// Definitions of a class that does the parsing and
// sanity checking of commnad line options for the 
// "eddy" application.
// 
// EddyCommandLineOptions.cpp
//
// Jesper Andersson, FMRIB Image Analysis Group
//
// Copyright (C) 2011 University of Oxford 
//
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#include <cstdlib>
#include <string>
#include <vector>
#include "utils/options.h"
#include "topup/topup_file_io.h"
#include "EddyHelperClasses.h"
#include "EddyCommandLineOptions.h"

using namespace EDDY;

EddyCommandLineOptions::EddyCommandLineOptions(int  argc, char *argv[]) : 
  _title("eddy \nCopyright(c) 2011, University of Oxford (Jesper Andersson)"),
  _examples("eddy --monsoon"),
  _verbose(string("-v,--verbose"),false,string("switch on diagnostic messages"),false, Utilities::no_argument), 
  _help(string("-h,--help"),false,string("display this message"),false, Utilities::no_argument),
  _imain(string("--imain"),string(""),string("File containing all the images to estimate distortions for"),true,Utilities::requires_argument), 
  _mask(string("--mask"),string(""),string("Mask to indicate brain"),true,Utilities::requires_argument),
  _acqp(string("--acqp"),string(""),string("File containing acquisition parameters"),true,Utilities::requires_argument),
  _index(string("--index"),string(""),string("File containing indices for all volumes in --imain into --acqp and --topup"),true,Utilities::requires_argument),
  _session(string("--session"),string(""),string("File containing session indices for all volumes in --imain"),false,Utilities::requires_argument),
  _topup(string("--topup"),string(""),string("Base name for output files from topup"),false,Utilities::requires_argument),
  _bvecs(string("--bvecs"),string(""),string("File containing the b-vectors for all volumes in --imain"),true,Utilities::requires_argument),
  _bvals(string("--bvals"),string(""),string("File containing the b-values for all volumes in --imain"),true,Utilities::requires_argument),
  _fwhm(string("--fwhm"),0.0,string("FWHM for conditioning filter when estimating the parameters"),false,Utilities::requires_argument),
  _niter(string("--niter"),5,string("Number of iterations (default 5)"),false,Utilities::requires_argument),
  _out(string("--out"),string(""),string("Basename for output"),true,Utilities::requires_argument),
  _flm(string("--flm"),string("quadratic"),string("First level EC model (linear/quadratic/cubic)"),false,Utilities::requires_argument),
  _rep_ol(string("--repol"),false,string("Detect and replace outlier slices"),false, Utilities::no_argument), 
  _resamp(string("--resamp"),string("jac"),string("Final resampling method (jac/lsr)"),false, Utilities::requires_argument), 
  _ol_nstd(string("--ol_nstd"),4.0,string("Number of std off to qualify as outlier (default 4)"),false,Utilities::requires_argument),
  _ol_nvox(string("--ol_nvox"),250,string("Min # of voxels in a slice for inclusion in outlier detection (default 250)"),false,Utilities::requires_argument),
  _very_verbose(string("--very_verbose"),false,string("Switch on detailed diagnostic messages"),false, Utilities::no_argument), 
  _dwi_only(string("--dwi_only"),false,string("Only register the dwi images"),false, Utilities::no_argument), 
  _b0_only(string("--b0_only"),false,string("Only register the b0 images"),false, Utilities::no_argument), 
  _fields(string("--fields"),false,string("Write EC fields as images"),false, Utilities::no_argument), 
  _history(string("--history"),false,string("Write history of mss and parameter estimates"),false, Utilities::no_argument), 
  _write_slice_stats(string("--wss"),false,string("Write slice-wise stats for each iteration"),false, Utilities::no_argument), 
  _init(string("--init"),string(""),string("Text file with parameters for initialisation"),false,Utilities::requires_argument),
  _debug(string("--debug"),0,string("Level of debug print-outs."),false,Utilities::requires_argument),
  _rdwi(true), _rb0(true)
{
  // Do the parsing implemented by the Option<T> class.
  do_initial_parsing(argc,argv);

  // Do sanity checking and some initial reading of files
  // Image file exists?
  NEWIMAGE::volume4D<float> imahdr;
  NEWIMAGE::read_volume4D_hdr_only(imahdr,_imain.value());  // Throws if there is a problem
  NEWIMAGE::volume<float> maskhdr;
  NEWIMAGE::read_volume_hdr_only(maskhdr,_mask.value());    // Throws if there is a problem
  if (!samesize(imahdr[0],maskhdr,true)) throw EddyException("--imain and --mask images must have the same dimensions");
  // Index file exists and makes sense given image file
  NEWMAT::Matrix index = MISCMATHS::read_ascii_matrix(_index.value());
  if (std::min(index.Nrows(),index.Ncols()) != 1 || std::max(index.Nrows(),index.Ncols()) != imahdr.tsize()) {
    throw EddyException("--index must be an 1xN or Nx1 matrix where N is the number of volumes in --imain");
  }
  // Session file either dont exist, or exists and makes sense.
  if (!this->session_indicies_kosher(_session.value(),imahdr.tsize())) {
    throw EddyException("--session file does not make sense");
  }
  // File with acquisition parameters exists and makes sense
  NEWMAT::Matrix acqpM = MISCMATHS::read_ascii_matrix(_acqp.value());
  if (acqpM.Ncols() != 4) throw EddyException("Each row of the --acqp file must contain 4 values");
  if (!this->indicies_kosher(index,acqpM)) throw EddyException("Mismatch between --index and --acqp");
  // bvals and bvecs exists and are consistent with image file
  NEWMAT::Matrix bvecsM = MISCMATHS::read_ascii_matrix(_bvecs.value());
  if (std::min(bvecsM.Nrows(),bvecsM.Ncols()) != 3 || std::max(bvecsM.Nrows(),bvecsM.Ncols()) != imahdr.tsize()) {
    throw EddyException("--bvecs should contain a 3xN or Nx3 matrix where N is the number of volumes in --imain");    
  }
  NEWMAT::Matrix bvalsM = MISCMATHS::read_ascii_matrix(_bvals.value());
  if (std::min(bvalsM.Nrows(),bvalsM.Ncols()) != 1 || std::max(bvalsM.Nrows(),bvalsM.Ncols()) != imahdr.tsize()) {
    throw EddyException("--bvals should contain a 1xN or Nx1 matrix where N is the number of volumes in --imain");    
  }
  // Topup file exists if one has been specified
  if (_topup.set() && _topup.value() != string("")) {
    try { TOPUP::TopupFileReader  tfr(_topup.value()); }
    catch (...) { throw EddyException("Error when attempting to read --topup files"); }
  }
  // Valid final resampling method?
  if (_resamp.value() != string("jac") && _resamp.value() != string("lsr")) throw EddyException("Invalid --resamp parameter");
  // Valid first level model?
  if (_flm.value() != string("linear") && _flm.value() != string("quadratic") && _flm.value() != string("cubic")) throw EddyException("Invalid --flm parameter");
  // Reasonable FWHM
  if (_fwhm.value() < 0.0 || _fwhm.value() > 15.0) throw EddyException("--fwhm value outside valid range");
  // If very_verbose is set we should also set verbose
  if (_very_verbose.value() && !_verbose.value()) _verbose.set_T(true);
  // Make sure the "only" flags are mutually exclusive
  if (_dwi_only.value() && _b0_only.value()) throw EddyException("--dwi_only and --b0_only cannnot both be set");
  if (_dwi_only.value()) _rb0 = false;
  else if (_b0_only.value()) _rdwi = false;
  // Initialisation file exists if one has been specified
  if (_init.set() && _init.value() != string("")) {
    try { NEWMAT::Matrix  tmp = MISCMATHS::read_ascii_matrix(_init.value()); }
    catch (...) { throw EddyException("Error when attempting to read --init file"); }
  }
}

EDDY::FinalResampling EddyCommandLineOptions::ResamplingMethod() const
{
  if (_resamp.value() == std::string("jac")) return(EDDY::JAC);
  else if (_resamp.value() == std::string("lsr")) return(EDDY::LSR);
  else return(EDDY::UNKNOWN_RESAMPLING);
}

EDDY::ECModel EddyCommandLineOptions::FirstLevelModel() const
{
  if (_flm.value() == string("linear")) return(EDDY::Linear);
  else if (_flm.value() == string("quadratic")) return(EDDY::Quadratic);
  else if (_flm.value() == string("cubic")) return(EDDY::Cubic);
  return(EDDY::Unknown);
}

void EddyCommandLineOptions::do_initial_parsing(int argc, char *argv[])
{
  Utilities::OptionParser options(_title,_examples);

  try {
    options.add(_imain);
    options.add(_mask);
    options.add(_index);
    options.add(_session);
    options.add(_acqp);
    options.add(_topup);
    options.add(_bvecs);
    options.add(_bvals);
    options.add(_flm);
    options.add(_fwhm);
    options.add(_niter);
    options.add(_out);
    options.add(_very_verbose);
    options.add(_dwi_only);
    options.add(_b0_only);
    options.add(_fields);
    options.add(_history);
    options.add(_resamp);
    options.add(_write_slice_stats);
    options.add(_rep_ol);
    options.add(_ol_nstd);
    options.add(_ol_nvox);
    options.add(_init);
    options.add(_debug);
    options.add(_verbose);
    options.add(_help);

    int i=options.parse_command_line(argc, argv);
    if (i < argc) {
      for (; i<argc; i++) {
        cerr << "Unknown input: " << argv[i] << endl;
      }
      exit(EXIT_FAILURE);
    }

    if (_help.value() || !options.check_compulsory_arguments(true)) {
      options.usage();
      exit(EXIT_FAILURE);
    }
  }  
  catch(Utilities::X_OptionError& e) {
    options.usage();
    cerr << endl << e.what() << endl;
    exit(EXIT_FAILURE);
  } 
  catch(std::exception &e) {
    cerr << e.what() << endl;
    exit(EXIT_FAILURE);
  } 
}

// Makes sure there is nothing obviously wrong with the session
// indicies, and stores them in _sessvec.
bool EddyCommandLineOptions::session_indicies_kosher(const std::string& fname, unsigned int ns)
{
  bool rval=true;

  if (!fname.length()) {
    _sessvec.resize(ns,1);
    _nsess = 1;
  }
  else {
    NEWMAT::Matrix session = MISCMATHS::read_ascii_matrix(fname);
    if (std::min(session.Nrows(),session.Ncols()) != 1 || std::max(session.Nrows(),session.Ncols()) != int(ns)) {
      throw EddyException("--session must be an 1xN or Nx1 matrix where N is the number of volumes in --imain");
    }
    if (session.Ncols() > session.Nrows()) session = session.t();
    _sessvec.resize(ns,0);
    unsigned int max_sess = static_cast<unsigned int>(session.Maximum());
    std::vector<unsigned int> scan_count(max_sess,0);
    for (unsigned int i=0; i<ns; i++) {
      _sessvec[i] = static_cast<unsigned int>(session(i+1,1));
      scan_count[_sessvec[i]-1]++;
    }
    for (unsigned int i=0; i<max_sess; i++) {
      if (!scan_count[i]) {
        rval=false;
	break;
      }
      else _nsess = max_sess;
    }
  }
  return(rval);
}

// Makes sure that the indicies makes sense w.r.t. pointing in to
// the acquistition parameter file, and stores them in _indvec.
bool EddyCommandLineOptions::indicies_kosher(NEWMAT::Matrix indx, NEWMAT::Matrix acqp)
{
  if (indx.Ncols() > indx.Nrows()) indx = indx.t();
  _indvec.resize(indx.Nrows());
  unsigned int max_indx = static_cast<unsigned int>(indx(1,1));
  for (int i=0; i<indx.Nrows(); i++) {
    _indvec[i] = static_cast<unsigned int>(indx(i+1,1));
    if (fabs(static_cast<double>(_indvec[i])-indx(i+1,1)) > 1e-6) return(false);
    max_indx = std::max(max_indx,_indvec[i]);
  }
  if (max_indx > static_cast<unsigned int>(acqp.Nrows())) return(false);
  else return(true);
}