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    // MatData.cpp
    #include <omp.h>
    #include <iostream>
    #include <fstream>
    #include <string>
    #include <sstream>
    #include <iomanip>
    #include <math.h>
    #include "pugixml.hpp"
    #include "MatData.h"
    #include "easylogging++.h"
    
    #ifdef _MSC_VER // tonipat:20131112
        #define SSCANF sscanf_s
    #else
        #define SSCANF sscanf
    			
    #endif
    
    namespace math1d_cl
    {
    	// Config constructor
    	MatData::MatData(std::string fileName)
    	{
    		const std::string measuredDischargeVolumesCsvFileName = "MeasuredDischargeVolumes.csv";
    		const std::string precipitationsCsvFileName = "Precipitations.csv";
    
    		const std::string qCsvFileName = "Q.csv";
    		const std::string hCsvFileName = "H.csv";
    		const std::string vCsvFileName = "V.csv";
    
    		m_configFilePath = fileName;
    		
    		CLOG(INFO, "model") << "Config file: " << m_configFilePath;
    
    		pugi::xml_document doc;
    		pugi::xml_parse_result result = doc.load_file(m_configFilePath.c_str());
    		 
    		if(result)
    		{
    			pugi::xml_node model = doc.child("conf").child("math1D");
    			//int logTarget = model.child("logTarget").text().as_int(); TODO: handle log targe for easyloggingcpp
    			std::string logFilePath = model.child("logFilePath").text().as_string();
    			// m_logger = new Logger(logTarget, logFilePath);
    
    			std::string resourcesPath = doc.child("conf").child("resourcesPath").text().as_string();
    
    			std::string matDataXmlFileName = model.child("matDataXmlFileName").text().as_string();
    
    			m_matDataXmlFilePath = resourcesPath + "/" + matDataXmlFileName;
    			m_measuredDischargeVolumesCsvFilePath = resourcesPath + "/" + measuredDischargeVolumesCsvFileName;
    			m_precipitationsCsvFilePath = resourcesPath + "/" + precipitationsCsvFileName;
    			
    			m_qCsvFilePath = resourcesPath + "/" + qCsvFileName;
    			m_hCsvFilePath = resourcesPath + "/" + hCsvFileName;
    			m_vCsvFilePath = resourcesPath + "/" + vCsvFileName;
    		}
    		else
    		{
    			CLOG(FATAL,"model") << "Config file " << m_configFilePath << " not loaded!";
    			std::exit(-1);
    		}
    
    		CLOG(DEBUG, "model") << "Measured discharge file: " << m_measuredDischargeVolumesCsvFilePath;
    		CLOG(DEBUG, "model") << "Precipitations file: " << m_precipitationsCsvFilePath;
    		CLOG(DEBUG, "model") << "Q output file: " << m_qCsvFilePath;
    		CLOG(DEBUG, "model") << "H output file: " << m_hCsvFilePath;
    		CLOG(DEBUG, "model") << "V output file: " << m_vCsvFilePath;
    	}//MatData
    
    	// Default constructor
    	/*MatData::MatData()
    	{
    		#ifdef _MSC_VER // tonipat:20131112
    			m_configFilePath = "..\\Resources\\Config.xml";
    			////getchar();
    		#else
    			m_configFilePath = "..//Resources//Config.linux.xml";	
    			////getchar();
    		#endif
    
    		CLOG(INFO, "model") << "Config file: " << m_configFilePath;
    
    		pugi::xml_document doc;
    		 
    		pugi::xml_parse_result result = doc.load_file(m_configFilePath.c_str());
    		 
    		if(result)
    		{
    			int logTarget = doc.child("math1D").child("logTarget").text().as_int();
    			std::string logFilePath = doc.child("math1D").child("logFilePath").text().as_string();
    			m_logger = new Logger(logTarget, logFilePath);
    
    			m_matDataXmlFilePath = doc.child("math1D").child("matDataXmlFilePath").text().as_string();
    			m_measuredDischargeVolumesCsvFilePath = doc.child("math1D").child("measuredDischargeVolumesCsvFilePath").text().as_string();
    			m_precipitationsCsvFilePath =  doc.child("math1D").child("precipitationsCsvFilePath").text().as_string();
    			m_qCsvFilePath =  doc.child("math1D").child("qCsvFilePath").text().as_string();
    			m_hCsvFilePath =  doc.child("math1D").child("hCsvFilePath").text().as_string();
    			m_vCsvFilePath =  doc.child("math1D").child("vCsvFilePath").text().as_string();
    		}
    		else
    		{
    			CLOG(ERROR,"model") << "Config file " << m_configFilePath << " not loaded!";
    			std::exit(-1);
    	}*/
    
    	// Copy constructor
    	MatData::MatData(const MatData& origin)
    	{
    		size_t i = 0;
    		// Source stations
    		for ( i = 0; i < origin.m_sourceStations.size(); i++)
    		{
    			this->m_sourceStations.push_back(*(new std::shared_ptr<Station>(new Station(*origin.m_sourceStations[i]))));
    		}
    		// River stations
    		for (  i = 0; i < origin.m_riverStations.size(); i++)
    		{
    			this->m_riverStations.push_back(*(new std::shared_ptr<Station>(new Station(*origin.m_riverStations[i]))));
    		}
    		// Basin ID
    		this->m_basinId = origin.m_basinId;
    		// Weather stations
    		for ( i = 0; i < origin.m_weatherStations.size(); i++)
    		{
    			this->m_weatherStations.push_back(*(new std::shared_ptr<Station>(new Station(*origin.m_weatherStations[i]))));
    		}
    		// Measure stations
    		for (  i = 0; i < origin.m_measureStations.size(); i++)
    		{
    			this->m_measureStations.push_back(*(new std::shared_ptr<Station>(new Station(*origin.m_measureStations[i]))));
    		}
    		// Channels
    		for ( i = 0; i < origin.m_channels.size(); i++)
    		{
    			this->m_channels.push_back(*(new std::shared_ptr<Channel>(new Channel(*origin.m_channels[i]))));
    		}
    		// Subbasins
    		for (  i = 0; i < origin.m_subbasins.size(); i++)
    		{
    			this->m_subbasins.push_back(*(new std::shared_ptr<Subbasin>(new Subbasin(*origin.m_subbasins[i]))));
    		}
    		// Measured discharge volume
    		this->m_measuredDischargeVolumes = origin.m_measuredDischargeVolumes;
    		// Precipitations
    		this->m_precipitations = origin.m_precipitations;
    		// Measured hydrographs Q
    		this->m_measuredHydrographsQ = origin.m_measuredHydrographsQ;
    		// Options
    		this->m_options = origin.m_options;
    		// Logger
    		//Logger logger = *origin.m_logger;
    		// TODO: Preserve log target 
    		//this->m_logger = new Logger(*(origin.m_logger));
    
    		this->m_configFilePath = origin.m_configFilePath;
    		this->m_matDataXmlFilePath = origin.m_matDataXmlFilePath;
    		this->m_measuredDischargeVolumesCsvFilePath = origin.m_measuredDischargeVolumesCsvFilePath;
    		this->m_precipitationsCsvFilePath = origin.m_precipitationsCsvFilePath;
    		this->m_qCsvFilePath = origin.m_qCsvFilePath;
    		this->m_hCsvFilePath = origin.m_hCsvFilePath;
    		this->m_vCsvFilePath = origin.m_vCsvFilePath;
    		this->m_nTimeSteps = origin.m_nTimeSteps;
    		this->m_minuteStep = origin.m_minuteStep;
    		this->m_precStationIds = origin.m_precStationIds;
    		this->m_mdvStationIds = origin.m_mdvStationIds;
    	}
    	
    	int MatData::runRR()
    	{
    		
    		//TIMED_FUNC(rrtimer);
    
    		// Set default options
    		setOptions();
    
    		// Load schematization and input data
    		collectMatDataCsv();
    		//PERFORMANCE_CHECKPOINT_WITH_ID(rrtimer, "loading csv data");
    
    		CLOG(INFO,"model") << "Solving Rainfall-Runoff simulation...";
    		CLOG(INFO,"model") << "Start time: " << printDateTime(m_options.getStartDate());
    		CLOG(INFO,"model") << "End time: " << printDateTime(m_options.getEndDate());
    		CLOG(INFO,"model") << "Minute step: " << intToString(m_options.getMinuteStep());
    		CLOG(INFO,"model") << "Scheme name: " << m_options.getRrSchemeName();
    		CLOG(INFO,"model") << "Meteorologic model: " << intToString(m_options.getMeteoModelId());
    		CLOG(INFO,"model") << "Creation time: " << printDateTime(m_options.getCreationDate());
    		
    		// compute model
    		rainfallRunoffModel();
    		//PERFORMANCE_CHECKPOINT_WITH_ID(rrtimer, "RR simulation");
    
    		// save results
    		collectRRResultCsv();
    		//PERFORMANCE_CHECKPOINT_WITH_ID(rrtimer, "saving results");
    
    		return m_options.getSimulationId();
    	}
    
    	void MatData::scsMethod(std::vector<double>& q, size_t& index)
    	{
    		double f = m_subbasins[index]->getArea();
    		double cn = m_subbasins[index]->getCn();
    		double q0 = m_subbasins[index]->getBaseflow();
    		int weatherStationIndex = m_subbasins[index]->getWeatherStationIndex();
    		double lost = 0;
    
    		// weather station index must be index in MatData.xml not id!
    		// value 144 just for testing reasons
    		// int wsId = 144;
    		int wsId = m_weatherStations[weatherStationIndex]->getId();
    		size_t order = -1;
    
    		// Not sure if some weather station id can appear more than once in m_precStationIds!
    		for(size_t i = 0; i < m_precStationIds.size(); i++)
    		{
    			if(m_precStationIds[i] == wsId)
    			{
    				order = i;
    			}
    		}
    
    		std::vector<double> p(m_precipitations.size());
    		// Cumulative sum of p
    		std::vector<double> cumSumP(m_precipitations.size());
    	    int lastNonZeroIndex = -1;
    
    		double firstValue = m_precipitations[0].second[order];
    		p[0] = firstValue;
    		cumSumP[0] = firstValue;
    		if(firstValue <= lost)
    		{
    			lastNonZeroIndex = 0;
    		}
    
    		for(size_t i = 1; i < m_precipitations.size(); i++)
    		{
    			p[i] = m_precipitations[i].second[order];
    			cumSumP[i] = cumSumP[i - 1] + p[i];
    			if(cumSumP[i] <= lost)
    			{
    				lastNonZeroIndex = i;
    			}
    		}
    
    		if(lastNonZeroIndex != -1)
    		{
    			double sumP = 0;
    			for(size_t i = 0; i < (size_t) lastNonZeroIndex + 1; i++)
    			{
    				if(lastNonZeroIndex < ((int)p.size() - 1))
    				{
    					sumP += p[i];
    				}
    				p[i] = 0;
    			}
    			if(lastNonZeroIndex < ((int)p.size() - 1))
    			{
    				p[lastNonZeroIndex + 1] -= lost - sumP;
    			}
    		}
    
    
    		/* Unit hydrograph */
    		double sumQ1 = 0.7 + 0.96 + 1 + 0.75 + 0.55 + 0.35;
    		std::vector<double> q1 = {0, 0.7, 0.96, 1, 0.75, 0.55, 0.35};
    		/*------------------*/
    
    		/* Hypodermic flow */
    		for(int i = 0; i < 73; i++)
    		{
    			double value = 0.18 * exp(-0.05*i);
    			q1.push_back(value);
    			sumQ1 += value;
    		}
    		/*------------------*/
    
    		for(int i = 0; i < 80; i++)
    		{
    			// Take subbasin area into account
    			// Suspected magic ??? 3.6 ???
    			q1[i] = q1[i] / sumQ1 * f / 3.6;
    		}
    
    		std::vector<double> CN(m_precipitations.size(), cn);
    		std::vector<double> p24(m_precipitations.size(), 0);
    		size_t m = m_precipitations.size();
    		size_t n = q1.size();
    		std::vector<double> Q(m + n - 1); // Suspicious dimension ??? 
    
    		for(size_t i = 0; i < m_precipitations.size(); i++)
    		{
    			//int iL = 0 < i - 120 ? i - 120 : 0;
    			// Compute which values are predicted
    			int iL = 0 < (int )(i - 120 + 1) ? (int )(i - 120 + 1 ): 0;
    			double sumPTmp = 0;
    
    			for(size_t j = iL; j < i + 1; j++)
    			{
    				sumPTmp += p[j];
    			}
    
    			if(sumPTmp > 53) // CHMI Official value = 40
    			{
    				// When cumulative precipitations for previous 5 days are
    				// bigger than 53 <- ??? HOW, WHY ???, change CN, just a little bit...
    				CN[i] = cn * exp(0.00673 * (100 - cn));
    			}
    
    			// Cumulative precipitations for last 24 hours
    			iL = 0 < (int)(i - 24 + 1) ? (int ) (i - 24 + 1 ): 0;
    			sumPTmp = 0;
    			for(size_t j = iL; j < i + 1; j++)
    			{
    				sumPTmp += p[j];
    			}
    			p24[i] = sumPTmp;
    
    
    			// Retention potential (S)
    			std::vector<double> rp(m_precipitations.size());
    
    			// Initial abstraction (Ia)
    			std::vector<double> r1(m_precipitations.size());
    
    			// Intermediate result
    			std::vector<double> h24ef(m_precipitations.size());
    
    			// Percentual infulence
    			std::vector<double> proc(m_precipitations.size());
    
    			// Effective height of overland flow
    			std::vector<double> pef(m_precipitations.size());
    
    			double h24 = 50; // <- ???? Educated guess
    			for(size_t j = 0; j < (size_t) m; j++)
    			{
    				rp[j] = 25.4 * (1000 / CN[j] - 10);
    				r1[j] = 0.2 * rp[j];
    				//h24ef[j] = (h24 > r1[j]) * (pow((h24 - r1[j]), 2) / (h24 + rp[j] - r1[j]));
    				h24ef[j] = (h24 > r1[j]) * ((h24 - r1[j]) * (h24 - r1[j])) / (h24 + rp[j] - r1[j]);
    				proc[j] = h24ef[j] / h24;
    				pef[j] = proc[j] * p[j];
    			}
    
    			/*
    			testing data
    			m = 5;
    			n = 3;
    			double u[] = {1,2,3,4,5};
    			double v[] = {1,2,3};
    			std::vector<double> d(m + n - 1, 0);*/
    
    			// Convulation
    			
    			//for(int j = 0; j < m + n + 1; j++)
    			//{
    			//	int k = 0 > (j - n + 1) ? 0 : (j - n + 1);
    			//	int kTo = (j < (m)) ? j : m;
    			//	for(k; k < kTo + 1; k++)
    			//	{
    			//		//Q[j] += pef[k] * q1[j - k - 1];
    			//		d[j] += u[k] * v[j - k];
    			//	}
    			//}
    
    		
    			/* Convolution of precipitations and unit hydrograph*/			
    			int j=0, j1=0, k=0;
    			//#pragma omp parallel for schedule(auto)
    			for(j = 0; j < ((int)(m + n) - 1); j++)
    			{
    			    j1 = j;
    				Q[j]=0;	
    				
    				for( k = 0; k < (int)n; k++)
    				{
    					if(j1 >= 0 && j1 < (int)m)
    					{
    					Q[j]  += (pef[j1]*q1[k]);
    					
    					}//if
    					j1--;
    
    				}//fork
    			}//forj
    		}//?
    
    		/* Add base flow to computed runoff */
    		for(size_t i = 0; i < (size_t ) m; i++)
    		{
    			q[i] = Q[i] + q0;
    		}
    	}
    
    	void MatData::rainfallRunoffModel()
    	{
    		// Clear hydrograms
    		clearResults();
    		
    		int rectangleProfile = 0;
    		if(m_options.getRrProfileShape() == "rectangle")
    		{
    			rectangleProfile = 1;
    		}
    		
    		CLOG(DEBUG, "model") << "Runoff computations...";
    		
    		// Iterate through channels
    		for(size_t i = 0; i < m_channels.size(); i++)
    		{
    			CLOG(DEBUG, "model") << "Computing channel "  << i;
    			//m_logger->log("Computing channel " + intToString((int )i));
    			
    			std::vector<double> qIn(m_nTimeSteps, 0);
    			std::vector<double> qOut(m_nTimeSteps, 0);
    			std::vector<double> hIn(m_nTimeSteps, 0);
    
    			// Initial channels
    			if(m_channels[i]->getUpstreams().size() == 0)
    			{
    				// Subbasin contribution
    				if(m_options.getRrType() == SCS_CN)
    				{
    					scsMethod(qOut, i);
    					m_channels[i]->getHydrograph().setQOut(qOut);
    				}
    			}
    			else // Ordinary channels
    			{
    				m_channels[i]->getHydrograph().setQOut(qOut);
    
    				// Add upstreams contributions to QIn
    				for(size_t upstream = 0; upstream < m_channels[i]->getUpstreams().size(); upstream++)
    				{
    					int index = m_channels[i]->getUpstreams()[upstream];
    
    					if(index >= 0)
    					{
    						for(int j = 0; j < m_nTimeSteps; j++ )
    						{
    							qIn[j] += m_channels[index]->getHydrograph().getQOut()[j];
    						}
    					}
    				}
    
    				m_channels[i]->getHydrograph().setQIn(qIn);
    
    				// Compute corresponding Hin
    				m_channels[i]->getHydrograph().setHIn(qToH(qIn, m_channels[i], rectangleProfile));
    
    				// Compute channel contributions
    				switch(m_options.getRrHdType())
    				{
    				case SV1D:
    					break;
    				case KWA_Comsol:
    					break;
    				case KWA_FV:
    					break;
    				case Vel:
    					{
    						double v = velocity(m_channels[i]);
    						double it = floor(m_channels[i]->getLength() / (3600 * v) + 0.5);
    						for(int j = 0; j < it; j++)
    						{
    							qOut[j] = qIn[0];
    						}
    						for(int j = (int )it; j < m_nTimeSteps; j++)
    						{
    							qOut[j] = qIn[j - (int )it];
    						}
    						m_channels[i]->getHydrograph().setQOut(qOut);
    					}
    					break;
    				case FDM:
    					break;
    				}
    
    				// Add subbasin contributions
    				std::vector<double> qSub(m_nTimeSteps, 0);
    
    				switch(m_options.getRrType())
    				{
    				case SCS_CN:
    					size_t subbasin = m_channels[i]->getSubbasinIndex();
    					scsMethod(qSub, subbasin);
    					break;
    				}
    
    				for(int j = 0; j < m_nTimeSteps; j++)
    				{
    					m_channels[i]->getHydrograph().getQOut()[j] += qSub[j];
    				}
    			}
    
    			// Fitting
    			if(m_options.getFitting())
    			{
    				for(size_t j = 0; j < m_measureStations.size(); j++)
    				{
    					if(m_measureStations[j]->getChannelIndex() == m_channels[i]->getSubbasinIndex())
    					{
    						// remove all zero elements over last nonzero element
    						size_t size = 0;
    						for(size_t k = m_measuredHydrographsQ[j].size(); k-- > 0;)
    						{
    							while(m_measuredHydrographsQ[j][k] == 0)
    								continue;
    							size = k + 1;
    							break;
    						}
    
    						std::vector<double> measQ(size, 0);
    						std::vector<double> compQ(size, 0);
    						std::vector<double> wageQ(size, 1);
    
    						std::vector<double> added = m_channels[i]->getHydrograph().getQOut();
    
    						for(size_t k = 0; k < size; k++)
    						{
    							measQ[k] = m_measuredHydrographsQ[j][k];
    							compQ[k] = added[k];
    						}
    
    						double alpha, beta;
    						fit(alpha, beta, measQ, compQ, wageQ);
    
    						for(int k = 0; k < m_nTimeSteps; k++)
    						{
    							added[k] = alpha * added[k] + beta;
    							if(added[k] <= 0)
    							{
    								added[k] = 0.1;
    							}
    						}
    
    						m_channels[i]->getHydrograph().setQOut(added);
    					}
    				}
    			}
    		}
    
    		// Iterate through channels
    		for(size_t i = 0; i < m_channels.size(); i++)
    		{
    			if(m_channels[i]->getUpstreams().size() == 1 && m_channels[i]->getUpstreams()[0] == 0)
    			{
    				int index = m_channels[i]->getDownstream();
    				if(index < 0)
    					continue;
    				m_channels[i]->getHydrograph().setHOut(qToH(m_channels[i]->getHydrograph().getQOut(),
    					m_channels[index], rectangleProfile));
    			}
    			else
    			{
    				m_channels[i]->getHydrograph().setHOut(qToH(m_channels[i]->getHydrograph().getQOut(),
    					m_channels[i],	rectangleProfile));
    			}
    		}
    
    		m_simulationDone = true;
    	}
    
    	void MatData::collectRRResultCsv()
    	{
    		CLOG(INFO, "model") << "Saving results...";
    		int nChannels =(int ) m_channels.size();
    
    		std::ofstream qFile(m_qCsvFilePath.c_str());
    		// std::ofstream vFile(m_vCsvFilePath.c_str()); // only zeros
    		std::ofstream hFile(m_hCsvFilePath.c_str());
    
    		std::string firstLine = "time\\id;";
    
    		for(size_t i = 0; i < (size_t ) nChannels; i++)
    		{
    			firstLine += intToString(m_channels[i]->getStationId());
    			if(i <(unsigned int ) (nChannels - 1))
    			{
    				firstLine += ";";
    			}
    			else
    			{
    				firstLine += "\n";
    			}
    		}
    
    		qFile << firstLine;
    		//vFile << firstLine;
    		hFile << firstLine;
    
    		for(int i = 0; i < m_nTimeSteps; i++)
    		{	
    			qFile << printDateTime(m_precipitations[i].first) << ";";
    			//vFile << printDateTime(m_precipitations[i].first);
    			hFile << printDateTime(m_precipitations[i].first) << ";";
    			for(size_t j = 0; j < (size_t) nChannels; j++)
    			{
    				qFile << std::fixed << std::setprecision(6) << m_channels[j]->getHydrograph().getQOut()[i];
    				
    				//if(m_channels[j]->getHydrograph().getHOut().size() > i)
    				hFile << std::fixed << std::setprecision(6) << m_channels[j]->getHydrograph().getHOut()[i];
    				//else
    				//	hFile << ";";
    				if(j < (unsigned int )(nChannels - 1))
    				{
    					qFile << ";  ";
    					hFile << ";  ";
    				}
    			}
    			qFile << "\n";
    			//vFile << "\n";
    			hFile << "\n";
    		}
    
    		qFile.close();
    		//vFile.close();
    		hFile.close();
    	}
    
    	void MatData::fit(double& alpha, double& beta, std::vector<double>& x, std::vector<double>& y, std::vector<double>& wage)
    	{
    		size_t size = x.size();
    		std::vector<double> yTest(size, 0);
    		double tmp = 0;
    
    		for(size_t i = 0; i < size; i++)
    		{
    			yTest[i] = y[i] - y[0];
    			tmp += yTest[i] * yTest[i];
    		}
    
    		// 2-norm of vector yTest == 0
    		if(sqrt(tmp) == 0)
    		{
    			alpha = 1;
    			double diff = 0;
    			
    			for(size_t i = 0; i < size; i++)
    			{
    				diff += x[i] - y[i];
    			}
    			beta = diff / size;
    		}
    		else
    		{
    			double wageX = 0;
    			double wageY = 0;
    			double a = 0;
    			double b = 0;
    			std::vector<double> yMod(size, 0);
    			std::vector<double> xMod(size, 0);
    			std::vector<double> yyMod(size, 0);
    			std::vector<double> yxMod(size, 0);
    
    			for(size_t i = 0; i < size; i++)
    			{
    				wageX += x[i];
    				wageY += y[i];
    			}
    
    			for(size_t i = 0; i < size; i++)
    			{
    				xMod[i] = x[i] - (wageX / size);
    				yMod[i] = y[i] * size - wageY;
    				yxMod[i] = y[i] * xMod[i];
    				yyMod[i] = y[i] * yMod[i];
    				a += yxMod[i];
    				b += yyMod[i] / size;
    			}
    
    			alpha = a / b;
    			beta = 0;
    
    			if(alpha < 0)
    			{
    				alpha = 1;
    				for(size_t i = 0; i < size; i++)
    				{
    					beta += (x[i] - y[i]) / size;
    				}
    			}
    			else
    			{
    				std::vector<double> alphaY(size);
    				for(size_t i = 0; i < size; i++)
    				{
    					alphaY[i] = alpha * y[i];
    					beta += (x[i] - alphaY[i]) / size;
    				}
    			}
    		}
    	}
    
    	double MatData::velocity(std::shared_ptr<Channel> channel)
    	{
    		double n = channel->getN(); // Manning coefficient
    		double iS = channel->getSlope(); // Channel slope
    		double w = channel->getWidth(); // Channel width
    		double iB = channel->getBankSlope(); // Channel bank slope
    		double q = channel->getHydrograph().getQIn()[0];
    
    		if(iS == 0)
    		{
    			iS += 0.001;
    		}
    
    		// Version 2 (rectangle profile)
    		double x = q * n / (w * sqrt(iS));
    		double h = pow(x, 3.0/5.0);
    		double s = h * (w + h / iB);
    		return q/s;
    	}
    
    	std::vector<double> MatData::qToH(std::vector<double>& q, std::shared_ptr<Channel> channel, int& rectangleProfile)
    	{
    		std::vector<double> h(m_nTimeSteps, 0);
    		double n = channel->getN(); // Manning coefficient
    		double iS = channel->getSlope(); // Channel slope
    		double w = channel->getWidth(); // Channel width
    		//double iB = channel->getBankSlope(); // Channel bank slope
    
    		if(rectangleProfile == 1) // Version 1 (rectangle profile)
    		{
    			for(int i = 0; i < m_nTimeSteps; i++)
    			{
    				h[i] = pow(n / (w * sqrt(iS)) * q[i], 3/5);
    			}
    		}
    		else // Version 1 (rectangle profile)
    		{
    			// not implemented yet
    		}
    
    		return h;
    	}
    
    	void MatData::setOptions()
    	{
    		m_options.setUri("http://release.floreon.vsb.cz:8088/WS_Database/M9_M11.asmx?WSDL");
    
    		tm startDate;
    		startDate.tm_mday = 10;
    		startDate.tm_mon = 8;
    		startDate.tm_year = 107;
    		startDate.tm_hour = 0;
    		startDate.tm_min = 0;
    		startDate.tm_sec = 0;
    		time_t start = mktime(&startDate);
    		m_options.setStartDate(start);
    
    		tm endDate;
    		endDate.tm_mday = 15;
    		endDate.tm_mon = 8;
    		endDate.tm_year = 107;
    		endDate.tm_hour = 10;
    		endDate.tm_min = 0;
    		endDate.tm_sec = 0;
    		time_t end = mktime(&endDate);
    		m_options.setEndDate(end);
    
    		m_options.setMinuteStep(60);
    
    		m_options.setMeteoModelId(2);
    		m_options.setMeteoModelName("Measured");
    		m_options.setRr(true);
    		m_options.setHd(false);
    		   
    		m_options.setRrSchemeId(1);
    		m_options.setRrSchemeName("RRschematizace");
    		m_options.setRrModelId(3);
    		m_options.setRrModelName("Math_1D");
    		m_options.setRrType(SCS_CN);
    		m_options.setRrHdType(Vel);
    		m_options.setRrProfileShape("rectangle");
    		m_options.setHdModelId(0);
    		m_options.setHdType("KWA_Comsol");
    		m_options.setHdProfileShape("rectangle");
    		m_options.setLog(true);
    			   
    		m_options.setSimulationId(0);
    		m_options.setFitting(true);
    		m_options.setCalibtemp(true);
    
    		time_t now = time(NULL);
    		m_options.setCreationDate(now);
    	}
    	
    	void MatData::collectMatDataCsv()
    	{
    		CLOG(INFO, "model") << "Loading MatData and meteodata...";
    		
    		// Loads MatData schematization
    		MatData::loadSchematization();
    
    		// Measured Discharge Volumes
    		loadMeasuredDischargeVolumesFromCsv();
    		
    		// Precipitations
    		loadPrecipitationsFromCsv();
    
    		m_nTimeSteps =(int ) m_precipitations.size();
    		m_minuteStep = 60; // Hardcoded
    		m_options.setStartDate(m_precipitations[0].first);
    		m_options.setEndDate(m_precipitations[m_precipitations.size() - 1].first);
    
    
    		// Prefill vectors with default values
    		for(size_t i = 0; i < m_channels.size(); i++)
    		{
    			for(size_t j = 0; j < m_precipitations.size(); j++)
    			{
    				Hydrograph h = m_channels[i]->getHydrograph();
    				h.getHIn().push_back(0);
    				h.getQIn().push_back(0);
    				h.getHOut().push_back(0);
    				h.getQOut().push_back(0);
    			}
    		}
    
    		for(size_t i = 0; i < m_precipitations.size(); i++)
    		{
    			for(size_t j = 0; j < m_precStationIds.size(); j++)
    			{
    				if(m_precipitations[i].second[j] == -999)
    				{
    					m_precipitations[i].second[j] = -1;
    				}
    			}
    		}
    
    		// Creates Hydrographs
    		getMeasuredHydrographs();
    	}
    
    	void MatData::loadSchematization()
    	{
    		CLOG(DEBUG, "model") << "Loading schematization..";
    		pugi::xml_document doc;
    		pugi::xml_parse_result result = doc.load_file(m_matDataXmlFilePath.c_str());
    		if(result.status != pugi::status_ok)
    		{
    			CLOG(FATAL, "model") << "Schematization load result: " << result.description();
    			std::exit(EXIT_FAILURE);
    		}
    
    		// Source stations
    		pugi::xml_node sourceStations = doc.child("MatData").child("SourceStations");
    		loadStationsFromXml(m_sourceStations, sourceStations);
    
    		// River stations
    		pugi::xml_node riverStations = doc.child("MatData").child("RiverStations");
    		loadStationsFromXml(m_riverStations, riverStations);
    
    		// Weather stations
    		// Weather station contains only Id, Name, Code and Location
    		pugi::xml_node weatherStations = doc.child("MatData").child("WeatherStations");
    		loadStationsFromXml(m_weatherStations, weatherStations);
    
    		// Channels
    		pugi::xml_node channels = doc.child("MatData").child("Channels");
    		loadChannelsFromXml(m_channels, channels);
    
    		// Subbasins
    		pugi::xml_node subbasins = doc.child("MatData").child("Subbasins");
    		loadSubbasinsFromXml(m_subbasins, subbasins);
    	}
    
    	void MatData::loadStationsFromXml(std::vector<std::shared_ptr<Station>>& stations, pugi::xml_node& xml_stations)
    	{
    		for (pugi::xml_node xml_station = xml_stations.first_child(); xml_station; xml_station = xml_station.next_sibling())
    		{
    			std::shared_ptr<Station> station(new Station());
    
    			station->setId(xml_station.child("Id").text().as_int());
    			station->setDescription(xml_station.child_value("Description"));
    			station->setName(xml_station.child_value("Name"));
    			Location location;
    			location.setX(xml_station.child("Location").child("X").text().as_float());
    			location.setY(xml_station.child("Location").child("Y").text().as_float());
    			location.setZ(xml_station.child("Location").child("Z").text().as_float());
    			station->setLocation(location);
    			station->setClockStep(xml_station.child("ClockStep").text().as_double());
    			station->setCode(xml_station.child_value("Code"));
    			station->setPrecipitationFlag(xml_station.child("PrecipitationFlag").text().as_bool());
    			station->setTemperatureFlag(xml_station.child("TemperatureFlag").text().as_bool());
    			station->setSnowFlag(xml_station.child("SnowFlag").text().as_bool());
    			station->setWindVelocityFlag(xml_station.child("WindVelocityFlag").text().as_bool());
    			station->setRadarFlag(xml_station.child("RadarFlag").text().as_bool());
    			station->setIsVirtual(xml_station.child("Virtual").text().as_bool());
    			station->setSpa1(xml_station.child("Spa1").text().as_double());
    			station->setSpa2(xml_station.child("Spa2").text().as_double());
    			station->setSpa3(xml_station.child("Spa3").text().as_double());
    			station->setQ(xml_station.child("Q").text().as_double());
    			//station->setOwner(xml_station.child_value("Owner")); // Not known what is owner yet.
    			std::string wgcString = xml_station.child_value("WaterGaugingCategory");
    			WaterGaugingCategory wgcResult;
    			if(wgcString == "A") wgcResult = A;
    			else if(wgcString == "B") wgcResult = B;
    			else if(wgcString == "N") wgcResult = N;
    			station->setWaterGaugingCategory(wgcResult);
    			station->setHSpa1(xml_station.child("HSpa1").text().as_double());
    			station->setHSpa2(xml_station.child("HSpa2").text().as_double());
    			station->setHSpa3(xml_station.child("HSpa3").text().as_double());
    			station->setH(xml_station.child("H").text().as_int());
    			//station->setChmuProfileId(xml_station.child("ChmuProfileId").text().as_int());
    			
    			//station->setChannelIndex(xml_station.child("Channel").child("Id").text().as_int());
    			station->setChannelIndex(xml_station.child("ChannelIndex").text().as_int() - 1);
    			
    			stations.push_back(station);
    		}
    	}
    
    	void MatData::loadChannelsFromXml(std::vector<std::shared_ptr<Channel>>& channels, pugi::xml_node& xml_channels)
    	{
    		for (pugi::xml_node xml_channel = xml_channels.first_child(); xml_channel; xml_channel = xml_channel.next_sibling())
    		{
    			std::shared_ptr<Channel> channel(new Channel());
    
    			channel->setId(xml_channel.child("Id").text().as_int());
    			channel->setName(xml_channel.child_value("Name"));
    			channel->setSourceStationId(xml_channel.child("SourceStationId").text().as_int());
    			channel->setSourceStationIndex(xml_channel.child("SourceStationIndex").text().as_int() - 1);
    			channel->setStationId(xml_channel.child("StationId").text().as_int());
    			channel->setStationIndex(xml_channel.child("StationIndex").text().as_int() - 1);
    			channel->setH(xml_channel.child("H").text().as_double());
    			channel->setD(xml_channel.child("D").text().as_double());
    			channel->setLength(xml_channel.child("Length").text().as_double());
    			channel->setSlope(xml_channel.child("Slope").text().as_double());
    			channel->setBankSlope(xml_channel.child("BankSlope").text().as_double());
    			channel->setDepth(xml_channel.child("Depth").text().as_double());
    			channel->setWidth(xml_channel.child("Width").text().as_double());
    			channel->setN(xml_channel.child("N").text().as_double());
    			channel->setSubbasinId(xml_channel.child("SubbasinId").text().as_int());
    			channel->setSubbasinIndex(xml_channel.child("SubbasinIndex").text().as_int() - 1);
    
    			pugi::xml_node xml_upstreams = xml_channel.child("Upstreams");
    			for (pugi::xml_node xml_upstream = xml_upstreams.first_child(); xml_upstream; xml_upstream = xml_upstream.next_sibling())
    			{
    				channel->getUpstreams().push_back(xml_upstream.child("Index").text().as_int() - 1);
    			}
    			//channel->setDownstream(xml_channel.child("Downstreams").child("Downstream").child("Index").text().as_int());
    			channel->setDownstream(xml_channel.child("DownstreamIndex").text().as_int() - 1);
    			channels.push_back(channel);
    		}
    	}
    
    	void MatData::loadSubbasinsFromXml(std::vector<std::shared_ptr<Subbasin>>& subbasins, pugi::xml_node& xml_subbasins)
    	{
    		for (pugi::xml_node xml_subbasin = xml_subbasins.first_child(); xml_subbasin; xml_subbasin = xml_subbasin.next_sibling())
    		{
    			std::shared_ptr<Subbasin> subbasin(new Subbasin());
    
    			subbasin->setId(xml_subbasin.child("Id").text().as_int());
    			subbasin->setName(xml_subbasin.child_value("Name"));
    			subbasin->setArea(xml_subbasin.child("Area").text().as_double());
    			subbasin->setH(xml_subbasin.child("H").text().as_double());
    			subbasin->setD(xml_subbasin.child("D").text().as_double());
    			subbasin->setLength(xml_subbasin.child("Length").text().as_double());
    			subbasin->setSlope(xml_subbasin.child("Slope").text().as_double());
    			subbasin->setBaseflow(xml_subbasin.child("BaseFlow").text().as_double());
    			subbasin->setCn(xml_subbasin.child("Cn").text().as_double());
    			subbasin->setN(xml_subbasin.child("N").text().as_double());
    			subbasin->setLai(xml_subbasin.child("Lai").text().as_double());
    			subbasin->setInitAbstraction(xml_subbasin.child("InitAbstraction").text().as_double());
    			subbasin->setTimeConcentration(xml_subbasin.child("TimeConcentration").text().as_double());
    			subbasin->setStorageCoeff(xml_subbasin.child("StorageCoeff").text().as_double());
    			subbasin->setChannelIndex((int )(xml_subbasin.child("ChannelIndex").text().as_double() - 1));
    			subbasin->setWeatherStationIndex(xml_subbasin.child("WeatherStationIndex").text().as_int() - 1); // Change to Index!
    
    			subbasins.push_back(subbasin);
    		}
    	}
    
    	void MatData::loadMeasuredDischargeVolumesFromCsv()
    	{
    		std::ifstream measuredDischargeVolumesFile(m_measuredDischargeVolumesCsvFilePath.c_str());
    		std::string value, firstLine, mdv;
    		int nColumns = 0;
    		
    
    		// Gets number of columns
    		// First line is header consisting of string "Time" and Station Ids
    		if(getline(measuredDischargeVolumesFile, firstLine))
    		{
    			std::istringstream iss(firstLine);
    			while(getline(iss, value, ';'))
    			{
    				if(value != "Time")
    				{
    					m_mdvStationIds.push_back(atoi(value.c_str()));
    				}
    				nColumns++;
    			}
    		}
    
    		// Parse data
    		while(getline(measuredDischargeVolumesFile, value))