSynchronizer::~ClockSynchronizer(){};
+
+void ClockSynchronizer::setup(){
+	if(staticConstructed==false) //This should be called in the constructor, but because of the current limitations of
+		// BeagleRT, it is here and setup() needs to be called in BeagleRT setup();
+		staticConstructor();
+}
+void ClockSynchronizer::reset(){
+	localCounter=0;
+	remoteCounter=0;
+	lastTime=0;
+	localOffset=-1;
+	remoteOffset=-1;
+	timeOffset=-1;
+	currentSamplingRate=44100;
+}
+
+void ClockSynchronizer::update(int aLocalCounter, int aRemoteCounter, RTIME aLastTime){
+	if(threadRunning==true){ //do nothing if clock is being adjusted
+		rt_printf("do nothing if clock is being adjusted\n");
+		return;
+	}
+	if(threadWasRunning > 0){ //reset variables after clock has been adjusted
+		threadWasRunning--;  // wait a few calls to make sure the clock stabilizes
+		rt_printf("wait a few calls to make sure the clock stabilizes\n");
+		return;
+	}/*
+	if(threadWasRunning==1){
+		threadWasRunning=0;
+		// reset offsets after a correction
+		localOffset=aLocalCounter;
+		remoteOffset=aRemoteCounter;
+		timeOffset=aLastTime;
+		rt_printf("reset variables after clock has been adjusted\n");
+		return;
+	}*/
+	if (localOffset<=0 || remoteOffset<=0){ // probably this is the first run
+		localOffset=aLocalCounter;
+		remoteOffset=aRemoteCounter;
+		timeOffset=aLastTime;
+		rt_printf("First run of update(), localOffset: %d, remoteOffset: %d, timeOffset: %llu\n",
+				localOffset, remoteOffset, timeOffset);
+		return;
+	}
+	localCounter=aLocalCounter-localOffset;
+	remoteCounter=aRemoteCounter-remoteOffset;
+	lastTime=aLastTime-timeOffset;
+	if (localCounter<=0 || remoteCounter<=0 || timeOffset<=0) {// did anything wrong happened?
+		rt_printf("fourth\n");
+		return;
+	}
+	// TODO: make sure we do not get actually adjust the clock too often (e.g.: limits on the timestamp)
+	// Should keep track of last time a change has been made, so that when a large compensation is needed
+	// (e.g.: as the program has just started), adjustClock() is called more frequently
+	// but gets called less often later.
+	// Should also try to avoid drastic correction after a while that the program
+	// has started, so to avoid glitches. But this can maybe be handled by the thread itself.
+	// TODO: should keep a log and maybe compensate for (and prevent) overshoot according to previous changes
+	static RTIME lastlastTime=0;
+//	rt_printf("interval: %f, \n",(double)(remoteCounter*300.0)/lastTime*1000000000.0);
+	lastlastTime=lastTime;
+	currentSamplingRate=gAudioCodec->getAudioSamplingRate();
+	float T=1/currentSamplingRate;
+	int elapsedSamples=remoteCounter*(NetworkBuffer::bufferLength-NetworkBuffer::headerLength);
+	double expectedTimeUs=T*elapsedSamples*1000000;
+	double actualTimeS=lastTime/1000000000.0;
+	double actualTimeUs=lastTime/1000.0;
+	static float averageBuffer[101]={0};
+	static int averageBufferPointer=0;
+	static float average=0;
+	static int bufferFull=0;
+	average-=averageBuffer[averageBufferPointer];
+	averageBuffer[averageBufferPointer]=elapsedSamples/actualTimeS;
+	average+=averageBuffer[averageBufferPointer];
+	averageBufferPointer++;
+	if(averageBufferPointer==101){
+		averageBufferPointer=0;
+		bufferFull++;
+	}
+
+//	rt_printf("Fs: %f, expectedTimeUs: %f, lastTime: %ul\n", expectedTimeUs, lastTime);
+//	rt_printf("Fs: %.1f, actualTimeS: %4.6f, targetFs_ %.3f\n",
+	if((averageBufferPointer&3)==0){
+		static float oldTargetSamplingRate=0;
+		targetSamplingRate=average/101;
+		if(bufferFull>=3 && fabsf(targetSamplingRate-oldTargetSamplingRate) < 1){
+			rt_printf("%.1f, %4.6f, %.3f;\n",
+				gAudioCodec->getAudioSamplingRate(),  actualTimeS, targetSamplingRate, targetSamplingRate-oldTargetSamplingRate);
+			adjustClock();
+		}
+		oldTargetSamplingRate=targetSamplingRate;
+	}
+}
+
+void ClockSynchronizer::adjustClock(){
+	if(fabsf(currentSamplingRate-targetSamplingRate)>0.7){ //TODO: actually check that the difference is less than the quantization error in the PLL
+		BeagleRT_scheduleAuxiliaryTask(setClockTask);
+	}
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/NetworkSend.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,294 @@
+#include "NetworkSend.h"
+
+#ifdef USE_JUCE
+#else
+//initialize the static members of NetworkSend
+bool NetworkSend::staticConstructed=false;
+int NetworkSend::sleepTimeMs;
+bool NetworkSend::threadIsExiting;
+bool NetworkSend::threadRunning;
+std::vector<NetworkSend*> NetworkSend::objAddrs(0);
+AuxiliaryTask NetworkSend::sendDataTask=NULL;
+
+void sendData(){
+	NetworkSend::run();
+}
+void NetworkSend::staticConstructor(){
+	if(staticConstructed==true)
+		return;
+	staticConstructed=true;
+	threadIsExiting=false;
+	threadRunning=false;
+	sendDataTask = BeagleRT_createAuxiliaryTask(::sendData, 95, "sendDataTask"); //TODO: allow variable priority
+}
+void NetworkSend::sendAllData(){
+	for(unsigned int n=0; n<NetworkSend::objAddrs.size(); n++){
+		NetworkSend::objAddrs[n]->sendData();
+	}
+}
+int NetworkSend::getNumInstances(){
+	return objAddrs.size();
+}
+void NetworkSend::startThread(){
+	BeagleRT_scheduleAuxiliaryTask(sendDataTask);
+}
+void NetworkSend::stopThread(){
+	threadIsExiting=true;
+}
+bool NetworkSend::threadShouldExit(){
+	return(gShouldStop || threadIsExiting);
+}
+bool NetworkSend::isThreadRunning(){
+	return threadRunning;
+}
+#endif /* USE_JUCE */
+
+#ifdef USE_JUCE
+NetworkSend::NetworkSend(const String &threadName):
+		Thread(threadName)
+#else
+NetworkSend::NetworkSend()
+#endif /* USE_JUCE */
+{
+	channel.buffers=NULL;
+	channel.doneOnTime=NULL;
+	channel.readyToBeSent=NULL;
+	channel.enabled=false;
+	sleepTimeMs=2; //This should actually be initialized in the staticConstructor for non-Juce code, but doing it here makes it more portable
+	channel.sampleCount=0;
+}
+
+NetworkSend::~NetworkSend(){
+#ifdef USE_JUCE
+	stopThread(1000);
+#else
+	stopThread();
+	for(unsigned int n=0; n<objAddrs.size(); n++){ //keep track of deleted instances;
+		if(objAddrs[n]==this){
+			objAddrs.erase(objAddrs.begin()+n);
+			break;
+		}
+	}
+#endif
+	dealloc();
+}
+void NetworkSend::dealloc(){
+	channel.enabled=false;
+	if(channel.buffers!=NULL){
+		for(int n=0; n<channel.numBuffers; n++){
+			free(channel.buffers[n]);
+			channel.buffers[n]=NULL;
+		}
+		free(channel.buffers);
+		channel.buffers=NULL;
+	}
+	free(channel.readyToBeSent);
+	channel.readyToBeSent=NULL;
+	free(channel.doneOnTime);
+	channel.doneOnTime=NULL;
+}
+void NetworkSend::cleanup(){
+	dealloc();
+}
+
+void NetworkSend::setup(float aSampleRate, int blockSize, int aChannelNumber, int aPort, const char *aServer){
+#ifdef USE_JUCE
+#else
+	staticConstructor(); //FIXME: ideally this should be in the constructor, but this is not currently possible
+						//because of limitations in BeagleRT_createAuxiliaryTask()
+	//keep track of added active instances
+	objAddrs.push_back(this);//TODO: this line should be in the constructor, but something weird happens if
+	// an instance of NetworkSend is then declared globally: the constructor gets called,
+	// and objAddrs.size()==1 but when you get to setup, objAddrs.size() has reverted back to 0, without
+	// any destructor being called in between ...
+#endif /* USE_JUCE */
+	cleanup();
+	int numSamples=blockSize*4>4*channel.bufferLength ? blockSize*4 : 4*channel.bufferLength;
+	channel.numBuffers= 1+numSamples/channel.bufferLength; //the +1 takes the ceil() of the division
+	channel.buffers=(float**)malloc(channel.numBuffers*sizeof(float*));
+	printf("NumBuffers: %d\n", channel.numBuffers);
+	if(channel.buffers==NULL)
+		return;
+	for(int n=0; n<channel.numBuffers; n++){
+		channel.buffers[n]=(float*)malloc(channel.bufferLength*sizeof(float));
+		if(channel.buffers[n]==NULL)
+			return;
+	}
+	channel.readyToBeSent=(bool*)malloc(channel.numBuffers*sizeof(bool));
+	channel.doneOnTime=(bool*)malloc(channel.numBuffers*sizeof(bool));
+	for(int n=0; n<channel.numBuffers; n++){
+		channel.readyToBeSent[n]=false;
+		channel.doneOnTime[n]=true;
+	}
+	if(channel.readyToBeSent==NULL || channel.doneOnTime==NULL)
+		return;
+	channel.writePointer=0;
+	channel.writeBuffer=0;
+	channel.readBuffer=0;
+	setChannelNumber(aChannelNumber);
+	setPort(aPort); //TODO: check for the return value
+	setServer(aServer); //TODO: check for the return value
+	printf("Channel %d is sending messages to: %s:%d at %fHz\n", getChannelNumber(), aServer, aPort, aSampleRate);
+	channel.enabled=true;
+}
+
+void NetworkSend::log(float value){ //TODO: add a vectorized version of this method
+	if(channel.enabled==false)
+		return;
+	if(channel.writePointer==channel.bufferLength){ // when the buffer is filled ...
+		channel.readyToBeSent[channel.writeBuffer]=true; // flag it as such
+//		printf("Scheduling for send %d\n",(int)channel.buffers[channel.writeBuffer][channel.headerTimestampIndex]);
+		channel.writePointer=channel.headerLength; //reset the writePointer
+		channel.writeBuffer=(channel.writeBuffer+1); //switch buffer
+		if(channel.writeBuffer==channel.numBuffers) // and wrap it
+			channel.writeBuffer=0;
+//		printf("WriteBuffer:%d\n", channel.writeBuffer);
+		if(channel.doneOnTime[channel.writeBuffer]==false){ //check if this buffer's last sending has completed on time ...
+			printf("Network buffer underrun. timestamp: %d :-{\n",
+					(int)channel.buffers[channel.writeBuffer][channel.headerTimestampIndex]);
+		}
+		channel.doneOnTime[channel.writeBuffer]=false; // ... and then reset the flag
+#ifdef USE_JUCE
+		if(isThreadRunning()==false){
+			startThread(10);
+		}
+#else
+		if(isThreadRunning()==false){
+			startThread();
+		}
+#endif /* USE_JUCE */
+	}
+	if(channel.writePointer==channel.headerLength){ // we are about to start writing in the buffer, let's set the header
+		//set dynamic header values here. Static values are set in setup() and setChannelNumber().
+		channel.buffers[channel.writeBuffer][channel.headerTimestampIndex]=(float)channel.sampleCount; //timestamp
+		channel.sampleCount++;
+		//add here more header fields
+	}
+    channel.buffers[channel.writeBuffer][channel.writePointer++]=value;
+//	sampleCount++;
+};
+
+void NetworkSend::setServer(const char *aServer){
+#ifdef USE_JUCE
+	remoteHostname=String::fromUTF8(aServer);
+#else
+	udpClient.setServer(aServer);
+#endif /* USE_JUCE */
+}
+void NetworkSend::setPort(int aPort){
+#ifdef USE_JUCE
+	remotePortNumber=aPort;
+#else
+	udpClient.setPort(aPort);
+#endif /* USE_JUCE */
+}
+
+void NetworkSend::setChannelNumber(int aChannelNumber){
+	channel.channelNumber=aChannelNumber;
+	for(int n=0; n<channel.numBuffers; n++){ //initialize the header
+		channel.buffers[n][channel.headerChannelIndex]=channel.channelNumber;
+		//add here more static header fields
+	}
+};
+int NetworkSend::getChannelNumber(){
+	return channel.channelNumber;
+};
+
+int NetworkSend::getTimestamp(){
+	return channel.buffers[channel.readBuffer][channel.headerTimestampIndex];
+}
+
+void NetworkSend::sendData(){
+	if(channel.enabled==false)
+		return;
+	while(channel.readyToBeSent[channel.readBuffer]==true){
+		channel.readyToBeSent[channel.readBuffer]=false;
+		void* sourceBuffer=channel.buffers[channel.readBuffer];
+//		printf("Trying to send timestamp %d\n",(int)((float*)sourceBuffer)[channel.headerTimestampIndex]);
+//		printf("ReadBuffer:%d\n", channel.readBuffer);
+		unsigned int numBytesToSend=NETWORK_AUDIO_BUFFER_SIZE*sizeof(float);
+		//TODO: call waitUntilReady before trying to write/send, to avoid blocks! (OR NOT?)
+#ifdef USE_JUCE
+		if(1==udpClient.waitUntilReady(0, 5)){
+			udpClient.write(remoteHostname, remotePortNumber, sourceBuffer, numBytesToSend);
+			channel.doneOnTime[channel.readBuffer]=true;
+			//  printf ("Sent timestamp: %d\n", (int)((float*)sourceBuffer)[1]);
+		} else {
+			//  printf ("Not ready timestamp: %d\n", (int)((float*)sourceBuffer)[1]);
+		}
+#else
+		udpClient.send(sourceBuffer, numBytesToSend);
+		channel.doneOnTime[channel.readBuffer]=true;
+#endif /* USE_JUCE */
+		channel.readBuffer++;
+		if(channel.readBuffer==channel.numBuffers)
+			channel.readBuffer=0;
+	}
+}
+
+void NetworkSend::run(){
+#ifdef USE_JUCE
+	//  std::chrono::high_resolution_clock::time_point t1;
+    //  std::chrono::high_resolution_clock::time_point t2;
+    //  std::chrono::high_resolution_clock::time_point t3;
+	while(threadShouldExit()==false){
+		//  t3 = std::chrono::high_resolution_clock::now();
+		//  t1 = std::chrono::high_resolution_clock::now();
+		sendData();
+		//  t2 = std::chrono::high_resolution_clock::now();
+		//  auto duration1 = std::chrono::duration_cast<std::chrono::microseconds>( t3 - t1 ).count();
+		//  auto duration2 = std::chrono::duration_cast<std::chrono::microseconds>( t2 - t1 ).count();
+		//  if(duration2>0)
+			//  std::cout << "Duration is: " << duration2 <<". Whole loop is: " << duration1 << "\n";
+		sleep(1);
+	}
+#else
+	threadRunning=true;
+	while(threadShouldExit()==false){
+		sendAllData();
+		usleep(sleepTimeMs*1000);
+	}
+	threadRunning=false;
+#endif
+}
+#ifdef USE_JUCE
+#else
+Scope::Scope(int aNumChannels):
+		channels(aNumChannels)
+{};
+Scope::~Scope(){};
+
+void Scope::log(int channel, float value){
+	if(channel>=getNumChannels()) //TODO: assert this
+		return;
+	channels[channel].log(value);
+}
+
+void Scope::setup(){
+	setup(44100, 9999, "127.0.0.1");
+}
+
+void Scope::setup(float sampleRate, int aPort, const char* aServer){
+	for(int n=0; n<getNumChannels(); n++){
+		channels[n].setup(sampleRate, 128, n, aPort, aServer); //TODO: replace 128 with the actual block size
+	}
+}
+
+void Scope::setPort(int port){
+	for(int n=0; n<getNumChannels(); n++){
+		channels[n].setPort(port);
+	}
+}
+void Scope::setPort(int channel, int aPort){
+	channels[channel].setPort(aPort);
+	printf("Channel %d is now sending to port %d\n", channel, aPort);
+}
+
+int Scope::getNumChannels(){
+	return channels.size();
+}
+
+void Scope::sendData(){
+	NetworkSend::sendAllData();
+}
+#endif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/ReceiveAudioThread.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,310 @@
+#include "ReceiveAudioThread.h"
+
+#ifdef USE_JUCE
+#else
+//initialise static members
+bool ReceiveAudioThread::staticConstructed=false;
+AuxiliaryTask ReceiveAudioThread::receiveDataTask=NULL;
+std::vector<ReceiveAudioThread *> ReceiveAudioThread::objAddrs(0);
+bool ReceiveAudioThread::threadRunning;
+bool ReceiveAudioThread::threadIsExiting;
+int ReceiveAudioThread::sleepTime;
+
+void receiveData(){
+	ReceiveAudioThread::run();
+}
+void ReceiveAudioThread::staticConstructor(){
+	if(staticConstructed==true)
+		return;
+	staticConstructed=true;
+    threadIsExiting=false;
+	receiveDataTask=BeagleRT_createAuxiliaryTask(receiveData, 90, "receiveDataTask"); //TODO: allow different priorities
+}
+#endif /* USE_JUCE */
+
+void ReceiveAudioThread::dealloc(){
+    free(buffer);
+    buffer=NULL;
+    free(stackBuffer);
+    stackBuffer=NULL;
+}
+void ReceiveAudioThread::wrapWritePointer(){
+    //this is not quite a simple wrapping as you would do in a circular buffer,
+    //as there is no guarantee the buffer will be full at all times, given that there must alwas be enough space at the end of it
+    //to hold a full payload
+    // lastValidPointer indicates the last pointer in the buffer containing valid data
+    //
+    if(writePointer+payloadLength+headerLength>bufferLength){ //if we are going to exceed the length of the buffer with the next reading
+        //  lastValidPointer=writePointer+headerLength; //remember where the last valid data are
+        //  for(int n=headerLength;n<lastValidPointer; n++){
+            //  fprintf(fd2, "%f\n",buffer[n]); //DEBUG
+        //  }
+        writePointer=0; //and reset to beginning of the buffer
+    }
+}
+void ReceiveAudioThread::pushPayload(int startIndex){ //backup the payload samples that will be overwritten by the new header
+    for(int n=0; n<headerLength; n++){
+        stackBuffer[n]=buffer[startIndex+n];
+    }
+}
+void ReceiveAudioThread::popPayload(int startIndex){
+    for(int n=0; n<headerLength; n++){
+        buffer[startIndex+n]=stackBuffer[n];
+    }
+}
+
+int ReceiveAudioThread::readUdpToBuffer(){
+    if(listening==false || bufferReady==false)
+        return 0;
+    if(writePointer<0)
+        return 0;
+    if(socket.waitUntilReady(true, waitForSocketTime)){// TODO: if waitForSocketTime here is >>5, the
+#ifdef USE_JUCE
+#else
+		lastTime=rt_timer_read();
+//        rt_printf("lastTimeread= %llu\n", lastTime);
+#endif /* USE_JUCE */
+    	// destructor (always or sometimes) never actually gets called, despite run() returns ...see issue #1381
+        pushPayload(writePointer); //backup headerLength samples. This could be skipped if writePointer==0
+        //read header+payload
+        int numBytes=socket.read(buffer+writePointer, bytesToRead, true); //read without waiting.
+            //TODO: (if using variable-length payload) validate the actual numBytes read against the size declared in the header
+        if(numBytes<0){
+            printf("error numBytes1\n");
+            return -3; //TODO: something went wrong, you have to discard the rest of the packet!
+        }
+        if(numBytes==0){//TODO: this should not happen unless you actually receive a packet of size zero (is it at all possible?)
+//        	printf("received 0 bytes\n");
+        	return 0;
+        }
+        if(numBytes != bytesToRead){ //this is equivalent to (numBytes<bytesToRead)
+            printf("error numBytes2: %d\n", numBytes);
+            return -4; //TODO: something went wrong, less bytes than expected in the payload.
+        }
+        if(channel!=(int)buffer[writePointer]){
+//        	printf("I am channel %d, but I received data for channel %d\n", channel, (int)buffer[writePointer]);
+        	return -5;
+        }
+        if(buffer[writePointer+1]!=timestamp+1)
+        	printf("missing a timestamp: %d\n",timestamp+1);
+        timestamp=buffer[writePointer+1];
+//        rt_printf("Received a message of length %d, it was on channel %d and timestamp %d\n", numBytes, (int)buffer[writePointer], (int)buffer[writePointer+1]);
+
+        popPayload(writePointer); //restore headerLength payload samples. This could be skipped if writePointer==0
+        //even though we just wrote (payloadLength+headerLength) samples in the buffer,
+        //we only increment by payloadLength. This way, next time a socket.read is performed, we will
+        //backup the last headerLength samples that we just wrote and we will overwrite them with
+        //the header from the new read. After parsing the header we will then restore the backed up samples.
+        //This way we guarantee that, apart from the first headerLength samples, buffer is a circular buffer!
+        writePointer+=payloadLength;
+        wrapWritePointer();
+        return numBytes;
+    }
+    return 0; //timeout occurred
+}
+//USE_JUCE    Thread(threadName),
+#ifdef USE_JUCE
+ReceiveAudioThread::ReceiveAudioThread(const String &threadName) :
+			Thread(threadName),
+#else
+ReceiveAudioThread::ReceiveAudioThread() :
+#endif /* USE_JUCE */
+	socket(0),
+    listening(false),
+    bufferReady(false),
+    buffer(NULL),
+    stackBuffer(NULL),
+    bufferLength(0),
+    lastValidPointer(0),
+    waitForSocketTime(5),
+#ifdef USE_JUCE
+    threadPriority(5)
+#else
+    threadPriority(88)
+#endif /* USE_JUCE */
+{};
+ReceiveAudioThread::~ReceiveAudioThread(){
+#ifdef USE_JUCE
+	stopThread(1000);
+#else
+	stopThread();
+	while(threadRunning){
+		usleep(sleepTime*2);	//wait for thread to stop
+		std::cout<< "Waiting for receiveAudioTask to stop" << std::endl;
+	}
+#endif /* USE_JUCE */
+	//TODO: check if thread stopped, otherwise kill it before dealloc
+    dealloc();
+}
+void ReceiveAudioThread::init(int aPort, int aSamplesPerBlock, int aChannel){
+  dealloc();
+#ifdef USE_JUCE
+#else
+  staticConstructor();
+  objAddrs.push_back(this);//TODO: this line should be in the constructor
+#endif /* USE_JUCE */
+  bindToPort(aPort);
+  channel=aChannel;
+  printf("Channel %d is receiving on port %d\n",aChannel, aPort);
+  //  fd=fopen("output.m","w"); //DEBUG
+  //  fprintf(fd,"var=["); //DEBUG
+  headerLength=2;
+  payloadLength=300; //TODO: make sure that payloadLength and headerLength are the same as the client is sending.
+  bufferLength=std::max(headerLength+(payloadLength*4), headerLength+(aSamplesPerBlock*4)); //there are many considerations that can be done here ...
+                      //We keep a headerLength padding at the beginning of the array to allow full reads from the socket
+  buffer=(float*)malloc(sizeof(float)*bufferLength);
+  if(buffer==NULL) // something wrong
+    return;
+  lastValidPointer=headerLength+ ((bufferLength-headerLength)/payloadLength)*payloadLength;
+  memset(buffer,0,bufferLength*sizeof(float));
+  stackBuffer=(float*)malloc(sizeof(float)*headerLength);
+  if(stackBuffer==NULL) // something wrong
+      return;
+  bufferReady=true;
+  bytesToRead=sizeof(float)*(payloadLength + headerLength);
+  writePointer=-1;
+  readPointer=0;
+  sleepTime=payloadLength/(float)44100 /4.0; //set sleepTime so that you do not check too often or too infrequently
+  timestamp=0;
+#ifdef USE_JUCE
+  startThread(threadPriority);
+#else
+  //TODO: the thread cannot be started here at the moment because init() is called in setup(), where tasks cannot be scheduled
+#endif /* USE_JUCE */
+}
+
+void ReceiveAudioThread::bindToPort(int aPort){
+    listening=socket.bindToPort(aPort);
+#ifdef USE_JUCE
+#else
+    if(listening==false) //this condition is valid also for USE_JUCE, but we do not printf in USE_JUCE
+    	printf("Could not bind to port %d\n",aPort);
+#endif /* USE_JUCE */
+}
+bool ReceiveAudioThread::isListening(){
+    return listening;
+}
+float* ReceiveAudioThread::getCurrentBuffer(int length){ // NOTE: this cannot work all the time unless samplesPerBuffer and payloadLength are multiples
+    //TODO: make it return the number of samples actually available at the specified location
+    if(isListening()==false || length>bufferLength)
+        return NULL;
+    readPointer+=length;
+    if(readPointer>lastValidPointer){
+        readPointer=headerLength;
+    }
+    return buffer+(int)readPointer;
+};
+int ReceiveAudioThread::getSamplesSrc(float *destination, int length,
+		float samplingRateRatio, int numChannelsInDestination,
+		int channelToWriteTo)
+{
+    if (!(samplingRateRatio>0 && samplingRateRatio<=2))
+        return -2;
+    if(isListening()==false)
+        return -1;
+    static int numCalls=0;
+    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);
+    	readPointer=0;
+#endif /* USE_JUCE */
+        writePointer=2*length;  // do it, so that it starts writing at a safety margin from where we write.
+                            // This will help keeping them in sync.
+                            //TODO: handle what happens when the remote stream is interrupted and then restarted
+    }
+    numCalls++;
+    if(length>lastValidPointer) {
+        //not enough samples available, we fill the buffer with what is available, but the destination buffer will not be filled completely
+        //at this very moment the other thread might be writing at most one payload into the buffer.
+        //To avoid a race condition, we need to let alone the buffer where we are currently writing
+        //as writing the payload also temporarily overwrites the previous headerLength samples, we need to account for them as well
+        //TODO: This assumes that the writePointer and readPointer do not drift. When doing clock synchronization we will find out that it is not true!
+        length=lastValidPointer-payloadLength-headerLength;
+        if(length<0) //no samples available at all!
+            return 0;
+    }
+    for(int n=0; n<length; n++){
+        destination[n*numChannelsInDestination+channelToWriteTo]=buffer[(int)(0.5+readPointer)];//simple ZOH non-interpolation (nearest neighbour)
+        //  fprintf(fd,"%f, %d, %f;\n",readPointer,writePointer,destination[n]); //DEBUG
+        readPointer+=samplingRateRatio;
+        if((int)(0.5+readPointer)>=lastValidPointer){
+            readPointer=readPointer-lastValidPointer+headerLength;
+        }
+    }
+    return length;
+}
+int ReceiveAudioThread::getSamplesSrc(float *destination, int length, float samplingRateRatio){
+	return getSamplesSrc(destination, length, samplingRateRatio, 1,0);
+	// TODO: rewriting this so that it does not call the override method we can save a multiply and add
+	// for each sample.
+}
+bool ReceiveAudioThread::isBufferReady(){
+    return bufferReady;
+}
+#ifdef USE_JUCE
+#else
+void ReceiveAudioThread::startThread(){
+	BeagleRT_scheduleAuxiliaryTask(receiveDataTask);
+}
+void ReceiveAudioThread::stopThread(){
+	threadIsExiting=true;
+}
+bool ReceiveAudioThread::threadShouldExit(){
+	return(gShouldStop || threadIsExiting );
+}
+RTIME ReceiveAudioThread::getLastTime(){
+	return lastTime;
+}
+#endif /* USE_JUCE */
+int ReceiveAudioThread::getTimestamp(){
+	return timestamp;
+}
+void ReceiveAudioThread::run(){
+    //  fd2=fopen("buffer.m","w"); //DEBUG
+    //  fprintf(fd2, "buf=["); //DEBUG
+	threadRunning=true;
+	int maxCount=10;
+	int count=0;
+	// Clean the socket from anything that is currently in it.
+#ifdef USE_JUCE
+	// this is borrowed from BeagleRT's UdpServer class.
+	int n;
+	do {
+		float waste;
+		if(socket.waitUntilReady(true, 0)==0)
+			break;
+		n=socket.read((void*)&waste, sizeof(float), false);
+		count++;
+		if(n<0){
+			printf("error\n");
+			break;
+		}
+		printf("n: %d\n",n);
+	} while (n>0 && (maxCount<=0 || count<maxCount));
+#else
+	for(unsigned int n=0; n<objAddrs.size(); n++){
+		count=objAddrs[n]->socket.empty(maxCount);
+	}
+#endif /* USE_JUCE */
+	printf("socket emptied with %d reads\n", count);
+
+    while(!threadShouldExit()){ //TODO: check that the socket buffer is empty before starting
+#ifdef USE_JUCE
+        readUdpToBuffer(); // read into the oldBuffer
+        sleep(sleepTime);
+#else
+		for(unsigned int n=0; n<ReceiveAudioThread::objAddrs.size(); n++){
+//			printf("%d\n", n);
+			ReceiveAudioThread::objAddrs[n]->readUdpToBuffer();
+		}
+		usleep(sleepTime); //TODO: use rt_task_sleep instead
+#endif /* USE_JUCE */
+    }
+    threadRunning=false;
+    printf("Thread is not running \n");
+    //  fprintf(fd,"];readPointer,writePointer,lastValidPointer,destination]=deal(var(:,1), var(:,2), var(:,3), var(:,4));"); //DEBUG
+    //  fclose(fd);//DEBUG
+    //  fprintf(fd2,"];");//DEBUG
+    //  fclose(fd2); //DEBUG
+}
--- a/core/UdpClient.cpp	Mon Sep 14 17:31:24 2015 +0100
+++ b/core/UdpClient.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -1,57 +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;
-	};
-
+/*
+ * 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/UdpServer.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,119 @@
+/*
+ * udpServer.cpp
+ *
+ *  Created on: 19 May 2015
+ *      Author: giulio moro
+ */
+#include "UdpServer.h"
+
+UdpServer::UdpServer(int aPort){
+	init(aPort);
+};
+UdpServer::UdpServer(){
+	init(0);
+}
+UdpServer::~UdpServer(){
+	close();
+};
+bool UdpServer::init(int aPort){
+	enabled=true;
+	stZeroTimeOut.tv_sec = 0; //set timeout to 0
+	stZeroTimeOut.tv_usec = 0;
+	inSocket=socket(AF_INET, SOCK_DGRAM, 0);
+	if (inSocket < 0){
+		enabled=false;
+	}
+	length = sizeof(server);
+	server.sin_family=AF_INET;
+	server.sin_addr.s_addr=INADDR_ANY;
+	enabled=bindToPort(aPort);
+	wasteBufferSize=2048;
+	wasteBuffer=malloc(wasteBufferSize);
+  memset(&stTimeOut,0,sizeof(struct timeval));
+	return enabled;
+}
+
+bool UdpServer::bindToPort(int aPort){
+	port=aPort;
+	if(port<1){
+		enabled=false;
+		return false;
+	}
+	server.sin_port=htons(port);
+	if (bind(inSocket,(struct sockaddr *)&server,length)<0){
+		enabled=false;
+		return false;
+	}
+	enabled=true;
+	return true;
+}
+
+void UdpServer::close(){
+	int ret=::close(inSocket);
+	if(ret != 0)
+		printf("Error while closing socket, errno: %d\n", errno);//Stop receiving data for this socket. If further data arrives, reject it.
+	inSocket=0;
+}
+
+int UdpServer::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(inSocket+1, &stReadFDS, NULL, NULL, NULL); //calling this with a NULL timeout will block indefinitely
+	FD_ZERO(&stReadFDS);
+	FD_SET(inSocket, &stReadFDS);
+	if(timeoutMsecs>=1000){
+		float timeOutSecs=timeoutMsecs*0.001;
+		stTimeOut.tv_sec=(long int)timeOutSecs;
+		timeOutSecs-=(int)timeOutSecs;
+		stTimeOut.tv_usec=(long int)(timeOutSecs*1000000);
+	} else //faster!
+		stTimeOut.tv_usec=(long int)timeoutMsecs*1000;
+	int descriptorReady= select(inSocket+1, &stReadFDS, NULL, NULL, &stTimeOut);
+	return descriptorReady>0? 1 : descriptorReady;
+}
+
+int UdpServer::read(//Returns the number of bytes read, or -1 if there was an error.
+					void *destBuffer,
+					int maxBytesToRead,
+					bool blockUntilSpecifiedAmountHasArrived)
+{
+	if(enabled==false)
+		return -1;
+	FD_ZERO(&stReadFDS);
+	FD_SET(inSocket, &stReadFDS);
+	int descriptorReady= select(inSocket+1, &stReadFDS, NULL, NULL, &stZeroTimeOut); //TODO: this is not JUCE-compliant
+	if(descriptorReady<0){ //an error occurred
+		return -1;
+	}
+	int numberOfBytes=0;
+//	do
+	{
+		if (FD_ISSET(inSocket, &stReadFDS))
+		{
+	//		numberOfBytes=recvfrom(inSocket,destBuffer,maxBytesToRead,0,(struct sockaddr *)&from,&fromLength);
+			numberOfBytes+=recv(inSocket,destBuffer,maxBytesToRead-numberOfBytes,0);
+			if(numberOfBytes<0)
+				return -1;
+		}
+	}
+//	while (blockUntilSpecifiedAmountHasArrived && numberOfBytes==maxBytesToRead);
+	return numberOfBytes;
+}
+int UdpServer::empty(){
+	return empty(0);
+}
+int UdpServer::empty(int maxCount){
+	int count=0;
+	int n;
+	do {
+		if(waitUntilReady(true, 0)==0)
+			return 0;
+		float waste;
+		n=read(&waste, sizeof(float), false);
+		count++;
+	} while (n>0 && (maxCount<=0 || maxCount<count));
+	printf("socket emptied with %d reads\n", count);
+	return count;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/VirtualClock.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,69 @@
+#include "VirtualClock.h"
+void VirtualClock::init(){
+	firstRun=true;
+	movingAverage.setLength(101); //TODO: a better filtering algorithm ( Did you say Kalman?)
+	period=-1;
+	elapsedPeriods=0;
+	startTime=0;
+	startTimeOffset=0;
+	elapsedPeriodsOffset=0;
+}
+
+VirtualClock::VirtualClock(){
+	init();
+}
+void VirtualClock::sync(){
+	sync(1);
+}
+void VirtualClock::sync(double numPeriods){
+	myClock_t currentTime=Clock::getTimeUs();
+	static int calls=0;
+	elapsedPeriods+=numPeriods;
+	if(calls==50){ //TODO: this is dangerous as the clock might jump suddenly if currentTime is not precise
+		calls=0;
+		startTimeOffset=startTime;
+		startTime=currentTime;
+		elapsedPeriodsOffset=elapsedPeriods;
+	}
+	calls++;
+	if(firstRun==true){
+		firstRun=false;
+		startTime=currentTime;
+	} else {
+		double newPeriod=(currentTime-lastSync)/numPeriods;
+		double expectedPeriod=22.67;
+		double maxPeriodDeviation=10;
+		if(fabs(newPeriod-expectedPeriod)<maxPeriodDeviation){ // filtering outliers
+			period=movingAverage.add(newPeriod); //TODO: replace with Kalman filter
+		} else {
+			printf("period out of range: %f\n", newPeriod);
+		}
+	}
+	lastSync=currentTime;
+//	printf("lastSync: %lld\n",lastSync-startTime);
+}
+
+double VirtualClock::getNow(){
+	myClock_t currentSystemTime=Clock::getTimeUs();
+	if(period<=0){
+		return currentSystemTime; // TODO: this is not very meaningful.
+	}
+	//  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=(currentSystemTime-startTime);
+	double now=elapsedPeriodsOffset + elapsed/(double)period;
+//	printf("elapsed=%lld;  sincelastSync=%lld; period=%f; now=%f\n", elapsed, currentSystemTime-lastSync, period, now);
+	return now;
+}
+
+void VirtualClock::addOffset(double periodOffset){
+	elapsedPeriods-=periodOffset;
+	if(elapsedPeriods<0){
+		printf("ERROR: periodOffset adjustment of %f resulted in elapsedPeriods=%f\n", periodOffset, elapsedPeriods);
+		exit(1);
+	}
+	movingAverage.reset();
+}
+double VirtualClock::getPeriod(){
+	return period;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core/intervals.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,94 @@
+/*
+ * intervals.h
+ *
+ *  Created on: 18 May 2015
+ *      Author: unmanaged
+ */
+
+#include <unistd.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include <native/timer.h>
+#include <rtdk.h>
+
+#include "../include/intervals.h"
+void Interval::init(int aNumAverages, int aNumFrames, float aSamplingRate, const char *aName){
+	enabled=false;
+	numAverages=aNumAverages;
+	intervals=(RTIME *)malloc(sizeof(RTIME)*numAverages);
+	samplingRate=aSamplingRate;
+	numFrames=aNumFrames;
+	maxTimeus=0;
+	intervalsPointer=0;
+	sum=0;
+	startTime=0;
+
+	if(intervals!=0)
+		enabled=true;
+	int len=strlen(aName);
+	name=(char *)malloc(sizeof(char)*(len+1));
+	strcpy(name, aName);
+	if(name == 0)
+		enabled=false;
+};
+Interval::Interval(){
+	init(100,1,44100,"");
+}
+Interval::Interval(int aNumAverages){
+	init(aNumAverages,1,44100,"");
+}
+Interval::Interval(int aNumAverages, int aNumFrames, float aSamplingRate, const char *aName){
+	init(aNumAverages,aNumFrames,aSamplingRate,aName);
+}
+Interval::~Interval(){
+	free(intervals);
+//			free(name);
+}
+void Interval::setNumFrames(int aNumFrames){
+	numFrames=aNumFrames;
+};
+
+int Interval::start(){
+//	printf("start: intervals: 0x%x, intervalsPointer: %d, numAverages: %d\n", intervals,intervalsPointer,numAverages);
+	if(!enabled)
+		return 0;
+	startTime=rt_timer_read();
+	return 1;
+}
+int Interval::resetMax(){
+	maxTimeus=0;
+	return 1;
+}
+int Interval::split(){ //updates
+	if(!enabled)
+		return 0;
+	int currentInterval=rt_timer_read()-startTime;
+	RTIME *currentPointer=&(intervals[intervalsPointer]);
+	sum-=*currentPointer; //take out the oldest value from the sum
+	*currentPointer=currentInterval;
+	sum+=*currentPointer; //add the new value to the sum
+	timeus=((float)sum)/numAverages/1000.0;
+	maxTimeus=timeus>maxTimeus?timeus:maxTimeus;
+	intervalsPointer++;
+	if(intervalsPointer>=(numAverages-1)){
+		intervalsPointer=0;
+	}
+	return 1;
+}
+void Interval::setEnabled(bool aActive){
+	enabled=aActive;
+}
+float Interval::getTimeus(){
+	return timeus;
+}
+float Interval::getMaxTimeus(){
+	return maxTimeus;
+}
+void Interval::print(){
+	rt_printf(//"sleepTimer time: 29.484us, (1.30 samples, numFrames: 2, 65.01%%). MaxTime: 30.439us, (1.34 samples, 67.12%%)\n");
+"%s time: %.3fus, (%.2f samples, numFrames: %d, %.2f%%). MaxTime: %.3fus, (%.2f samples, %.2f%%)\n",
+			name,
+			timeus, timeus/1000000.0*samplingRate, numFrames, timeus/1000000.0*samplingRate/numFrames * 100,
+			maxTimeus, maxTimeus/1000000.0*samplingRate, maxTimeus/1000000.0*samplingRate/numFrames * 100);
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/Clock.h	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,18 @@
+#ifndef CLOCK_H_INCLUDED
+#define CLOCK_H_INCLUDED
+#include <sys/time.h>
+#include <stdio.h>
+
+#ifdef USE_JUCE
+#else
+//#include <BeagleRT.h>
+#include <native/timer.h>
+#endif /* USE_JUCE */
+
+typedef long long int myClock_t;
+
+namespace Clock
+{
+  myClock_t getTimeUs();
+}
+#endif /* CLOCK_H_INCLUDED */
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/ClockSync.h	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,84 @@
+#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;
+	void resetTs();
+	bool areTsValid();
+	void processOffset(double offset);
+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 */
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/ClockSyncThread.h	Mon Sep 14 17:35:18 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/ClockSynchronizer.h	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,42 @@
+/*
+ * ClockSynchronizer.h
+ *
+ *  Created on: 26 Aug 2015
+ *      Author: giulio
+ */
+
+#ifndef CLOCKSYNCHRONIZER_H_
+#define CLOCKSYNCHRONIZER_H_
+
+#include <BeagleRT.h>
+#include <I2c_Codec.h>
+#include <NetworkSend.h>
+#include <native/timer.h>
+extern I2c_Codec *gAudioCodec;
+
+class ClockSynchronizer {
+private:
+	int localOffset;
+	int remoteOffset;
+	RTIME timeOffset;
+	int localCounter;
+	int remoteCounter;
+	RTIME lastTime;
+	void reset();
+	static bool staticConstructed;
+	static void staticConstructor();
+	static float currentSamplingRate;
+	static float targetSamplingRate;
+	static bool threadRunning;
+	static int threadWasRunning;
+	static AuxiliaryTask setClockTask;
+public:
+	ClockSynchronizer();
+	~ClockSynchronizer();
+	void setup();
+	void update(int aLocalCounter, int aRemoteCounter, RTIME aLastTime);
+	void adjustClock();
+	static void setClock();
+};
+
+#endif /* CLOCKSYNCHRONIZER_H_ */
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/NetworkSend.h	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,115 @@
+//scope.cpp
+#ifndef SCOPE_H_
+#define SCOPE_H_
+
+#ifdef USE_JUCE
+#include <JuceHeader.h>
+#else
+#include <BeagleRT.h>
+#include <rtdk.h>
+#include <cmath>
+#include <UdpClient.h>
+#include <vector>
+#include <string>
+extern bool gShouldStop;
+#endif /* USE_JUCE */
+
+#define NETWORK_AUDIO_BUFFER_SIZE 302
+#define UDP_BUFFER_HEADER_CHANNEL_INDEX 0
+#define UDP_BUFFER_HEADER_TIMESTAMP_INDEX 1
+#define UDP_BUFFER_HEADER_LENGTH 2
+
+struct NetworkBuffer{
+	int channelNumber;
+	int numBuffers;
+	int writeBuffer;
+	int readBuffer;
+	int writePointer;
+	float** buffers;
+	bool* doneOnTime;
+	bool* readyToBeSent;
+	bool enabled;
+	int sampleCount;
+	static const int bufferLength=NETWORK_AUDIO_BUFFER_SIZE;
+	static const int headerLength=UDP_BUFFER_HEADER_LENGTH;
+	static const int headerChannelIndex=UDP_BUFFER_HEADER_CHANNEL_INDEX;
+	static const int headerTimestampIndex=UDP_BUFFER_HEADER_TIMESTAMP_INDEX;
+};
+
+#ifdef USE_JUCE
+class NetworkSend: public Thread {
+#else
+class NetworkSend {
+#endif /* USE_JUCE */
+	float sampleRate;
+#ifdef USE_JUCE
+	DatagramSocket udpClient;
+	int sleepTimeMs;
+	String remoteHostname;
+	int remotePortNumber;
+#else
+	UdpClient udpClient;
+	bool isThreadRunning();
+	static int sleepTimeMs;
+	static bool threadShouldExit();
+	static bool threadIsExiting;
+	static bool threadRunning;
+	static bool staticConstructed;
+	static void staticConstructor();
+	static AuxiliaryTask sendDataTask; //TODO: allow different AuxiliaryTasks for different priorities (e.g.: audio vs scope)
+	static std::vector<NetworkSend *> objAddrs;
+#endif /* USE_JUCE */
+	void dealloc();
+public:
+	NetworkBuffer channel;
+#ifdef USE_JUCE
+	NetworkSend(const String &threadName);
+#else
+	NetworkSend();
+#endif
+	~NetworkSend();
+	void setup(float aSampleRate, int blockSize, int aChannelNumber, int aPort, const char *aServer);
+	void cleanup();
+	void sendData();
+	void log(float value);
+	void setPort(int aPort);
+	void setServer(const char* aServer);
+	void setChannelNumber(int aChannelNumber);
+	int getChannelNumber();
+	int getTimestamp();
+#ifdef USE_JUCE
+	void run();
+#else
+	static int getNumInstances();
+	static void sendAllData();
+    static void startThread();
+    static void stopThread();
+	static void run();
+#endif /* USE_JUCE */
+};
+
+#ifdef USE_JUCE
+#else
+/**
+ * An array of NetworkSend objects with some default parameters
+ *
+ * All sending on the same port (defaults to 9999)
+ * All sending to the same server (defaults to 127.0.0.1)
+*/
+class Scope {
+	std::vector<NetworkSend> channels;
+	void deallocate();
+public:
+	Scope(int aNumChannels);
+	~Scope();
+	void log(int channel, float value);
+    void setup();
+    void setup(float sampleRate, int aPort, const char* aServer);
+    void sendData();
+    void setPort(int port);
+    void setPort(int channel, int port);
+    int getNumChannels();
+};
+#endif /* USE_JUCE */
+
+#endif /* SCOPE_H */
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/ReceiveAudioThread.h	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,105 @@
+#ifndef RECEIVEAUDIOTHREAD_H_INCLUDED
+#define RECEIVEAUDIOTHREAD_H_INCLUDED
+
+#ifdef USE_JUCE
+#include <JuceHeader.h>
+#else
+#include <BeagleRT.h>
+#include <UdpServer.h>
+#include <vector>
+#include <iostream>
+#include <native/task.h>
+#include <native/timer.h>
+#include <math.h>
+
+#endif /*USE_JUCE*/
+
+#ifdef USE_JUCE
+class ReceiveAudioThread : public Thread {
+#else
+class ReceiveAudioThread{
+#endif /* USE_JUCE */
+private:
+    //  FILE *fd; //DEBUG
+    //  FILE *fd2; //DEBUG
+#ifdef USE_JUCE
+	DatagramSocket socket;
+#else
+    UdpServer socket;
+#endif /* USE_JUCE */
+    bool listening;
+    bool bufferReady;
+#ifdef USE_JUCE
+    bool threadRunning; //do we really need this ?
+#else
+    static bool threadRunning;
+    static bool threadIsExiting;
+#endif
+    float *buffer;
+    float *stackBuffer;
+    int bufferLength;
+    float readPointer;
+    int writePointer;
+    int lastValidPointer;
+#ifdef USE_JUCE
+    int sleepTime;
+#else
+    static int sleepTime;
+#endif
+    int waitForSocketTime;
+    int payloadLength; //size of the payload of each datagram
+    int headerLength; //size of the header of each datagram
+    int bytesToRead;
+    int threadPriority;
+    int channel;
+    int timestamp;
+    void dealloc();
+    void wrapWritePointer();
+    void pushPayload(int startIndex);
+    void popPayload(int startIndex);
+    int readUdpToBuffer();
+#ifdef USE_JUCE
+#else
+    RTIME lastTime; // Used for clock synchronization
+    static bool threadShouldExit();
+	static bool staticConstructed;
+    static void staticConstructor();
+    static AuxiliaryTask receiveDataTask; //TODO: allow different AuxiliaryTasks for different priorities (e.g.: audio vs scope)
+    static std::vector<ReceiveAudioThread *> objAddrs;
+#endif
+public:
+#ifdef USE_JUCE
+    ReceiveAudioThread(const String &threadName);
+#else
+    ReceiveAudioThread();
+#endif
+    ~ReceiveAudioThread();
+    void init(int port, int aSamplesPerBlock, int channel);
+    void bindToPort(int aPort);
+    bool isListening();
+    float* getCurrentBuffer(int length);
+    /**
+     * Copies the samples to a non-interleaved buffer.
+     */
+    int getSamplesSrc(float *destination, int length, float samplingRateRatio);
+    /**
+     * Copies the samples to an interleaved buffer.
+     */
+    int getSamplesSrc(float *destination, int length,
+    		float samplingRateRatio, int numChannelsInDestination,
+    		int channelToWriteTo);
+    bool isBufferReady();
+    int getTimestamp();
+#ifdef USE_JUCE // if we are in Juce, then we run a separate thread for each receiver
+    		// (as each of them are typically receiving on a mono or stereo track)
+    void run();
+#else
+    RTIME getLastTime();
+    void static run(); //while in BeagleRT we have a single thread that receives for all the instances.
+    //TODO: make run() private in BeagleRT
+    static void startThread();
+    static void stopThread();
+    static int getNumInstances();
+#endif // USE_JUCE
+};
+#endif  // RECEIVEAUDIOTHREAD_H_INCLUDED
--- a/include/Scope.h	Mon Sep 14 17:31:24 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-//scope.cpp
-#include <BeagleRT.h>
-#include <rtdk.h>
-#include <cmath>
-#include <UdpClient.h>
-
-#define BUILD_FOR_UDPRECEIVE_PLUGIN
-#define NETWORK_AUDIO_BUFFER_SIZE 302
-struct networkAudio{
-	int timestamp;
-	int currentBuffer;
-	int index;
-	float buffers[2][NETWORK_AUDIO_BUFFER_SIZE];
-	int doneOnTime;
-	bool toBeSent;
-	UdpClient udpClient;
-};
-
-#define NUM_SCOPE_CHANNELS 6
-
-static void SendScopeData();
-
-class Scope {
-    int sampleCount;
-    float sampleRate;
-    AuxiliaryTask scopeTask;
-  public:
-    int numChannels;
-    networkAudio channel[NUM_SCOPE_CHANNELS];
-    Scope(){
-        numChannels = NUM_SCOPE_CHANNELS;
-        sampleCount = 0;
-#ifdef BUILD_FOR_UDPRECEIVE_PLUGIN
-        char server[]="192.168.7.1";
-#else
-        char server[]="127.0.0.1";
-#endif /* BUILD_FOR_UDPRECEIVE_PLUGIN */
-        printf("Sending messages to : %s\n", server);
-        for(int n=0; n<numChannels; n++){
-            channel[n].doneOnTime=1;
-            channel[n].index=2; //leave space for the heading message (channel, timestamp)
-            channel[n].timestamp=0;
-            channel[n].currentBuffer=0;
-            channel[n].toBeSent=false;
-            channel[n].udpClient.setServer(server);
-#ifdef BUILD_FOR_UDPRECEIVE_PLUGIN
-            channel[n].udpClient.setPort(9999+n);
-#else
-            channel[n].udpClient.setPort(9999);
-#endif /* BUILD_FOR_UDPRECEIVE_PLUGIN */
-    	}
-    }
-    void setup(float _sampleRate);
-    void log(float channel1=0.0, float channel2=0.0, float channel3=0.0, float channel4=0.0, float channel5=0.0, float channel6=0.0){
-
-        for(int j=0; j<numChannels; j++){
-			if(channel[j].index==(NETWORK_AUDIO_BUFFER_SIZE)){ // when the buffer is ready ...
-              channel[j].buffers[channel[j].currentBuffer][0] = (float)j;
-              channel[j].buffers[channel[j].currentBuffer][1] = (float)channel[j].timestamp;
-				channel[j].toBeSent=true;
-				channel[j].index=2; //reset the counter
-				if(channel[j].doneOnTime==0)
-					rt_printf("Network buffer underrun :-{\n");
-				channel[j].timestamp=sampleCount;
-				channel[j].currentBuffer=!channel[j].currentBuffer; //switch buffer
-				channel[j].doneOnTime=0;
-				BeagleRT_scheduleAuxiliaryTask(scopeTask); //send the buffer
-			}
-		}
-
-      	channel[0].buffers[channel[0].currentBuffer][channel[0].index++]=channel1;
-      	channel[1].buffers[channel[1].currentBuffer][channel[1].index++]=channel2;
-      	channel[2].buffers[channel[2].currentBuffer][channel[2].index++]=channel3;
-      	channel[3].buffers[channel[3].currentBuffer][channel[3].index++]=channel4;
-      	channel[4].buffers[channel[4].currentBuffer][channel[4].index++]=channel5;
-      	channel[5].buffers[channel[5].currentBuffer][channel[5].index++]=channel6;
-
-	sampleCount++;
-    }
-};
-
-Scope* gOscilloscopeInstance;
-
-void Scope::setup(float _sampleRate){
-    sampleRate = _sampleRate;
-    gOscilloscopeInstance = this;
-    scopeTask = BeagleRT_createAuxiliaryTask(*SendScopeData, 98, "transmit-receive-audio");
-}
-
-//Scope scope;
-
-static void SendScopeData(){
-    for(int n=0; n<gOscilloscopeInstance->numChannels; n++){
-		if(gOscilloscopeInstance->channel[n].toBeSent){
-			gOscilloscopeInstance->channel[n].toBeSent=false;
-			gOscilloscopeInstance->channel[n].udpClient.send(
-				gOscilloscopeInstance->channel[n].buffers[!gOscilloscopeInstance->channel[n].currentBuffer],
-				NETWORK_AUDIO_BUFFER_SIZE*sizeof(float)
-			);
-			gOscilloscopeInstance->channel[n].doneOnTime=1;
-		}
-	}
-}
--- a/include/UdpClient.h	Mon Sep 14 17:31:24 2015 +0100
+++ b/include/UdpClient.h	Mon Sep 14 17:35:18 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;
@@ -33,6 +35,8 @@
 		void setPort(int aPort);
 		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);
 };
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/UdpServer.h	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,70 @@
+/*
+ * udpServer.h
+ *
+ *  Created on: 19 May 2015
+ *      Author: giulio moro
+ */
+
+#ifndef UDPSERVER_H_
+#define UDPSERVER_H_
+
+#include <sys/types.h>
+#include <sys/socket.h>
+#include <netinet/in.h>
+#include <arpa/inet.h>
+#include <errno.h>
+#include <netdb.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+
+class UdpServer{
+	private:
+		int port;
+		int enabled;
+		int inSocket;
+		struct sockaddr_in server;
+		struct timeval stTimeOut;
+		struct timeval stZeroTimeOut;
+		fd_set stReadFDS;
+		int size;
+		void *wasteBuffer;
+		int wasteBufferSize;
+		int length;
+		socklen_t fromLength;
+		struct sockaddr_in from;
+	public:
+		UdpServer();
+		UdpServer(int aPort);
+		~UdpServer();
+		bool init(int aPort);
+		bool bindToPort(int aPort);
+		int getBoundPort() const;
+		/*
+		 * Reads bytes from the socket.
+		 *
+		 * Drop-in replacement for JUCE DatagramSocket::read()
+		 *
+			If blockUntilSpecifiedAmountHasArrived is true, the method will block until maxBytesToRead
+			bytes have been read, (or until an error occurs). If this flag is false, the method will
+			return as much data as is currently available without blocking.
+		 */
+		int read(void* destBuffer, int maxBytesToRead, bool blockUntilSpecifiedAmountHasArrived);
+		void close();
+		int empty();
+		int empty(int maxCount);
+		/*
+		 * Waits until the socket is ready for reading or writing.
+		 *
+			Drop-in replacement for JUCE DatagramSocket::waitUntilReady.
+			If readyForReading is true, it will wait until the socket is ready for reading; if false, it will wait until it's ready for writing.
+			If the timeout is < 0, it will wait forever, or else will give up after the specified time.
+			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.
+		 */
+		int waitUntilReady(bool readyForReading, int timeoutMsecs);
+};
+
+
+
+#endif /* UDPSERVER_H_ */
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/VirtualClock.h	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,53 @@
+#ifndef VIRTUAL_CLOCK_H_INCLUDED
+#define VIRTUAL_CLOCK_H_INCLUDED
+
+#include "math.h"
+#include "stats.hpp"
+#include "Clock.h"
+#ifdef USE_JUCE
+#else
+#include <BeagleRT.h>
+#endif /* USE_JUCE */
+
+class VirtualClock{
+private:
+	myClock_t startTime;
+	myClock_t startTimeOffset;
+	myClock_t lastSync;
+	bool firstRun;
+	double elapsedPeriods;
+	double elapsedPeriodsOffset;
+	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 numPeriods);
+/**
+	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();
+/**
+ * Add an offset to the number of elapsed periods.
+ *
+ * Add an offset to the number of elapsed periods. It also compensates for the corresponding time offset.
+ */
+	void addOffset(double periodOffset);
+};
+
+#endif /* VIRTUAL_CLOCK_H_INCLUDED */
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/intervals.h	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,50 @@
+/*
+ * intervals.h
+ *
+ *  Created on: 18 May 2015
+ *      Author: unmanaged
+ */
+
+#ifndef INTERVALS_H_
+#define INTERVALS_H_
+
+#define TEN_POW_9 1000000000
+
+#include <unistd.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include <native/timer.h>
+#include <rtdk.h>
+
+class Interval
+{
+	private:
+		int intervalsPointer;
+		long sum;
+		RTIME startTime;
+		RTIME *intervals;
+		float maxTimeus;
+		float timeus;
+		float samplingRate; //used for getPrint()
+		int numFrames;
+		bool enabled; //whether it actually reads the clock or not
+		int numAverages;
+		char *name;
+		void init(int aNumAverages, int aNumFrames, float aSamplingRate, const char *aName);
+	public:
+		Interval();
+		Interval(int aNumAverages);
+		Interval(int aNumAverages, int aNumFrames, float aSamplingRate, const char *aName);
+		~Interval();
+		void setNumFrames(int aNumFrames);
+		int start();
+		int resetMax();
+		int split();
+		void setEnabled(bool aActive);
+		float getTimeus();
+		float getMaxTimeus();
+		void print();
+};
+
+#endif /* INTERVALS_H_ */
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/stats.hpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,76 @@
+#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;
+  bool bufferFull;
+  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);
+    reset();
+  }
+public:
+  MovingAverage(){
+    init(0);
+  }
+  MovingAverage(int aLength){
+    init(aLength);
+  }
+  ~MovingAverage(){
+    dealloc();
+  }
+  int getLength(){
+    return bufferFull ? length : pointer;
+  }
+  void setLength(int aLength){
+    dealloc();
+    init(aLength);
+  }
+  double add(TYPE newElement){
+    sum-=array[pointer];
+    array[pointer]=newElement;
+    sum+=newElement;
+    if(bufferFull==true){
+    	average=sum*scale;
+    }
+    else{
+    	average=sum/(double)(1+pointer);
+    }
+    pointer++;
+    if(pointer==length){
+      pointer=0;
+      bufferFull=true;
+    }
+    return average;
+  }
+  double getAverage(){
+    return average;
+  }
+  void reset(){
+	  pointer=0;
+	  bufferFull=false;
+  }
+};
+
+#endif /* STATS_HPP_INCLUDED */
--- a/projects/basic_network/render.cpp	Mon Sep 14 17:31:24 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,150 +0,0 @@
-/*
- * render.cpp
- *
- *  Created on: Oct 24, 2014
- *      Author: parallels
- */
-
-#include <BeagleRT.h>
-//#include <rtdk.h>
-#include <cmath>
-#include <UdpClient.h>
-#include <Utilities.h>
-
-AuxiliaryTask transmitReceiveDataTask;
-
-#define NETWORK_AUDIO_BUFFER_SIZE 400 //1400/4 //maximum payload for a UDP datagram over ethernet is 1472 bytes, I leave some headroom and divide by 4 to get the number of floats
-struct networkAudio{
-	int timestamp;
-	int currentBuffer;
-	int index;
-	float buffers[2][NETWORK_AUDIO_BUFFER_SIZE];
-	int doneOnTime;
-	bool toBeSent;
-	UdpClient udpClient;
-};
-
-float gFrequency;
-float gPhase;
-float gInverseSampleRate;
-int gCount=0;
-//networkData networkObject;
-#define numNetAudio 3
-networkAudio netAudio[numNetAudio];
-AuxiliaryTask printIntervalTask;
-AuxiliaryTask transmitReceiveAudioTask;
-
-void transmitReceiveAudio(){ //transmit and receive audio buffers
-	for(int n=0;n<numNetAudio; n++){
-		if(netAudio[n].toBeSent){
-			netAudio[n].toBeSent=false;
-			netAudio[n].udpClient.send(netAudio[n].buffers[!netAudio[n].currentBuffer],NETWORK_AUDIO_BUFFER_SIZE*sizeof(float));
-			netAudio[n].doneOnTime=1;
-		}
-	}
-}
-
-// setup() is called once before the audio rendering starts.
-// Use it to perform any initialisation and allocation which is dependent
-// on the period size or sample rate.
-//
-// userData holds an opaque pointer to a data structure that was passed
-// in from the call to initAudio().
-//
-// Return true on success; returning false halts the program.
-bool setup(BeagleRTContext *context, void *userData)
-{
-	// Retrieve a parameter passed in from the initAudio() call
-	gFrequency = *(float *)userData;
-
-	gInverseSampleRate = 1.0 / context->audioSampleRate;
-	gPhase = 0.0;
-
-//	networkObject.counter=&gCount;
-//	networkObject.variables[0]=&gFrequency;
-//	networkObject.variables[1]=&gPhase;
-//	networkObject.numVariables=2;
-	for(int n=0; n<numNetAudio; n++){
-		netAudio[n].doneOnTime=1;
-		netAudio[n].index=0;
-		netAudio[n].currentBuffer=0;
-		netAudio[n].toBeSent=false;
-//		netAudio[n].udpClient.setPort(settings->transmitPort+n);
-//		netAudio[n].udpClient.setServer(settings->serverName);
-		netAudio[n].udpClient.setPort(9999+n);
-		netAudio[n].udpClient.setServer("192.168.7.1");
-	}
-//	setupSockets(settings->receivePort, settings->transmitPort, settings->serverName);
-
-//	transmitReceiveDataTask=createAuxiliaryTask(*transmitReceiveData, 10, "transmit-receive-data");
-//	scheduleAuxiliaryTask(transmitReceiveDataTask); //here it does not work
-	transmitReceiveAudioTask=BeagleRT_createAuxiliaryTask(*transmitReceiveAudio, 98, "transmit-receive-audio");
-	return true;
-}
-
-// render() is called regularly at the highest priority by the audio engine.
-// Input and output are given from the audio hardware and the other
-// ADCs and DACs (if available). If only audio is available, numMatrixFrames
-// will be 0.
-
-void render(BeagleRTContext *context, void *userData)
-{/*
-	for(unsigned int n = 0; n < context->audioFrames; n++) {
-		float out = 0.7f * sinf(gPhase);
-		gPhase += 2.0 * M_PI * gFrequency * gInverseSampleRate;
-		if(gPhase > 2.0 * M_PI)
-			gPhase -= 2.0 * M_PI;
-
-		for(unsigned int channel = 0; channel < context->audioChannels; channel++)
-			context->audioOut[n * context->audioChannels + channel] = out;
-
-		if(gCount == 0){
-			BeagleRT_scheduleAuxiliaryTask(transmitReceiveDataTask);
-		}
-		gCount++;
-	}
-
-
-*/
-	for(int n = 0; n < context->audioFrames; n++) {
-		float out = 0.7f * sinf(gPhase);
-		gPhase += 2.0 * M_PI * gFrequency * gInverseSampleRate;
-		if(gPhase > 2.0 * M_PI)
-			gPhase -= 2.0 * M_PI;
-
-//		for(int channel = 0; channel < context->audioChannels; channel++)
-//			context->audioOut[n * context->audioChannels + channel] = context->audioIn[n * context->audioChannels + 0]+context->audioIn[n * context->audioChannels + 1];
-		context->audioOut[n * context->audioChannels] = context->audioIn[n*context->audioChannels+0];
-		context->audioOut[n * context->audioChannels+1]=out;
-		if(0==gCount){
-//			scheduleAuxiliaryTask(transmitReceiveDataTask);
-		}
-		for(int j=0; j<numNetAudio; j++){
-			if(netAudio[j].index==(NETWORK_AUDIO_BUFFER_SIZE)){ // when the buffer is ready ...
-				netAudio[j].toBeSent=true;
-				netAudio[j].index=0; //reset the counter
-				if(netAudio[j].doneOnTime==0)
-					rt_printf("Network buffer underrun :-{\n");
-				netAudio[j].timestamp=gCount;
-				netAudio[j].currentBuffer=!netAudio[j].currentBuffer; //switch buffer
-				netAudio[j].doneOnTime=0;
-				BeagleRT_scheduleAuxiliaryTask(transmitReceiveAudioTask); //send the buffer
-			}
-		}
-		if((gCount&1)==0){
-			netAudio[1].buffers[netAudio[1].currentBuffer][netAudio[1].index++]=analogReadFrame(context,n/2,0)+context->audioOut[n*context->audioChannels + 0];
-			netAudio[2].buffers[netAudio[2].currentBuffer][netAudio[2].index++]=analogReadFrame(context,n/2,1)+context->audioOut[n*context->audioChannels + 0];
-		}
-		netAudio[0].buffers[netAudio[0].currentBuffer][netAudio[0].index++]=0.5*(out+context->audioOut[n*context->audioChannels + 0]);//copy channel 0 to the buffer
-//		netAudio[1].buffers[netAudio[1].currentBuffer][netAudio[1].index++]=0.5*(out+context->audioOut[n*context->audioChannels + 0]);
-//		netAudio[2].buffers[netAudio[2].currentBuffer][netAudio[2].index++]=0.5*(out+context->audioOut[n*context->audioChannels + 0]);
-		gCount++;
-	}
-}
-
-// cleanup() is called once at the end, after the audio has stopped.
-// Release any resources that were allocated in setup().
-
-void cleanup(BeagleRTContext *context, void *userData)
-{
-}
--- a/projects/scope/render.cpp	Mon Sep 14 17:31:24 2015 +0100
+++ b/projects/scope/render.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -1,12 +1,16 @@
 #include <BeagleRT.h>
-#include <Scope.h>
+#include <NetworkSend.h>
+#include <ReceiveAudioThread.h>
+#include <ClockSynchronizer.h>
 #include <cmath>
+#include <ClockSyncThread.h>

 float gPhase1, gPhase2;
 float gFrequency1, gFrequency2;
 float gInverseSampleRate;

-Scope scope;    //create a scope object
+//Scope scope(2);   //create a scope object with 2 channels
+//NetworkSend networkSend;

 // initialise_render() is called once before the audio rendering starts.
 // Use it to perform any initialisation and allocation which is dependent
@@ -16,10 +20,37 @@
 // in from the call to initAudio().
 //
 // Return true on success; returning false halts the program.
+//ReceiveAudioThread receiveAudio0;
+//ReceiveAudioThread receiveAudio1;
+ClockSynchronizer clockSynchronizer;
+extern I2c_Codec* gAudioCodec;
+VirtualClock virtualClock;
+ClockSyncThread clockSyncThread;
+AuxiliaryTask testTime;
+void testTimeFunction(){
+	rt_printf("time=[");
+	while(!gShouldStop){
+		rt_task_sleep(50000*1e3);
+		rt_printf("%f, ", virtualClock.getNow());
+		rt_printf("%f, ", virtualClock.getPeriod());
+		rt_task_sleep(20000);
+		rt_printf("%f,", virtualClock.getNow());
+		rt_printf("%f\n", virtualClock.getPeriod());
+	}
+	rt_printf("];");
+}
 bool setup(BeagleRTContext *context, void *userData)
 {
-	scope.setup(context->audioSampleRate);  //call this once in setup to initialise the scope
-
+//	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");
+//	clockSynchronizer.setup();
+	virtualClock.init();
+	clockSyncThread.init(true, 5000, virtualClock); //start as slave
 	gInverseSampleRate = 1.0/context->audioSampleRate;

 	gPhase1 = 0.0;
@@ -27,6 +58,8 @@

 	gFrequency1 = 200.0;
 	gFrequency2 = 201.0;
+
+//	testTime=BeagleRT_createAuxiliaryTask(testTimeFunction, 80, "testTimeTask");
 	return true;
 }

@@ -37,33 +70,94 @@

 void render(BeagleRTContext *context, void *userData)
 {
+	virtualClock.sync(context->audioFrames);
+	static int count=0;
+	if(count==0){
+//		BeagleRT_scheduleAuxiliaryTask(testTime);
+		clockSyncThread.startThread(); //make sure you uncomment .init in setup()
+	}
+	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))==0)){
+//		rt_printf("b %d\n", count);
+		clockSynchronizer.update(networkSend.getTimestamp(), receiveAudio0.getTimestamp(), receiveAudio0.getLastTime());
+//		nextCall=count+100000;
+//		rt_printf("a %d\n", count);
+	}
+//	if(count == nextCall){
+//		clockSynchronizer.update(networkSend.getTimestamp(), receiveAudio0.getTimestamp(), receiveAudio0.getLastTime());
+//	}
+	if(count==0){
+		gAudioCodec->setAudioSamplingRate( 44100);
+		rt_printf("startHread\n");
+		ReceiveAudioThread::startThread();
+	}
 	for(unsigned int n = 0; n < context->audioFrames; n++) {

-	    float chn1 = sinf(gPhase1);
-	    float chn2 = sinf(gPhase2);
-
-	    float chn3 = context->audioIn[n*2 + 0];
-	    float chn4 = context->audioIn[n*2 + 1];
-
-	    float chn5 = context->analogIn[(int)n/2*8 + 0];
-	    float chn6 = context->analogIn[(int)n/2*8 + 1];
+		float chn0 = sinf(gPhase1);
+//		float chn1 = sinf(gPhase2);
+
+    //  float chn2 = context->audioIn[n*2 + 0];
+    //  float chn3 = context->audioIn[n*2 + 1];
+
+    //  float chn4 = context->analogIn[(int)n/2*8 + 0];
+    //  float chn5 = context->analogIn[(int)n/2*8 + 1];
+//		networkSend.log(context->audioIn[n]);
+		networkSend.log(chn0);
+//		scope.log(0, chn0);
+//		scope.log(1, chn1);
+		//  scope.log(2, chn2);
+		//  scope.log(3, chn3);
+		//  scope.log(4, chn4);
+		//  scope.log(5, chn5);

 //	    scope.log(chn1, chn2, chn3, chn4, chn5, chn6);
-	    scope.log(chn1);
 	    //call this once every audio frame
 	    //takes six or fewer floats as parameters
 	    //first parameter becomes channel 1 etc
 	    //to view, click the 'oscilloscope' button on the toolbar while BeagleRT is NOT running
 	    //then click the big red button on the toolbar on this page

-	    gPhase1 += 2.0 * M_PI * gFrequency1 * gInverseSampleRate;
-	    gPhase2 += 2.0 * M_PI * gFrequency2 * gInverseSampleRate;
+	    gPhase1 += 2.0 * M_PI * gFrequency1 * gInverseSampleRate * ((count&65535)/65535.0+1);
+			gPhase2 += 2.0 * M_PI * gFrequency2 * gInverseSampleRate;
 		if(gPhase1 > 2.0 * M_PI)
 			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=1;
+		int length=receiveAudio0.getSamplesSrc(context->audioOut, context->audioFrames,
+				samplingRateRatio, channelsInDestinationBuffer, channelToWriteTo);
+		if((unsigned int)length!=context->audioFrames){
+			rt_printf("Length mismatch: %d\n", length);
+		}
+//		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];
+	}
+	*/
+
 }

 // cleanup_render() is called once at the end, after the audio has stopped.
--- a/resources/network/udp-server.c	Mon Sep 14 17:31:24 2015 +0100
+++ b/resources/network/udp-server.c	Mon Sep 14 17:35:18 2015 +0100
@@ -47,11 +47,12 @@
        n = recvfrom(sock,buf,2048,0,(struct sockaddr *)&from,&fromlen);
        if (n < 0) error("recvfrom");
        printf("Received a datagram of size %d: \n", n);
-       for(i=0; i<n/sizeof(float); i+=8)
-	       printf("[%05d]: %+f, %+f, %+f, %+f, %+f, %+f, %+f, %+f\n",i,buf[0+i],buf[1+i],buf[2+i],buf[3+i],buf[4+i],buf[5+i],buf[6+i],buf[7+i]);
-       n = sendto(sock,"Got your message\n",17,
-                  0,(struct sockaddr *)&from,fromlen);
-       if (n  < 0) error("sendto");
+       printf("Header: channel: %d, timestamp: %d\n", (int)buf[0], (int)buf[1]);
+       //  for(i=2; i<n/sizeof(float); i+=8)
+	       //  printf("%+f, %+f, %+f, %+f, %+f, %+f, %+f, %+f\n",buf[0+i],buf[1+i],buf[2+i],buf[3+i],buf[4+i],buf[5+i],buf[6+i],buf[7+i]);
+       //  n = sendto(sock,"Got your message\n",17,
+                  //  0,(struct sockaddr *)&from,fromlen);
+       //  if (n  < 0) error("sendto");
    }
    return 0;
  }
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resources/tests/UdpClientUdpServerTest.cpp	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,128 @@
+#include "../../include/UdpServer.h"
+#include "../../include/UdpClient.h"
+#include <unistd.h>
+
+int test1(UdpServer *server, UdpClient *client){
+	int buffer;
+	int tot=100;
+	int errors=0;
+	for(int n=0; n<tot; n++){
+		if(client->send(&n,sizeof(int))!=1){
+			printf("error: while sending\n");
+			errors++;
+		}
+	}
+	for(int n=0; n<tot; n++){
+		if(server->read(&buffer,sizeof(int))<0){
+			printf("error: unable to read\n");
+			errors++;
+			continue;
+		};
+		if(n!=buffer){
+			printf("error: %d!=%d\n",n,buffer);
+			errors++;
+		}
+	}
+	int n=server->emptySocket();
+	if(n!=0)
+		printf("Error: the socket had %d bytes\n",n);
+	return errors;
+}
+int compareStrings(char * str1, char * str2){
+	if(strlen(str1)!=strlen(str2))
+		return -1;
+	for(int n=0; n<strlen(str1); n++){
+		if(str1[n]!=str2[n])
+			return -1;
+	}
+	return 0;
+}
+
+int test2(UdpServer *server, UdpClient *client){
+	char buffer[1000];
+	int tot=100;
+	int errors=0;
+	for(int n=0; n<tot; n++){
+		int num=sprintf(buffer,"%08.8f",n/1000.0);
+		client->send(&buffer,sizeof(char)*(num+1));
+	}
+	char auxBuffer[100];
+	for(int n=0; n<tot; n++){
+		int num=sprintf(auxBuffer,"%08.8f",n/1000.0);
+		server->read(&buffer,num*sizeof(char));
+		if(compareStrings(auxBuffer,buffer)==-1){
+			printf("error: %s!=%s\n",auxBuffer,buffer);
+			errors++;
+		}
+	}
+
+	return errors;
+}
+
+int test3(UdpServer *server, UdpClient *client){
+	char buffer[1000];
+	int tot=100;
+	int errors=0;
+    int totNum=0;
+	for(int n=0; n<tot; n++){
+		int num=sprintf(buffer,"%.8f",n/1000.0);
+		client->send(&buffer,sizeof(char)*(num+1));
+        totNum+=1+num;
+	}
+    int n=server->emptySocket();
+    if(n!=totNum){
+        errors=1;
+        printf("retrieved bytes differs from sent bytes: %d!=%d\n",n,totNum);
+    }
+	return errors;
+}
+
+
+int main(){
+	int port=1234;
+	char serverName[]="127.0.0.1";
+	UdpServer server(port);
+	UdpClient client(port,serverName);
+	int errors=0;
+	int ret=0;
+	ret=test1(&server,&client);
+	errors+=ret;
+	if(ret)
+		printf("test1 failed with %d errors\n", ret);
+	else
+		printf("test1 passed\n");
+
+	ret=test2(&server,&client);
+	errors+=ret;
+	if(ret)
+		printf("test2 failed with %d errors\n", ret);
+	else
+		printf("test2 passed\n");
+
+	ret=test3(&server,&client);
+	errors+=ret;
+	if(ret)
+		printf("test3 failed with %d errors\n", ret);
+	else
+		printf("test3 passed\n");
+//now test if the setPort and setServer methods work
+	client.~UdpClient();
+	server.~UdpServer();
+	port=1235;
+	UdpServer server1;
+	UdpClient client1;
+	client1.setPort(port);
+	client1.setServer(serverName);
+	if(server1.bindToPort(port)==false){
+		printf("unable to bind to port %d\n",port);
+		errors+=1;
+	}
+	ret=test1(&server1, &client1);
+	errors+=ret;
+	if(ret)
+		printf("test1 failed with %d errors\n", ret);
+	else
+		printf("test1 passed\n");
+
+	return errors;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resources/tests/make_tests.sh	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,7 @@
+#!/bin/bash
+mkdir -p build
+mkdir -p bin
+g++ -o build/UdpServer.o -O2 -c ../../core/UdpServer.cpp &&\
+g++ -O2 -o build/UdpClient.o -c ../../core/UdpClient.cpp && \
+g++ -O2 -o build/UdpClientUdpServerTest.o -c UdpClientUdpServerTest.cpp && \
+g++ -o bin/UdpClientUdpServerTest build/UdpClientUdpServerTest.o build/UdpClient.o build/UdpServer.o
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resources/tests/run_tests.sh	Mon Sep 14 17:35:18 2015 +0100
@@ -0,0 +1,2 @@
+#!/bin/bash
+bin/*