#ifdef SLS_RECEIVER_FUNCTION_LIST
/********************************************//**
 * @file slsReceiverFunctionList.cpp
 * @short does all the functions for a receiver, set/get parameters, start/stop etc.
 ***********************************************/


#include "slsReceiverFunctionList.h"

#include <signal.h>  		// SIGINT
#include <sys/stat.h> 		// stat
#include <sys/socket.h>		// socket(), bind(), listen(), accept(), shut down
#include <arpa/inet.h>		// sock_addr_in, htonl, INADDR_ANY
#include <stdlib.h>			// exit()
#include <iomanip>			//set precision
#include <sys/mman.h>		//munmap



#include <string.h>
#include <iostream>
using namespace std;

FILE* slsReceiverFunctionList::sfilefd(NULL);
int slsReceiverFunctionList::receiver_threads_running(0);

slsReceiverFunctionList::slsReceiverFunctionList(detectorType det):
														myDetectorType(det),
														maxFramesPerFile(MAX_FRAMES_PER_FILE),
														enableFileWrite(1),
														fileIndex(0),
														frameIndexNeeded(0),
														framesCaught(0),
														acqStarted(false),
														measurementStarted(false),
														startFrameIndex(0),
														frameIndex(0),
														totalFramesCaught(0),
														totalPacketsCaught(0),
														startAcquisitionIndex(0),
														acquisitionIndex(0),
														packetsInFile(0),
														prevframenum(0),
														listening_thread_running(0),
														writing_thread_running(0),
														status(IDLE),
														latestData(NULL),
														udpSocket(NULL),
														server_port(DEFAULT_UDP_PORTNO),
														fifo(NULL),
														fifofree(NULL),
														fifosize(GOTTHARD_FIFO_SIZE),
														shortFrame(-1),
														bufferSize(GOTTHARD_BUFFER_SIZE),
														packetsPerFrame(GOTTHARD_PACKETS_PER_FRAME),
														guiDataReady(0),
														guiData(NULL),
														guiFileName(NULL),
														currframenum(0),
														nFrameToGui(0),
														frameIndexMask(GOTTHARD_FRAME_INDEX_MASK),
														frameIndexOffset(GOTTHARD_FRAME_INDEX_OFFSET),
														dataCompression(false),
														numJobsPerThread(GOTTHARD_NUM_JOBS_P_THREAD),
														userDefinedNumJobsPerThread(0),
														startAcquisitionCallBack(NULL),
														pStartAcquisition(NULL),
														acquisitionFinishedCallBack(NULL),
														pAcquisitionFinished(NULL),
														rawDataReadyCallBack(NULL),
														pRawDataReady(NULL)



{
	int aligned_frame_size = GOTTHARD_ALIGNED_FRAME_SIZE;

	if(myDetectorType == MOENCH){
		aligned_frame_size = MOENCH_ALIGNED_FRAME_SIZE;
		fifosize = MOENCH_FIFO_SIZE;
		maxFramesPerFile = MOENCH_MAX_FRAMES_PER_FILE;
		bufferSize = MOENCH_BUFFER_SIZE;
		packetsPerFrame = MOENCH_PACKETS_PER_FRAME;
		frameIndexMask = MOENCH_FRAME_INDEX_MASK;
		frameIndexOffset = MOENCH_FRAME_INDEX_OFFSET;
		numJobsPerThread = MOENCH_NUM_JOBS_P_THREAD;
	}

	if(userDefinedNumJobsPerThread)
		numJobsPerThread = userDefinedNumJobsPerThread;


	oneBufferSize = bufferSize/packetsPerFrame;

	strcpy(savefilename,"");
	strcpy(filePath,"");
	strcpy(fileName,"run");
	guiFileName = new char[MAX_STR_LENGTH];
	strcpy(guiFileName,"");
	eth = new char[MAX_STR_LENGTH];
	strcpy(eth,"");

	latestData = new char[bufferSize];
	fifofree = new CircularFifo<char>(fifosize);
	fifo = new CircularFifo<char>(fifosize);



	mem0=(char*)malloc(aligned_frame_size*fifosize);
	if (mem0==NULL) {
		cout<<"++++++++++++++++++++++ COULD NOT ALLOCATE MEMORY!!!!!!!+++++++++++++++++++++" << endl;
	}
	buffer=mem0;
	while (buffer<(mem0+aligned_frame_size*(fifosize-1))) {
		fifofree->push(buffer);
		buffer+=aligned_frame_size;
	}


	int16_t* map;
	int16_t* mask;
	int initial_offset = 2;
	int later_offset = 1;

	int mask_y_offset = 120;
	int mask_adc = 0x7fff;
	int num_packets_in_col = 4;
	int num_packets_in_row = 10;
	int num_pixels_per_packet_in_row = 40;
	int num_pixels_per_packet_in_col = 16;
	int offset,ipacket;


	int x,y,i,j;
	int ipx,ipy,ix,iy;

	/** not for roi */
	//filter
	switch(myDetectorType){
	case MOENCH:
		x = MOENCH_PIXELS_IN_ONE_ROW;
		y = MOENCH_PIXELS_IN_ONE_ROW;

		mask = new int16_t[x*y];
		map = new int16_t[x*y];

		//set up mask for moench
		for(i=0;i<x; i++)
			for(j=0;j<y; j++){
				if (j<mask_y_offset)
					mask[i*y+j] = mask_adc;
				else
					mask[i*y+j] = 0;
			}

		//set up mapping for moench
		for (ipy = 0; ipx < num_packets_in_col; ipx++ )
			for (ipx = 0; ipy < num_packets_in_row; ipy++ ){
				offset = initial_offset;
				for (ix = 0; ix < num_pixels_per_packet_in_col; ix++ ){
					for (iy = 0; iy < num_pixels_per_packet_in_row; iy++ ){
						ipacket = (ipx + 1) + (ipy * num_packets_in_row);
						if (ipacket == MOENCH_PACKETS_PER_FRAME)
							ipacket = 0;
						map[ (ipx * num_pixels_per_packet_in_col + ix) * y + (ipy * num_pixels_per_packet_in_row + iy) ] =
								ipacket * MOENCH_ONE_PACKET_SIZE + offset;
						offset += later_offset;
					}

				}
			}


		filter = new singlePhotonFilter(x,y, MOENCH_FRAME_INDEX_MASK, MOENCH_PACKET_INDEX_MASK, MOENCH_FRAME_INDEX_OFFSET,
				0, MOENCH_PACKETS_PER_FRAME, 0,map, mask,fifofree,MOENCH_BUFFER_SIZE);
		break;
	default:
		x = 1;
		y = (GOTTHARD_DATA_BYTES/GOTTHARD_PACKETS_PER_FRAME);/*bufferSize/sizeof(int16_t)*/
		offset = initial_offset;

		mask = new int16_t[x*y];
		map = new int16_t[x*y];

		//set up mask for gotthard
		for (i=0; i < x; i++)
			for (j=0; j < y; j++){
				mask[i*y+j] = 0;
			}

		//set up mapping for gotthard
		for (i=0; i < x; i++)
			for (j=0; j < y; j++){
				//since there are 2 packets
				if (j == y/2){
					offset += initial_offset;
					offset += 1;
				}
				map[i*y+j] = offset;
				/*cout<<"offset["<<i*y+j<<"]:"<<map[i*y+j]<<"\t";*/
				offset += 1;
			}
cout<<endl;

		filter = new singlePhotonFilter(x,y,GOTTHARD_FRAME_INDEX_MASK, GOTTHARD_PACKET_INDEX_MASK, GOTTHARD_FRAME_INDEX_OFFSET,
				0, GOTTHARD_PACKETS_PER_FRAME, 1,map, mask,fifofree,GOTTHARD_BUFFER_SIZE);
		break;
	}



	pthread_mutex_init(&status_mutex,NULL);
	pthread_mutex_init(&dataReadyMutex,NULL);


	dataCompression = false;
}



slsReceiverFunctionList::~slsReceiverFunctionList(){
	if(latestData) delete [] latestData;
	if(fifofree) delete [] fifofree;
	if(fifo) delete [] fifo;
	if(guiFileName) delete [] guiFileName;
	if(eth) delete [] eth;
	if(mem0) free(mem0);
}




int slsReceiverFunctionList::setEnableFileWrite(int i){
	if(i!=-1)
		enableFileWrite=i;
	return enableFileWrite;
}


void slsReceiverFunctionList::setEthernetInterface(char* c){
	strcpy(eth,c);
}



uint32_t slsReceiverFunctionList::getFrameIndex(){
	if(!framesCaught)
		frameIndex=0;
	else
		frameIndex = currframenum - startFrameIndex;
	return frameIndex;
}



uint32_t slsReceiverFunctionList::getAcquisitionIndex(){
	if(!totalFramesCaught)
		acquisitionIndex=0;
	else
		acquisitionIndex = currframenum - startAcquisitionIndex;
	return acquisitionIndex;
}



char* slsReceiverFunctionList::setFileName(char c[]){
	if(strlen(c))
		strcpy(fileName,c);

	return getFileName();
}



char* slsReceiverFunctionList::setFilePath(char c[]){
	if(strlen(c)){
		//check if filepath exists
		struct stat st;
		if(stat(c,&st) == 0)
			strcpy(filePath,c);
		else{
			strcpy(filePath,"");
			cout<<"FilePath does not exist:"<<filePath<<endl;
		}
	}
	return getFilePath();
}



int slsReceiverFunctionList::setFileIndex(int i){
	if(i>=0)
		fileIndex = i;
	return getFileIndex();
}


void slsReceiverFunctionList::resetTotalFramesCaught(){
	acqStarted = false;
	startAcquisitionIndex = 0;
	totalFramesCaught = 0;
	totalPacketsCaught = 0;
}



int slsReceiverFunctionList::startReceiver(char message[]){
#ifdef VERBOSE
	cout << "Starting Receiver" << endl;
#endif
	cout << endl;

	int err = 0;
	if(!receiver_threads_running){
#ifdef VERBOSE
		cout << "Starting new acquisition threadddd ...." << endl;
#endif
		//change status
		pthread_mutex_lock(&status_mutex);
		status = IDLE;
		listening_thread_running = 0;
		writing_thread_running = 0;
		receiver_threads_running = 1;
		pthread_mutex_unlock(&(status_mutex));


		// creating listening thread----------
		err = pthread_create(&listening_thread, NULL,startListeningThread, (void*) this);
		if(err){
			//change status
			pthread_mutex_lock(&status_mutex);
			status = IDLE;
			listening_thread_running = 0;
			receiver_threads_running = 0;
			pthread_mutex_unlock(&(status_mutex));

			sprintf(message,"Cant create listening thread. Status:%d\n",status);
			cout << endl << message << endl;
			return FAIL;
		}
		//wait till udp socket created
		while(!listening_thread_running);
		if(listening_thread_running==-1){
			//change status
			pthread_mutex_lock(&status_mutex);
			status = IDLE;
			listening_thread_running = 0;
			receiver_threads_running = 0;
			pthread_mutex_unlock(&(status_mutex));
			strcpy(message,"Could not create UDP Socket.\n");
			return FAIL;
		}
#ifdef VERBOSE
		cout << "Listening thread created successfully." << endl;
#endif

		// creating writing thread----------
		err = 0;
		err = pthread_create(&writing_thread, NULL,startWritingThread, (void*) this);
		if(err){
			//change status
			pthread_mutex_lock(&status_mutex);
			status = IDLE;
			writing_thread_running = 0;
			receiver_threads_running = 0;
			pthread_mutex_unlock(&(status_mutex));

			//stop listening thread
			pthread_join(listening_thread,NULL);
			sprintf(message,"Cant create writing thread. Status:%d\n",status);
			cout << endl << message << endl;
			return FAIL;
		}
		//wait till file is created
		while(!writing_thread_running);
		if(writing_thread_running==-1){
			//change status
			pthread_mutex_lock(&status_mutex);
			status = IDLE;
			listening_thread_running = 0;
			receiver_threads_running = 0;
			pthread_mutex_unlock(&(status_mutex));
			if(udpSocket) udpSocket->ShutDownSocket();
			pthread_join(listening_thread,NULL);
			sprintf(message,"Could not create file %s.\n",savefilename);
			return FAIL;
		}
#ifdef VERBOSE
		cout << "Writing thread created successfully." << endl;
#endif


		//change status----------
		pthread_mutex_lock(&status_mutex);
		status = RUNNING;
		pthread_mutex_unlock(&(status_mutex));
		cout << "Threads created successfully." << endl;




		struct sched_param tcp_param, listen_param, write_param;
		int policy= SCHED_RR;

		tcp_param.sched_priority = 50;
		listen_param.sched_priority = 99;
		write_param.sched_priority = 90;


		if (pthread_setschedparam(listening_thread, policy, &listen_param) == EPERM)
			cout << "WARNING: Could not prioritize threads. You need to be super user for that." << endl;
		if (pthread_setschedparam(writing_thread, policy, &write_param) == EPERM)
			cout << "WARNING: Could not prioritize threads. You need to be super user for that." << endl;
		if (pthread_setschedparam(pthread_self(),5 , &tcp_param) == EPERM)
			cout << "WARNING: Could not prioritize threads. You need to be super user for that." << endl;


		//pthread_getschedparam(pthread_self(),&policy,&tcp_param);
		//cout << "current priority of main tcp thread is " << tcp_param.sched_priority << endl;

	}

	//initialize semaphore
	sem_init(&smp,0,1);

	return OK;
}





int slsReceiverFunctionList::stopReceiver(){
//#ifdef VERBOSE
	cout << "Stopping Receiver" << endl;
//#endif

	if(receiver_threads_running){
//#ifdef VERBOSE
		cout << "Stopping new acquisition thread" << endl;
//#endif
		//stop listening thread
		pthread_mutex_lock(&status_mutex);
		receiver_threads_running=0;
		pthread_mutex_unlock(&(status_mutex));

		if(udpSocket) udpSocket->ShutDownSocket();
		pthread_join(listening_thread,NULL);
		pthread_join(writing_thread,NULL);
		/*if(dataCompression)
			filter->enableCompression(false);*/
	}
	//change status
	pthread_mutex_lock(&status_mutex);
	status = IDLE;
	pthread_mutex_unlock(&(status_mutex));;

	//semaphore destroy
	sem_post(&smp);
	sem_destroy(&smp);


	cout << "Receiver Stopped.\nStatus:" << status << endl;
	return OK;
}



void* slsReceiverFunctionList::startListeningThread(void* this_pointer){
	((slsReceiverFunctionList*)this_pointer)->startListening();

	return this_pointer;
}










int slsReceiverFunctionList::startListening(){
#ifdef VERYVERBOSE
	cout << "In startListening()\n");
#endif
	int rc=0;
	measurementStarted = false;
	startFrameIndex = 0;
	int offset=0;
	int ret=1;
	int i=0;
	char *tempchar = new char[oneBufferSize];


	//to increase socket receiver buffer size and max length of input queue by changing kernel settings
	if(system("echo $((100*1024*1024)) > /proc/sys/net/core/rmem_max"))
		cout << "\nWARNING: Could not change socket receiver buffer size in file /proc/sys/net/core/rmem_max" << endl;
	else if(system("echo 250000 > /proc/sys/net/core/netdev_max_backlog"))
		cout << "\nWARNING: Could not change max length of input queue in file /proc/sys/net/core/netdev_max_backlog" << endl;

	/** permanent setting heiner
		net.core.rmem_max = 104857600 # 100MiB
		net.core.netdev_max_backlog = 250000
		sysctl -p
		// from the manual
		sysctl -w net.core.rmem_max=16777216
		sysctl -w net.core.netdev_max_backlog=250000
	 */

	//creating udp socket
	if (strchr(eth,'.')!=NULL) strcpy(eth,"");
	if(!strlen(eth)){
		cout<<"warning:eth is empty.listening to all"<<endl;
		if(udpSocket){
			delete udpSocket;
			udpSocket = NULL;
		}
		udpSocket = new genericSocket(server_port,genericSocket::UDP,oneBufferSize,1);//packetsPerFrame);
	}else{
		cout<<"eth:"<<eth<<endl;
		udpSocket = new genericSocket(server_port,genericSocket::UDP,oneBufferSize,1,eth);//packetsPerFrame,eth);
	}
	int iret = udpSocket->getErrorStatus();
	if (iret){
		//#ifdef VERBOSE
		std::cout<< "Could not create UDP socket on port "<< server_port  << " error:"<<iret<<std::endl;
		//#endif
		pthread_mutex_lock(&status_mutex);
		listening_thread_running = -1;
		pthread_mutex_unlock(&status_mutex);
		return 0;
	}else{

		/*filter->setupAcquisitionParameters();*/


		while (receiver_threads_running) {

			if (!fifofree->isEmpty()) {
				if (ret!=0)
					fifofree->pop(buffer);


				if(ret == -3){
					memcpy(buffer,tempchar,oneBufferSize);
					offset = oneBufferSize;
					//set all the new frame header and remaining headers invalid
					for(i = offset; i < bufferSize; i += oneBufferSize)
						(*((uint32_t*)(buffer+i))) = 0xFFFFFFFF;
					//start from beginning
					offset = 0;
					ret = 0;
				}
				else{
					if(ret == -2){/** for moench, in between nxt, means ots -1*/
						memcpy(buffer,tempchar,oneBufferSize);
						offset = oneBufferSize;
						ret = 0;
					}


					if(!startFrameIndex){
						if(!listening_thread_running){
							pthread_mutex_lock(&status_mutex);
							listening_thread_running = 1;
							pthread_mutex_unlock(&(status_mutex));
						}
					}
					//receiver 2 half frames / 1 short frame / 40 moench frames
					rc = udpSocket->ReceiveDataOnly(buffer+offset,oneBufferSize);
					if( rc <= 0){
						//#ifdef VERYVERBOSE
						cerr << "recvfrom() failed:"<<endl;;// << receiver_threads_running<<endl;
						fifofree->push(buffer);
						//#endif
						continue;
					}


					//manipulate buffer number to inlude frame number and packet number for gotthard
					if ((myDetectorType == GOTTHARD) && (shortFrame == -1))
						(*((uint32_t*)(buffer+offset)))++;


					ret = filter->verifyFrame(buffer+offset);

					//start for each scan
					if(!measurementStarted){
						startFrameIndex = ((((uint32_t)(*((uint32_t*)buffer))) & (frameIndexMask)) >> frameIndexOffset);
						cout<<"startFrameIndex:"<<startFrameIndex<<endl;
						prevframenum=startFrameIndex;
						measurementStarted = true;
					}

					//start of acquisition
					if(!acqStarted){
						startAcquisitionIndex=startFrameIndex;
						currframenum = startAcquisitionIndex;
						acqStarted = true;
						cout<<"startAcquisitionIndex:"<<startAcquisitionIndex<<endl;
					}

					//last packet, but not the full frame, must push previous frame
					if(ret == -1){
						//set reminaing headers invalid
						for( i = offset+ oneBufferSize; i < bufferSize; i += oneBufferSize)
							(*((uint32_t*)(buffer+i))) = 0xFFFFFFFF;
						offset = 0;
					}

					else if(ret == -3){
						//copy the new frame to a temp
						memcpy(tempchar, buffer+offset, oneBufferSize);
						//set all the new frame header and remaining headers invalid
						for(i = offset; i < bufferSize; i += oneBufferSize)
							(*((uint32_t*)(buffer+i))) = 0xFFFFFFFF;
					}
					//first packet of new frame, must push previous frame
					else if(ret == -2){
						//copy the new frame to a temp
						memcpy(tempchar, buffer+offset, oneBufferSize);
						//set all the new frame header and remaining headers invalid
						for(i = offset; i < bufferSize; i += oneBufferSize)
							(*((uint32_t*)(buffer+i))) = 0xFFFFFFFF;
					}
					//wait for new packets of same frame
					else if (ret == 0){
						offset += oneBufferSize;
						continue;
					}
					//wait for next frame
					else
						offset = 0;

				}

				//so that it doesnt write the last frame twice
				if((receiver_threads_running) && (!fifo->isFull())){
					fifo->push(buffer);
				}

			}
		}
	}

	delete  tempchar;
	return 0;
}






void* slsReceiverFunctionList::startWritingThread(void* this_pointer){
	((slsReceiverFunctionList*)this_pointer)->startWriting();
	return this_pointer;
}




int slsReceiverFunctionList::startWriting(){
#ifdef VERYVERBOSE
	cout << "In startWriting()" <<endl;
#endif

	char *wbuf;
	int sleepnumber=0;
	int frameFactor=0;
	int i,p;

/*	char* trialarr[GOTTHARD_COMPRESSION_FIFO_SIZE];*/
	int iJob = -2;
	char* startingmem = 0;
	int header_of_last_packet = (packetsPerFrame-1)*oneBufferSize;
	int pointinfifo=0;
	int firsttime = 1;

	packetsInFile=0;
	framesCaught=0;
	frameIndex=0;
	if(sfilefd) sfilefd=NULL;
	strcpy(savefilename,"");



	//reset this before each acq or you send old data
	guiData = NULL;
	guiDataReady=0;
	strcpy(guiFileName,"");

	cout << "Max Frames Per File:" << maxFramesPerFile << endl;
	if (rawDataReadyCallBack)
		cout << "Note: Data Write has been defined exernally" << endl;
	if (dataCompression)
		cout << "Data Compression is enabled with " << numJobsPerThread << " number of jobs per thread" << endl;
	if(nFrameToGui)
		cout << "Sending every " << nFrameToGui << "th frame to gui" <<  endl;

	//by default, we read/write everything
	cbAction = DO_EVERYTHING;
	//acquisition start call back returns enable write
	if (startAcquisitionCallBack)
		cbAction=startAcquisitionCallBack(filePath,fileName,fileIndex,bufferSize,pStartAcquisition);
	if(cbAction < DO_EVERYTHING)
		cout << endl << "Note: Call back activated. Data saving must be taken care of by user in call back." << endl;
	else if(enableFileWrite==0)
		cout << endl << "Note: Data will not be saved" << endl;


	cout << "Ready!" << endl;


	//will always run till acquisition over and then runs till fifo is empty
	while(receiver_threads_running || (!fifo->isEmpty())){

		//start a new file
		if ((strlen(savefilename) == 0) || ((packetsInFile/packetsPerFrame) >= maxFramesPerFile)){

			//create file name
			if(!dataCompression){
				if(frameIndexNeeded==-1)
					sprintf(savefilename, "%s/%s_%d.raw", filePath,fileName,fileIndex);
				else
					sprintf(savefilename, "%s/%s_f%012d_%d.raw", filePath,fileName,framesCaught,fileIndex);
			}

			//only for gui display
			else if(strlen(savefilename) == 0){
				sprintf(savefilename, "%s/%s_fxxx_%d.raw", filePath,fileName,fileIndex);
				filter->setupAcquisitionParameters(filePath,fileName,fileIndex);
			}



			if(enableFileWrite && cbAction > DO_NOTHING){
				if (dataCompression){
					//only the first time
					if ((!framesCaught) && (filter->initTree()== FAIL)){
						cout << " Error: Could not create file " << savefilename << endl;
						pthread_mutex_lock(&status_mutex);
						writing_thread_running = -1;
						pthread_mutex_unlock(&(status_mutex));
						break;
					}
				}


				//standard way
				else{
					//close and open file
					if(sfilefd){
						fclose(sfilefd);
						sfilefd = NULL;
					}
					if (NULL == (sfilefd = fopen((const char *) (savefilename), "w"))){
						cout << "Error: Could not create file " << savefilename << endl;
						pthread_mutex_lock(&status_mutex);
						writing_thread_running = -1;
						pthread_mutex_unlock(&(status_mutex));
						break;
					}
					//setting buffer
					setvbuf(sfilefd,NULL,_IOFBF,BUF_SIZE);


					//printing packet losses and file names
					if(!framesCaught)
						cout << savefilename << endl;
					else{
						cout << savefilename
								<< "\tpacket loss "
								<< setw(4)<<fixed << setprecision(4)<< dec <<
								(int)(((((currframenum-prevframenum)*packetsPerFrame)-(packetsInFile))/(double)((currframenum-prevframenum)*packetsPerFrame))*100.000)/*packetloss*/
								<< "%\tframenum "
								<< dec << currframenum //<< "\t\t p " << prevframenum
								<< "\tindex " << dec << getFrameIndex()
								<< "\tpackets lost " << dec << ((currframenum-prevframenum)*packetsPerFrame)-(packetsInFile) << endl;

					}
				}
			}

			//only the first time - state the thread is rinning
			if (!framesCaught){
				pthread_mutex_lock(&status_mutex);
				writing_thread_running = 1;
				pthread_mutex_unlock(&(status_mutex));
			}
			else if (!dataCompression){
				prevframenum = currframenum;
				packetsInFile=0;
			}
		}


		//pop fifo
		if(!fifo->isEmpty()){

			if(fifo->pop(wbuf)){
				currframenum = ((uint32_t)(*((uint32_t*)wbuf))& frameIndexMask) >>frameIndexOffset;
				//cout<<"currframenum2:"<<((((uint32_t)(*((uint32_t*)((char*)(wbuf+oneBufferSize)))))& frameIndexMask) >> frameIndexOffset)<<endl;;

				//write data call back
				if (cbAction < DO_EVERYTHING) {
					rawDataReadyCallBack(currframenum, wbuf, bufferSize, sfilefd, guiData,pRawDataReady);
				}

				//default writing to file
				else if(enableFileWrite){

					if(dataCompression){

						//if whole frame received
						if(((uint32_t)(*((uint32_t*)(wbuf+header_of_last_packet)))) != 0xFFFFFFFF){
							framesCaught++;
							totalFramesCaught++;
							packetsInFile += packetsPerFrame;
							totalPacketsCaught += packetsPerFrame;
							p = packetsPerFrame;
						}
						//to skip incompleete frames
						else  {
							/*cout<<"***not whole frame currframenum:"<<currframenum<<endl;*/
							(*((uint32_t*)(wbuf))) = 0xFFFFFFFF;
							p=0;
						}


						/*cout<<"wbuf:"<<(void*)wbuf<<endl;*/
						//filter and write
						if(iJob==-2){
							/*cout<<"startingmem changed"<<endl;*/
							startingmem = wbuf;
							/*cout<<"***************startingmem:"<<(void*)startingmem<<endl;
							cout<<"mem0:"<<(void*)mem0<<endl;*/
							iJob=0;
							if(firsttime){
								pointinfifo = (startingmem-mem0)/4096;
								firsttime = 0;
								/*cout<<"fist time pointinfifo :"<<pointinfifo+1<< " iJob:"<<iJob+1<<endl;*/
							}
						}
						++pointinfifo;
						++iJob;

						if(pointinfifo >= (fifosize-1)){
							/*cout<<"*** sending not normally  "<<iJob<<endl;
							cout<<"value:"<<((startingmem-mem0)/4096)+1<<endl;
							 cout<<"pointfifo:"<<pointinfifo<<endl;
							cout<<"iJob:"<<iJob<<endl;*/
							filter->assignJobsForThread(startingmem,iJob);
							startingmem = mem0;
							iJob = 0;
							pointinfifo = 0;
							/*cout<<"***************1trialmem:"<<(void*)startingmem<<endl;
							cout<<"1mem0:"<<(void*)mem0<<endl;
							cout<<"1fist time pointinfifo :"<<pointinfifo+1<< " iJob:"<<iJob+1<<endl;*/

						}
						else if(iJob>=(numJobsPerThread)){
							/*cout<<"*** sending normally "<<numJobsPerThread<<endl;
							cout<<"value:"<<((startingmem-mem0)/4096)+1<<endl;
							 cout<<"pointfifo:"<<pointinfifo<<endl;
							cout<<"iJob:"<<iJob<<endl;*/
							filter->assignJobsForThread(startingmem,numJobsPerThread);
							iJob = -2;
						}
					}


					//standard way
					else{
						//find number of packets received
						for(i=0,p=0; i < bufferSize; i+=oneBufferSize,++p){
							if(((uint32_t)(*((uint32_t*)((wbuf+i))))) == 0xFFFFFFFF){
								break;
							}
						}
						//increment counters
						totalPacketsCaught += p;
						packetsInFile += p;
						if(p == packetsPerFrame){
							framesCaught++;
							totalFramesCaught++;
						}
						//write to file
						if(sfilefd)
							fwrite(wbuf, 1, p*oneBufferSize, sfilefd);
						else{
							cout << "You do not have permissions to overwrite: " << savefilename << endl;
							usleep(50000);
						}
					}
				}



				//does not read every frame
				if(!nFrameToGui){
					if((guiData) && (p == packetsPerFrame)){/*change it in funcs*/
				/*	if(guiData){*/
						pthread_mutex_lock(&dataReadyMutex);
						guiDataReady=0;
						pthread_mutex_unlock(&dataReadyMutex);
						memcpy(latestData,wbuf,bufferSize);
						strcpy(guiFileName,savefilename);
						pthread_mutex_lock(&dataReadyMutex);
						guiDataReady=1;
						pthread_mutex_unlock(&dataReadyMutex);
					}else{
						pthread_mutex_lock(&dataReadyMutex);
						guiDataReady=0;
						pthread_mutex_unlock(&dataReadyMutex);
					}
				}
				//reads every nth frame
				else{
					if (p != packetsPerFrame)//so no 1 packet frame writing over previous 2 packet frame
						;
					else if(frameFactor){
						frameFactor--;
					}else{
						frameFactor = nFrameToGui-1;
						//block current process if the guireader hasnt read it yet
						sem_wait(&smp);
						//copy data and set guidataready
						pthread_mutex_lock(&dataReadyMutex);
						guiDataReady=0;
						pthread_mutex_unlock(&dataReadyMutex);
						memcpy(latestData,wbuf,bufferSize);
						strcpy(guiFileName,savefilename);
						pthread_mutex_lock(&dataReadyMutex);
						guiDataReady = 1;
						pthread_mutex_unlock(&dataReadyMutex);

					}
				}


				if(!dataCompression)
					fifofree->push(wbuf);
			}
		}
		else{//cout<<"************************fifo empty**********************************"<<endl;

			//acquisition in the detector is done
			if(status==TRANSMITTING){

				//compression
				if(dataCompression){
					//popped data
					if(iJob>0){
						cout<<"sending at the end  "<<iJob<<endl;
						filter->assignJobsForThread(startingmem,iJob);
						iJob = -2;
					}
					//no more popped data
					else{
						//all jobs done
						if(filter->checkIfJobsDone()){
							//its all done
							pthread_mutex_lock(&status_mutex);
							status = RUN_FINISHED;
							pthread_mutex_unlock(&(status_mutex));
							cout << "Status: Run Finished" << endl;
						}
					}
				}

				//standard way
				else{
					pthread_mutex_lock(&status_mutex);
					status = RUN_FINISHED;
					pthread_mutex_unlock(&(status_mutex));
					cout << "Status: Run Finished" << endl;
				}
			}
			//acquisition not done in detector
			else{
				sleepnumber++;
				usleep(50000);
			}
		}
	}


	cout << "Total Packets Caught:" << dec << totalPacketsCaught << endl;
	//cout << "RealTime Full Frames Caught:" << dec << framesCaught << endl;
	cout << "Total Full Frames Caught:"<< dec << totalFramesCaught << endl;


	if((!dataCompression)&&(sfilefd)){
#ifdef VERBOSE
		cout << "sfield:" << (int)sfilefd << endl;
#endif
		fclose(sfilefd);
		sfilefd = NULL;
	}

	//acquistion over call back
	if (acquisitionFinishedCallBack)
		acquisitionFinishedCallBack(totalFramesCaught, pAcquisitionFinished);

	return 0;
}








void slsReceiverFunctionList::readFrame(char* c,char** raw){
	//point to gui data
	if (guiData == NULL)
		guiData = latestData;
	//copy data and filename
	strcpy(c,guiFileName);
	//could not get gui data
	if(!guiDataReady){
		*raw = NULL;
	}
	//data ready, set guidata to receive new data
	else{
		*raw = guiData;
		guiData = NULL;
		pthread_mutex_lock(&dataReadyMutex);
		guiDataReady = 0;
		pthread_mutex_unlock(&dataReadyMutex);
		if((nFrameToGui) && (receiver_threads_running)){
			//release after getting data
			sem_post(&smp);
		}
	}
}




int slsReceiverFunctionList::setShortFrame(int i){
	shortFrame=i;

	if(shortFrame!=-1){
		bufferSize = GOTTHARD_SHORT_BUFFER_SIZE;
		maxFramesPerFile = SHORT_MAX_FRAMES_PER_FILE;
		packetsPerFrame = GOTTHARD_SHORT_PACKETS_PER_FRAME;
		frameIndexMask = GOTTHARD_SHORT_FRAME_INDEX_MASK;
		frameIndexOffset = GOTTHARD_SHORT_FRAME_INDEX_OFFSET;
		numJobsPerThread = GOTTHARD_SHORT_NUM_JOBS_P_THREAD;

	}else{
		bufferSize = GOTTHARD_BUFFER_SIZE;
		maxFramesPerFile = MAX_FRAMES_PER_FILE;
		packetsPerFrame = GOTTHARD_PACKETS_PER_FRAME;
		frameIndexMask = GOTTHARD_FRAME_INDEX_MASK;
		frameIndexOffset = GOTTHARD_FRAME_INDEX_OFFSET;
		numJobsPerThread = GOTTHARD_NUM_JOBS_P_THREAD;
	}

	if(userDefinedNumJobsPerThread)
		numJobsPerThread = userDefinedNumJobsPerThread;

	oneBufferSize = bufferSize/packetsPerFrame;

	//if the filter is inititalized with the wrong readout
	if(filter->getPacketsPerFrame() != packetsPerFrame){

		int16_t* map;
		int16_t* mask;

		int initial_offset = 2;
		int later_offset = 1;
		int x,y,i,j,offset = 0;

		switch(packetsPerFrame){
		case GOTTHARD_SHORT_PACKETS_PER_FRAME://roi readout for gotthard
			x = 1;
			y = (GOTTHARD_SHORT_DATABYTES/sizeof(int16_t));
			offset = initial_offset;


			mask = new int16_t[x*y];
			map = new int16_t[x*y];

			//set up mask for gotthard short
			for (int i=0; i < x; i++)
				for (int j=0; j < y; j++){
					mask[i*y+j] = 0;
				}
			//set up mapping for gotthard short
			for (int i=0; i < x; i++)
				for (int j=0; j < y; j++){
					map[i*y+j] = offset;
					offset += 2;
				}

			delete filter;
			filter = new singlePhotonFilter(x,y,frameIndexMask, GOTTHARD_PACKET_INDEX_MASK, frameIndexOffset,
					0, GOTTHARD_SHORT_PACKETS_PER_FRAME, 0,map, mask,fifofree,GOTTHARD_SHORT_BUFFER_SIZE);
			break;

		default: //normal readout for gotthard
			x = 1;
			y = (GOTTHARD_DATA_BYTES/sizeof(int16_t));
			offset = initial_offset;

			mask = new int16_t[x*y];
			map = new int16_t[x*y];

			//set up mask for gotthard
			for (int i=0; i < x; i++)
				for (int j=0; j < y; j++){
					mask[i*y+j] = 0;
				}

			//set up mapping for gotthard
			for (int i=0; i < x; i++)
				for (int j=0; j < y; j++){
					//since there are 2 packets
					if (j == y/2){
						offset += initial_offset;
						offset += 1;
					}
					map[i*y+j] = offset;
					offset += 1;
				}

			delete filter;
			filter = new singlePhotonFilter(x,y,frameIndexMask, GOTTHARD_PACKET_INDEX_MASK, frameIndexOffset,
					0, GOTTHARD_PACKETS_PER_FRAME, 1,map, mask,fifofree,GOTTHARD_BUFFER_SIZE);
			break;
		}



	}
	return shortFrame;
}




void slsReceiverFunctionList::startReadout(){
	pthread_mutex_lock(&status_mutex);
	status = TRANSMITTING;
	pthread_mutex_unlock(&status_mutex);
	cout << "Status: Transmitting" << endl;
}
#endif