Beispiel #1
0
void run ()
{
  auto sh_data = Image<value_type>::open(argument[0]);
  Math::SH::check (sh_data);

  auto amp_header = sh_data.original_header();

  Eigen::MatrixXd directions;

  if (get_options("gradient").size()) {
    Eigen::MatrixXd grad;
    grad = load_matrix(argument[1]);
    DWI::Shells shells (grad);
    directions = DWI::gen_direction_matrix (grad, shells.largest().get_volumes());
  } else {
    directions = load_matrix(argument[1]);
  }

  if (!directions.rows())
    throw Exception ("no directions found in input directions file");

  std::stringstream dir_stream;
  for (ssize_t d = 0; d < directions.rows() - 1; ++d)
    dir_stream << directions(d,0) << "," << directions(d,1) << "\n";
  dir_stream << directions(directions.rows() - 1,0) << "," << directions(directions.rows() - 1,1);
  amp_header.keyval().insert(std::pair<std::string, std::string> ("directions", dir_stream.str()));

  amp_header.size(3) = directions.rows();
  Stride::set_from_command_line (amp_header, Stride::contiguous_along_axis (3));
  amp_header.datatype() = DataType::from_command_line (DataType::Float32);

  auto amp_data = Image<value_type>::create(argument[2], amp_header);

  SH2Amp sh2amp (directions, Math::SH::LforN (sh_data.size(3)), get_options("nonnegative").size());
  ThreadedLoop("computing amplitudes", sh_data, 0, 3, 2).run(sh2amp, sh_data, amp_data);
  
}
void run ()
{
  Image::Buffer<value_type> dwi_data (argument[0]);

  if (dwi_data.ndim() != 4)
    throw Exception ("dwi image should contain 4 dimensions");

  Math::Matrix<value_type> grad = DWI::get_valid_DW_scheme<value_type> (dwi_data);
  DWI::Shells shells (grad);
  // Keep the b=0 shell (may be used for normalisation), but force single non-zero shell
  shells.select_shells (true, true);

  Math::Matrix<value_type> DW_dirs = DWI::gen_direction_matrix (grad, shells.largest().get_volumes());

  Options opt = get_options ("lmax");
  lmax = opt.size() ? opt[0][0] : Math::SH::LforN (shells.largest().count());
  INFO ("calculating even spherical harmonic components up to order " + str (lmax));

  Math::Matrix<value_type> HR_dirs;
  Math::Matrix<value_type> HR_SHT;
  opt = get_options ("normalise");
  if (opt.size()) {
    normalise = true;
    opt = get_options ("directions");
    if (opt.size())
      HR_dirs.load (opt[0][0]);
    else
      DWI::Directions::electrostatic_repulsion_300 (HR_dirs);
    Math::SH::init_transform (HR_SHT, HR_dirs, lmax);
  }

  // set Lmax
  int i;
  for (i = 0; Math::SH::NforL(i) < shells.largest().count(); i += 2);
  i -= 2;
  if (lmax > i) {
    WARN ("not enough data for SH order " + str(lmax) + ", falling back to " + str(i));
    lmax = i;
  }
  INFO("setting maximum even spherical harmonic order to " + str(lmax));

  // Setup response function
  int num_RH = (lmax + 2)/2;
  Math::Vector<value_type> sigs(num_RH);
  std::vector<value_type> AL (lmax+1);
  Math::Legendre::Plm_sph<value_type>(&AL[0], lmax, 0, 0);
  for (int l = 0; l <= lmax; l += 2) sigs[l/2] = AL[l];
  Math::Vector<value_type> response(num_RH);
  Math::SH::SH2RH(response, sigs);

  opt = get_options ("filter");
  Math::Vector<value_type> filter;
  if (opt.size()) {
    filter.load (opt[0][0]);
    if (filter.size() <= response.size())
      throw Exception ("not enough filter coefficients supplied for lmax" + str(lmax));
    for (int i = 0; i <= lmax/2; i++) response[i] *= filter[i];
    INFO ("using initial filter coefficients: " + str (filter));
  }

  Math::SH::Transform<value_type> FRT_SHT(DW_dirs, lmax);
  FRT_SHT.set_filter(response);

  Image::Header qbi_header (dwi_data);
  qbi_header.dim(3) = Math::SH::NforL (lmax);
  qbi_header.datatype() = DataType::Float32;
  Image::Stride::set (qbi_header, Image::Stride::contiguous_along_axis (3, dwi_data));
  Image::Buffer<value_type> qbi_data (argument[1], qbi_header);


  opt = get_options ("mask");
  if (opt.size()) {
    Image::Buffer<bool> mask_data (opt[0][0]);
    Image::ThreadedLoop ("estimating dODFs using Q-ball imaging...", dwi_data, 0, 3)
      .run (DWI2QBI (FRT_SHT.mat_A2SH(), HR_SHT, shells), mask_data.voxel(), dwi_data.voxel(), qbi_data.voxel());
  }
  else 
    Image::ThreadedLoop ("estimating dODFs using Q-ball imaging...", dwi_data, 0, 3)
      .run (DWI2QBI (FRT_SHT.mat_A2SH(), HR_SHT, shells), dwi_data.voxel(), qbi_data.voxel());
}
Beispiel #3
0
void run ()
{
  auto amp = Image<value_type>::open (argument[0]).with_direct_io (3);
  Header header (amp);

  std::vector<size_t> bzeros, dwis;
  Eigen::MatrixXd dirs;
  auto opt = get_options ("directions");
  if (opt.size()) {
    dirs = load_matrix (opt[0][0]);
  } 
  else {
    auto hit = header.keyval().find ("directions");
    if (hit != header.keyval().end()) {
      std::vector<default_type> dir_vector;
      for (auto line : split_lines (hit->second)) {
        auto v = parse_floats (line);
        dir_vector.insert (dir_vector.end(), v.begin(), v.end());
      }
      dirs.resize(dir_vector.size() / 2, 2);
      for (size_t i = 0; i < dir_vector.size(); i += 2) {
        dirs(i/2, 0) = dir_vector[i];
        dirs(i/2, 1) = dir_vector[i+1];
      }
    } 
    else {
      auto grad = DWI::get_valid_DW_scheme (amp);
      DWI::Shells shells (grad);
      shells.select_shells (true, true);
      if (shells.smallest().is_bzero())
        bzeros = shells.smallest().get_volumes();
      dwis = shells.largest().get_volumes();
      dirs = DWI::gen_direction_matrix (grad, dwis);
    }
  }

  auto sh2amp = DWI::compute_SH2amp_mapping (dirs, true, 8);


  bool normalise = get_options ("normalise").size();
  if (normalise && !bzeros.size())
    throw Exception ("the normalise option is only available if the input data contains b=0 images.");


  header.size (3) = sh2amp.cols();
  Stride::set_from_command_line (header);
  auto SH = Image<value_type>::create (argument[1], header);

  Amp2SHCommon common (sh2amp, bzeros, dwis, normalise);

  opt = get_options ("rician");
  if (opt.size()) {
    auto noise = Image<value_type>::open (opt[0][0]).with_direct_io();
    ThreadedLoop ("mapping amplitudes to SH coefficients", amp, 0, 3)
      .run (Amp2SH (common), SH, amp, noise);
  }
  else {
    ThreadedLoop ("mapping amplitudes to SH coefficients", amp, 0, 3)
      .run (Amp2SH (common), SH, amp);
  }
}