/*  contrast_mgr.cc

    Mark Woolrich, FMRIB Image Analysis Group

    Copyright (C) 1999-2000 University of Oxford  */

/*  CCOPYRIGHT  */

#include <iostream>
#include <fstream>
#include <strstream>
#define WANT_STREAM
#define WANT_MATH

#include "newmatap.h"
#include "newmatio.h"
#include "VolumeSeries.h"
#include "Volume.h"
#include "ContrastMgr.h"
#include "sigproc.h"
#include "miscmaths.h"
#include "Log.h"
#include "paradigm.h"
#include "ContrastMgrOptions.h"

#include <string>

#ifndef NO_NAMESPACE
using namespace NEWMAT;
using namespace SIGPROC;
using namespace TACO;
using namespace UTILS;
#endif

int main(int argc, char *argv[])
{
  try{
    // parse command line to find out directory name for logging:
    ofstream out2;
    ContrastMgrOptions& globalopts = ContrastMgrOptions::getInstance();
    globalopts.parse_command_line(argc, argv, out2);
    
    // Setup logging:
    Log& logger = Log::getInstance();
    logger.setLogFile("contrastlogfile");
    logger.setDir(globalopts.datadir);

    // parse command line again to output arguments to logfile
    globalopts.parse_command_line(argc, argv, logger.str());

    // Load contrasts: 
    Paradigm parad;
    parad.load("", globalopts.contrastfname, false, 0);
	
    if(globalopts.verbose)
      {
	logger.str() << "Contrast:" << endl << parad.getContrasts();
      }

    ContrastMgr conMgr(parad.getContrasts());
    
    cerr << "Loading data...";
    conMgr.Load();
    cerr << " Completed" << endl;

    // Loop through contrasts:
    for(int c = 1; c <= parad.getContrasts().Nrows(); c++)
      {
	cerr << "Computing data...";
	conMgr.SetContrast(c, c+globalopts.copenumber-1);
	conMgr.ComputeNeff(false);    
	conMgr.ComputeCope();
	conMgr.ComputeVarCope();
	conMgr.ComputeZStat();
	cerr << " Completed" << endl;
	
	cerr << "Saving data...";
	conMgr.Save(globalopts.suffix);
	cerr << " Completed" << endl;
      }
  }
  catch(Exception p_excp) 
    {
      cerr << p_excp.what() << endl;
    }
  catch(...) 
    {
      cerr << "Image error" << endl;
    } 
  return 0;
}