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

#include <iostream>

#include <fstream>

#include "SynchDatSerialize.h"

#include "Image.cpp"

#define D '\t'

using namespace std;

std::ostream & operator<<(std::ostream &o, const TraceChunk& tc) {

o << tc.mRowStart << D << tc.mColStart << D << tc.mFrameStart << D << tc.mFrameStep << D << tc.mHeight << D << tc.mWidth << D << tc.mDepth << D << tc.mT0 << D << tc.mTMidNuc << D << tc.mSigma << D << tc.mBaseFrameRate << D << tc.mChipRow << D << tc.mChipCol << D << tc.mOrigFrames << D << tc.mStartDetailedTime << D << tc.mStopDetailedTime << D << tc.mLeftAvg;

return o;

}

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

if(argc != 4) {

cout << "Usage:\n DumpSynchDat <in.sdat> <regionsout.txt> <dataout.txt>\n" << endl;

exit(1);

}

TraceChunkSerializer serializer;

SynchDat sdat;

cout << "Reading sdat." << endl;

serializer.SetRecklessAbandon(true);

serializer.Read(argv[1], sdat);

cout << "Writing text." << endl;

ofstream o(argv[3]);

cout << "Compressor: " << serializer.GetCompressionType() << endl;

cout << "Rows: " << sdat.NumRow() << endl;

cout << "Cols: " << sdat.NumCol() << endl;

int idx = (int)(sdat.mChunks.mRowBin*.25/sdat.mChunks.mRowBin) * sdat.mChunks.mColBin + (int)(sdat.mChunks.mColBin*.25/sdat.mChunks.mColBin);

TraceChunk &chunk = sdat.GetChunk(idx);

cout << "For region: " << idx << " T0: " << chunk.mT0 << " Tmid: " << chunk.mTMidNuc << " Sigma: " << chunk.mSigma << endl;

int keyCount = sdat.GetCount();

string key, value;

cout << endl << "Meta data:" << endl;

for (int i = 0; i < keyCount; i++) {

sdat.GetEntry(i, key, value);

cout << key << " = " << value << endl;

}

ofstream regOut(argv[2]);

for (size_t i = 0; i < sdat.mChunks.mBins.size(); i++) {

regOut << sdat.mChunks.mBins[i] << endl;

}

regOut.close();

cout << "Seconds: ";

for (size_t i = 0; i < sdat.mChunks.mBins[0].mTimePoints.size(); i++) {

cout << sdat.mChunks.mBins[0].mTimePoints[i] << ", ";

}

cout << endl;

for (size_t row = 0; row < sdat.NumRow(); row++) {

for (size_t col = 0; col < sdat.NumCol(); col++) {

o << row << D << col << D << sdat.GetT0(row, col);

for (int frame = 0; frame < sdat.GetFrames(); frame++) {

o << D << sdat.AtWell(row, col, frame);

}

o << endl;

}

}

o.close();

cout << "Finished." << endl;

}