/*  band_pass.cc

    Mark Woolrich, FMRIB Image Analysis Group

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

/*  CCOPYRIGHT  */

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

#include "newmatap.h"
#include "newmatio.h"
#include "miscmaths/volumeseries.h"
#include "miscmaths/volume.h"
#include "utils/log.h"
#include "BandPassOptions.h"
#include <string>

#ifndef NO_NAMESPACE
using namespace NEWMAT;
using namespace FILM;
using namespace Utilities;
#endif

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

    // parse command line again to output arguments to logfile
    globalopts.parse_command_line(argc, argv, logger.str());
   
    // load non-temporally filtered data
    VolumeSeries x;
    x.read(globalopts.inputfname);
    x.thresholdSeries(globalopts.thresh, true);
    SIGPROC::BandPass(x, globalopts.lowcut, globalopts.highcut);
    
    // Write out necessary data:
    cerr << "Saving results... ";
    x.unthresholdSeries();
    x.replaceMeans();
    x.writeAsFloat(logger.getDir() + "/bandpassed");
    cerr << "Completed" << endl;   
  }
  catch(Exception p_excp) 
    {
      cerr << p_excp.what() << endl;
    }
  catch(...) 
    {
      cerr << "Image error" << endl;
    } 
  return 0;
}