/* Copyright (C) 2010 Ion Torrent Systems, Inc. All Rights Reserved */

#include <iostream>

#include <iomanip>

#include <string>

#include <vector>

#include "OptArgs.h"

#include "Image.h"

using namespace std;

void usage() {

cout << "readDat - a little application to extract data from a dat file. Main purpose is" << endl;

cout << " to serve as an example of how to use the Image::LoadSlice() API to read a dat" << endl;

cout << " file." << endl;

cout << "" << endl;

cout << "Usage:" << endl;

cout << " readDat --col 0,3 --row 5,2 acq_0000.dat" << endl;

cout << " readDat --min-col 0 --max-col 9 --min-row 0 --max-col 9 acq_*.dat" << endl;

cout << "" << endl;

cout << "Options:" << endl;

cout << " col - comma-separated list of column indices to return" << endl;

cout << " row - comma-separated list of row indices to return" << endl;

cout << " min-col - min column for specifying a rectangular region (-1)" << endl;

cout << " max-col - max column for specifying a rectangular region (-1)" << endl;

cout << " min-row - min row for specifying a rectangular region (-1)" << endl;

cout << " max-row - max row for specifying a rectangular region (-1)" << endl;

cout << " uncompress - should data be VFC-decompressed (false)" << endl;

cout << " normalize - additive correction to zero the start of the trace (false)" << endl;

cout << " norm-start - start frame for additive correction (5)" << endl;

cout << " norm-end - end frame for additive correction (20)" << endl;

cout << " xtcorrect - apply electrical cross-talk correction, when appropriate (true)" << endl;

cout << " chiptype - explicitly set chip type (314/316/318,etc)" << endl;

cout << " baseline-min-time - start time in seconds for read baselining (0)" << endl;

cout << " baseline-max-time - end time in seconds for read baselining (-1)" << endl;

cout << " load-min-time - start time for frames to return (0)" << endl;

cout << " load-max-time - end time for frames to return (-1)" << endl;

cout << " help - this help message" << endl;

cout << "" << endl;

}

int main(int argc, const char *argv[]) {

vector<string> datFiles;

vector<unsigned int> col;

vector<unsigned int> row;

int minCol, maxCol, minRow, maxRow;

bool uncompress;

bool doNormalize;

int normStart;

int normEnd;

bool XTCorrect;

string chipType;

bool help;

double baselineMinTime,baselineMaxTime;

double loadMinTime,loadMaxTime;

OptArgs opts;

opts.ParseCmdLine(argc, argv);

opts.GetOption(col, "", '-', "col");

opts.GetOption(row, "", '-', "row");

opts.GetOption(minCol, "-1", '-', "min-col");

opts.GetOption(maxCol, "-1", '-', "max-col");

opts.GetOption(minRow, "-1", '-', "min-row");

opts.GetOption(maxRow, "-1", '-', "max-row");

opts.GetOption(uncompress, "false", '-', "uncompress");

opts.GetOption(doNormalize, "false", '-', "normalize");

opts.GetOption(normStart, "5", '-', "norm-start");

opts.GetOption(normEnd, "20", '-', "norm-end");

opts.GetOption(XTCorrect, "true", '-', "xtcorrect");

opts.GetOption(chipType, "", '-', "chip-type");

opts.GetOption(baselineMinTime, "0", '-', "baseline-min-time");

opts.GetOption(baselineMaxTime, "-1", '-', "baseline-max-time");

opts.GetOption(loadMinTime, "0", '-', "load-min-time");

opts.GetOption(loadMaxTime, "-1", '-', "load-max-time");

opts.GetOption(help, "false", 'h', "help");

opts.GetLeftoverArguments(datFiles);

//opts.CheckNoLeftovers();

if(help) {

usage();

return(0);

}

if (datFiles.empty()) {

usage();

return(1);

}

bool returnSignal=true;

bool returnMean=true;

bool returnSD=true;

bool returnLag=true;

unsigned int nCol,nRow,nFrame;

vector<unsigned int> colOut;

vector<unsigned int> rowOut;

vector< vector<double> > frameStart;

vector< vector<double> > frameEnd;

vector< vector< vector<short> > > signal;

vector< vector<short> > mean;

vector< vector<short> > sd;

vector< vector<short> > lag;

Image i;

if(!i.LoadSlice(datFiles,col,row,minCol,maxCol,minRow,maxRow,returnSignal,returnMean,returnSD,returnLag, uncompress,doNormalize,normStart,normEnd,XTCorrect,chipType,baselineMinTime,baselineMaxTime,loadMinTime,loadMaxTime,nCol,nRow,colOut,rowOut,nFrame,frameStart,frameEnd,signal,mean,sd,lag)) {

cerr << "Problem loading raw data" << endl;

return(1);

}

// frameStarts

cout << "NA\tNA\tNA\tNA";

for(unsigned int iDat=0; iDat < datFiles.size(); iDat++) {

for(unsigned int iFrame=0; iFrame < frameStart[iDat].size(); iFrame++) {

cout << "\t" << setprecision(3) << frameStart[iDat][iFrame];

}

}

cout << endl;

// frameEnds

cout << "NA\tNA\tNA\tNA";

for(unsigned int iDat=0; iDat < datFiles.size(); iDat++) {

for(unsigned int iFrame=0; iFrame < frameEnd[iDat].size(); iFrame++) {

cout << "\t" << setprecision(3) << frameEnd[iDat][iFrame];

}

}

cout << endl;

// signal values

unsigned int nWell = colOut.size();

for(unsigned int iWell=0; iWell<nWell; iWell++) {

cout << colOut[iWell];

cout << "\t" << rowOut[iWell];

for(unsigned int iDat=0; iDat < datFiles.size(); iDat++) {

if(returnMean)

cout << "\t" << mean[iDat][iWell];

else

cout << "\tNA";

if(returnSD)

cout << "\t" << sd[iDat][iWell];

else

cout << "\tNA";

if(returnSignal) {

for(unsigned int iFrame=0; iFrame < signal[iDat][iWell].size(); iFrame++) {

cout << "\t" << signal[iDat][iWell][iFrame];

}

}

}

cout << endl;

}

return(0);

}