void run ()
{
DWI::Tractography::Properties properties;
Image::Header input_header (argument[0]);
Image::BufferSparse<FixelMetric> input_data (input_header);
Image::BufferSparse<FixelMetric>::voxel_type input_fixel (input_data);
DWI::Tractography::Reader<float> reader (argument[1], properties);
properties.comments.push_back ("Created using fixel2tsf");
properties.comments.push_back ("Source fixel image: " + Path::basename (argument[0]));
properties.comments.push_back ("Source track file: " + Path::basename (argument[1]));
DWI::Tractography::ScalarWriter<float> tsf_writer (argument[2], properties);
float angular_threshold = 30.0;
Options opt = get_options ("angle");
if (opt.size())
angular_threshold = opt[0][0];
const float angular_threshold_dp = cos (angular_threshold * (Math::pi/180.0));
const size_t num_tracks = properties["count"].empty() ? 0 : to<int> (properties["count"]);
DWI::Tractography::Mapping::TrackMapperBase mapper (input_header);
mapper.set_use_precise_mapping (true);
ProgressBar progress ("mapping fixel values to streamline points...", num_tracks);
DWI::Tractography::Streamline<float> tck;
Image::Transform transform (input_fixel);
Point<float> voxel_pos;
while (reader (tck)) {
SetVoxelDir dixels;
mapper (tck, dixels);
std::vector<float> scalars (tck.size(), 0.0);
for (size_t p = 0; p < tck.size(); ++p) {
transform.scanner2voxel (tck[p], voxel_pos);
for (SetVoxelDir::const_iterator d = dixels.begin(); d != dixels.end(); ++d) {
if ((int)round(voxel_pos[0]) == (*d)[0] && (int)round(voxel_pos[1]) == (*d)[1] && (int)round(voxel_pos[2]) == (*d)[2]) {
Image::Nav::set_pos (input_fixel, (*d));
Point<float> dir (d->get_dir());
dir.normalise();
float largest_dp = 0.0;
int32_t closest_fixel_index = -1;
for (size_t f = 0; f != input_fixel.value().size(); ++f) {
float dp = std::abs (dir.dot (input_fixel.value()[f].dir));
if (dp > largest_dp) {
largest_dp = dp;
closest_fixel_index = f;
}
}
if (largest_dp > angular_threshold_dp)
scalars[p] = input_fixel.value()[closest_fixel_index].value;
else
scalars[p] = 0.0;
break;
}
}
}
tsf_writer (scalars);
progress++;
}
}
void run ()
{
auto in_data_image = Fixel::open_fixel_data_file<float> (argument[0]);
if (in_data_image.size(2) != 1)
throw Exception ("Only a single scalar value for each fixel can be output as a track scalar file, "
"therefore the input fixel data file must have dimension Nx1x1");
Header in_index_header = Fixel::find_index_header (Fixel::get_fixel_directory (argument[0]));
auto in_index_image = in_index_header.get_image<uint32_t>();
auto in_directions_image = Fixel::find_directions_header (Fixel::get_fixel_directory (argument[0])).get_image<float>().with_direct_io();
DWI::Tractography::Properties properties;
DWI::Tractography::Reader<float> reader (argument[1], properties);
properties.comments.push_back ("Created using fixel2tsf");
properties.comments.push_back ("Source fixel image: " + Path::basename (argument[0]));
properties.comments.push_back ("Source track file: " + Path::basename (argument[1]));
DWI::Tractography::ScalarWriter<float> tsf_writer (argument[2], properties);
float angular_threshold = get_option_value ("angle", DEFAULT_ANGULAR_THRESHOLD);
const float angular_threshold_dp = cos (angular_threshold * (Math::pi / 180.0));
const size_t num_tracks = properties["count"].empty() ? 0 : to<int> (properties["count"]);
DWI::Tractography::Mapping::TrackMapperBase mapper (in_index_image);
mapper.set_use_precise_mapping (true);
ProgressBar progress ("mapping fixel values to streamline points", num_tracks);
DWI::Tractography::Streamline<float> tck;
Transform transform (in_index_image);
Eigen::Vector3 voxel_pos;
while (reader (tck)) {
SetVoxelDir dixels;
mapper (tck, dixels);
vector<float> scalars (tck.size(), 0.0);
for (size_t p = 0; p < tck.size(); ++p) {
voxel_pos = transform.scanner2voxel * tck[p].cast<default_type> ();
for (SetVoxelDir::const_iterator d = dixels.begin(); d != dixels.end(); ++d) {
if ((int)round(voxel_pos[0]) == (*d)[0] && (int)round(voxel_pos[1]) == (*d)[1] && (int)round(voxel_pos[2]) == (*d)[2]) {
assign_pos_of (*d).to (in_index_image);
Eigen::Vector3f dir = d->get_dir().cast<float>();
dir.normalize();
float largest_dp = 0.0;
int32_t closest_fixel_index = -1;
in_index_image.index(3) = 0;
uint32_t num_fixels_in_voxel = in_index_image.value();
in_index_image.index(3) = 1;
uint32_t offset = in_index_image.value();
for (size_t fixel = 0; fixel < num_fixels_in_voxel; ++fixel) {
in_directions_image.index(0) = offset + fixel;
float dp = std::abs (dir.dot (Eigen::Vector3f (in_directions_image.row(1))));
if (dp > largest_dp) {
largest_dp = dp;
closest_fixel_index = fixel;
}
}
if (largest_dp > angular_threshold_dp) {
in_data_image.index(0) = offset + closest_fixel_index;
scalars[p] = in_data_image.value();
} else {
scalars[p] = 0.0;
}
break;
}
}
}
tsf_writer (scalars);
progress++;
}
}