#include "TListSpectrum.h"

#include "TSystemDirectory.h"
#include "TSystemFile.h"
#include "TFile.h"
#include "TCanvas.h"
#include "TMath.h"
#include "TF1.h"
#include "TVirtualFitter.h"
#include "TFitEditor.h"
#include "TFitResult.h"
#include "TMinuit.h"

// #include "Minuit/Minuit2Minimizer.h"

#include <ctime>
#include <cstring>
#include <iostream>
#include <sstream>
#include <string>
#include <stdexcept>
#include <fstream>
#include <limits>
#include <cmath>
#include <iterator>
#include <vector>
#include <iomanip>

using namespace std;

// using namespace ROOT::Minuit2;

ClassImp(TListSpectrum);

TListSpectrum::TListSpectrum() : TNamed("ListSpectrum", "Unnamed Rawdata File")
{
	kChannels = 0;
	kSampleNorm = 1.0;
	kStartofCounting = *(new TTimeStamp());
	kGeometry = "{EMPTY}";
	kSampleUnit = "sample";
	
	kListData.SetNameTitle("kListData","kListData");
	
	kEnergyCalibration = {0.0, 0.0, 0.0}; // this should be in TListSpectrumCal
}


TListSpectrum::TListSpectrum(TString fileTitle) : TListSpectrum()
{
	this->SetTitle(fileTitle);
}


TListSpectrum::~TListSpectrum()
{
}

Int_t factorial(int i) { return (i == 1 || i == 0) ? 1: i*factorial(i - 1);}

void TListSpectrum::SetChannels()
{
	kDescription.resize(kChannels);
	kDAQserialnmbr.resize(kChannels);;
	kChannelRange.resize(kChannels);
	kDAQchannelnmbr.resize(kChannels);
	kRealTime_ns.resize(kChannels);
	kDeadTime_ns.resize(kChannels);
	kLiveTime_ns.resize(kChannels);
	kFullSpectrum.resize(kChannels);
	kTemporalSpectrum.resize(kChannels);
	kDeadTime.resize(kChannels);
	kWindow_ns.resize(kChannels-1);
	kTimePhase_ns.resize(kChannels-1);
	
	kCombinations = factorial(kChannels)/(factorial(2)*factorial(kChannels-1));
	
	kCoincEvents.resize(kCombinations);
	kCoincidenceSpectrum.resize(kCombinations);
}

void TListSpectrum::ProgressBar(clock_t start, ULong64_t filePosition, ULong64_t fileLength, ULong64_t realtime, ULong64_t deadtime)
{
	clock_t currentTime = clock();
    printf("\e[A");
    printf("\e[A");
    printf("\e[A");
    printf("\r processed acq. time (sec) : %10.3f     estimated acq. time (sec) : %10.3f     est. dead-time (%%) : %10.5f\% \n", realtime*1.e-9, realtime*1.e-9/double(filePosition)*fileLength, double(deadtime)/realtime*100.0);
    printf("\r     %% complete: %6.3f%%      time (sec): %8.2f    Predicted completion time: %10.2f seconds \n", double(filePosition)/fileLength*100., double(currentTime-start)/CLOCKS_PER_SEC, double(currentTime-start)/CLOCKS_PER_SEC*fileLength/filePosition);

    printf("|");
    for (int i = 0; i < int(double(filePosition)/fileLength*100./2); i++)
    {
        printf("=");
    }
    printf(">");
    for (int i = 0; i < 50-int(double(filePosition)/fileLength*100./2)-1; i++)
    {
        printf(" ");
    }
    printf("|\n");
}

TList * TListSpectrum::ListDirectoryFiles(TString extension, TString directory = ".")
{
	TSystemDirectory dir(directory, directory);
	TList *allFiles = dir.GetListOfFiles();
	TList *myFiles = new TList();

	if (allFiles)
	{
		TSystemFile *file;
		TString fname;
		TIter next(allFiles);
		while ((file=(TSystemFile*)next()))
		{
			fname = file->GetName();

			if (!file->IsDirectory() && fname.EndsWith(extension))
			{
				TObjString *item = new TObjString(fname.Data());
				myFiles->Add(item);
			}
		}
	}

	return myFiles;
}

vector <string> TListSpectrum::FindinFile(ifstream *input, string search)
{
	vector <string> returnval;
	string tmp;
// 	bool notfound(true);

	unsigned long flag(-2);

	input->clear();
	input->seekg(0, ios::beg);

	if (input->good() && !input->eof())
	{
		while(!input->eof())
		{
			getline(*input, tmp);

			if (tmp.find(search) < flag) { returnval.push_back(tmp); }
		}
	} else {
		printf("Error: ifstream not good or already at eof \n");
	}

	return returnval;
}

void TListSpectrum::ParseCaenCompassROOT(TString rootFolder, Int_t boardnmbr, Int_t channelnmbr, TString description, TString geometry, TString type)
{
		kChannels = 1;
		SetChannels();
				
		TString rundataFile("//run.info");
		TString settingsFile("//settings.xml");

 		ifstream input(rootFolder+rundataFile);

 		TString dateString;
 		dateString = FindinFile(&input, "time.start=")[0];

 		dateString.Remove(0, dateString.First("=")+1);
 		dateString.ReplaceAll("/"," ");
 		dateString.ReplaceAll(":"," ");
 		dateString.ReplaceAll("."," ");
 		dateString.ReplaceAll("-"," ");

 		stringstream dateStream(dateString.Data());
 		UInt_t year, month, day, hour, min, sec, msec, timezone;
 		dateStream >> year >> month >> day >> hour >> min >> sec >> msec >> timezone;

 		kStartofCounting.Set(year, month, day, hour, min, sec, msec*1.e6, kFALSE, timezone);

 		input.close();
 		input.open(rootFolder+settingsFile);
		
 		kDescription[0] = description + " " + FindinFile(&input, "run")[0];
 		kDAQserialnmbr[0] = FindinFile(&input, "serial")[boardnmbr];
 		kGeometry = geometry;

 		kDAQchannelnmbr[0] = channelnmbr;

 		input.close();

 		TList *caenROOTdatafiles = ListDirectoryFiles(".root", rootFolder+type+"/");

 		TFile *caenROOTdata = new TFile();
 		for (int i = 0; i < caenROOTdatafiles->GetEntries(); i++)
		{
			if (((TObjString*)caenROOTdatafiles->At(i))->GetString().First("compass") == 0)
			{
				caenROOTdata = new TFile(rootFolder+"/"+type+"/"+((TObjString*)caenROOTdatafiles->At(i))->GetString());
			}
		}

		clock_t start(clock());
		UInt_t caenflag(0);
		UShort_t caenboard(0), caenchannel(0), caenenergy(0), caenextraflag(0);
		ULong64_t caenrealtime(0), inputCounts(0), outputCounts(0);
				
		vector<UShort_t> energy, flag, extraflag;
		vector<ULong64_t> realtime, deadtime;

		TTree *caenROOTtree = (TTree*)caenROOTdata->Get("Data");
		caenROOTtree->SetBranchAddress("Board",&caenboard);
		caenROOTtree->SetBranchAddress("Channel",&caenchannel);
		caenROOTtree->SetBranchAddress("Timestamp",&caenrealtime);
		caenROOTtree->SetBranchAddress("Energy",&caenenergy);
		caenROOTtree->SetBranchAddress("Flags",&caenflag);
		caenROOTtree->SetBranchAddress("EnergyShort",&caenextraflag);

		kListData.Branch("RealTime_ns","std::vector<ULong64_t>",&realtime);
		kListData.Branch("DeadTime_ns","std::vector<ULong64_t>",&deadtime);
    	kListData.Branch("Energy_channel","std::vector<UShort_t>",&energy);
		kListData.Branch("Flag_DAQ","std::vector<UShort_t>",&flag);
  		kListData.Branch("ExtraFlag_DAQ","std::vector<UShort_t>",&extraflag);

  		ULong64_t totalEntries(caenROOTtree->GetEntries());
  		ULong64_t pct(totalEntries/1000), iter(0);

  		printf("CAEN CoMPASS ROOT FILE PARSE\n\n\n\n\n");

		for (ULong64_t i = 0; i < totalEntries; i++)
		{
			caenROOTtree->GetEntry(i);
			
			if (caenboard == boardnmbr && caenchannel == channelnmbr)
			{
    	    	inputCounts++;
    	    	if (caenenergy > 0 && caenenergy < 32768 && caenflag == 0 || caenflag == 49152) { outputCounts++;}

    	    	energy.push_back(caenenergy);
    	    	extraflag.push_back(caenextraflag);
    	    	realtime.push_back(caenrealtime/1000);
    	    	flag.push_back(caenflag);
    	    	deadtime.push_back((1.0-double(outputCounts)/double(inputCounts))*realtime[0]);

				kListData.Fill();
				
				energy.clear();
				extraflag.clear();
				realtime.clear();
				flag.clear();
				deadtime.clear();
				
			}


    	   	if (iter > pct)
    	   	{
    	    	ProgressBar(start, i, totalEntries, realtime[0], deadtime[0]);
    	    	iter = 0;
    	    }

    	    iter++;
		}

		kChannelRange[0] = kListData.GetMaximum("Energy_channel");
}