void generate_header (Image::Header& header, const std::string& tck_file_path, const std::vector<float>& voxel_size)
{
Tractography::Properties properties;
Tractography::Reader<float> file (tck_file_path, properties);
Streamline<float> tck;
size_t track_counter = 0;
Point<float> min_values ( INFINITY, INFINITY, INFINITY);
Point<float> max_values (-INFINITY, -INFINITY, -INFINITY);
{
ProgressBar progress ("creating new template image...", 0);
while (file (tck) && track_counter++ < MAX_TRACKS_READ_FOR_HEADER) {
for (std::vector<Point<float> >::const_iterator i = tck.begin(); i != tck.end(); ++i) {
min_values[0] = std::min (min_values[0], (*i)[0]);
max_values[0] = std::max (max_values[0], (*i)[0]);
min_values[1] = std::min (min_values[1], (*i)[1]);
max_values[1] = std::max (max_values[1], (*i)[1]);
min_values[2] = std::min (min_values[2], (*i)[2]);
max_values[2] = std::max (max_values[2], (*i)[2]);
}
++progress;
}
}
min_values -= Point<float> (3.0*voxel_size[0], 3.0*voxel_size[1], 3.0*voxel_size[2]);
max_values += Point<float> (3.0*voxel_size[0], 3.0*voxel_size[1], 3.0*voxel_size[2]);
header.name() = "tckmap image header";
header.set_ndim (3);
for (size_t i = 0; i != 3; ++i) {
header.dim(i) = std::ceil((max_values[i] - min_values[i]) / voxel_size[i]);
header.vox(i) = voxel_size[i];
header.stride(i) = i+1;
//header.set_units (i, Image::Axis::millimeters);
}
//header.set_description (0, Image::Axis::left_to_right);
//header.set_description (1, Image::Axis::posterior_to_anterior);
//header.set_description (2, Image::Axis::inferior_to_superior);
Math::Matrix<float>& M (header.transform());
M.allocate (4,4);
M.identity();
M(0,3) = min_values[0];
M(1,3) = min_values[1];
M(2,3) = min_values[2];
file.close();
}
bool FixedNumPoints::operator() (const Streamline<>& in, Streamline<>& out) const
{
// Perform an explicit calculation of streamline length
// From this, derive the spline position of each sample
assert (in.size() > 1);
out.clear();
out.index = in.index;
out.weight = in.weight;
value_type length = 0.0;
vector<value_type> steps;
for (size_t i = 1; i != in.size(); ++i) {
const value_type dist = (in[i] - in[i-1]).norm();
length += dist;
steps.push_back (dist);
}
steps.push_back (value_type(0));
Math::Hermite<value_type> interp (hermite_tension);
Streamline<> temp (in);
const size_t s = temp.size();
temp.insert (temp.begin(), temp[0] + (temp[0] - temp[ 1 ]));
temp.push_back ( temp[s] + (temp[s] - temp[s-1]));
value_type cumulative_length = value_type(0);
size_t input_index = 0;
for (size_t output_index = 0; output_index != num_points; ++output_index) {
const value_type target_length = length * output_index / value_type(num_points-1);
while (input_index < s && (cumulative_length + steps[input_index] < target_length))
cumulative_length += steps[input_index++];
if (input_index == s) {
out.push_back (temp[s]);
break;
}
const value_type mu = (target_length - cumulative_length) / steps[input_index];
interp.set (mu);
out.push_back (interp.value (temp[input_index], temp[input_index+1], temp[input_index+2], temp[input_index+3]));
}
return true;
}