size_t number_of_threads ()
{
if (__number_of_threads)
return __number_of_threads;
const App::Options opt = App::get_options ("nthreads");
__number_of_threads = opt.size() ? opt[0][0] : File::Config::get_int ("NumberOfThreads", std::thread::hardware_concurrency());
return __number_of_threads;
}
Dynamic::Dynamic (const std::string& in, Image::Buffer<float>& fod_data, const Math::RNG& rng, const DWI::Directions::FastLookupSet& dirs) :
Base (in, rng, "dynamic", MAX_TRACKING_SEED_ATTEMPTS_DYNAMIC),
SIFT::ModelBase<Fixel_TD_seed> (fod_data, dirs),
total_samples (0),
total_seeds (0),
transform (SIFT::ModelBase<Fixel_TD_seed>::info())
#ifdef DYNAMIC_SEED_DEBUGGING
, seed_output ("seeds.tck", Tractography::Properties())
#endif
{
App::Options opt = App::get_options ("act");
if (opt.size())
act = new Dynamic_ACT_additions (opt[0][0]);
perform_FOD_segmentation (fod_data);
// Have to set a volume so that Seeding::List works correctly
for (std::vector<Fixel>::const_iterator i = fixels.begin(); i != fixels.end(); ++i)
volume += i->get_weight();
volume *= (fod_data.vox(0) * fod_data.vox(1) * fod_data.vox(2));
// Prevent divide-by-zero at commencement
SIFT::ModelBase<Fixel_TD_seed>::TD_sum = DYNAMIC_SEED_INITIAL_TD_SUM;
}
void load_tracking_seeds (Properties& properties)
{
List& list (properties.seeds);
App::Options opt = get_options ("seed_sphere");
for (size_t i = 0; i < opt.size(); ++i) {
Sphere* seed = new Sphere (opt[i][0], list.get_rng());
list.add (seed);
}
opt = get_options ("seed_image");
for (size_t i = 0; i < opt.size(); ++i) {
SeedMask* seed = new SeedMask (opt[i][0], list.get_rng());
list.add (seed);
}
opt = get_options ("seed_random_per_voxel");
for (size_t i = 0; i < opt.size(); ++i) {
Random_per_voxel* seed = new Random_per_voxel (opt[i][0], list.get_rng(), opt[i][1]);
list.add (seed);
}
opt = get_options ("seed_grid_per_voxel");
for (size_t i = 0; i < opt.size(); ++i) {
Grid_per_voxel* seed = new Grid_per_voxel (opt[i][0], list.get_rng(), opt[i][1]);
list.add (seed);
}
opt = get_options ("seed_rejection");
for (size_t i = 0; i < opt.size(); ++i) {
Rejection* seed = new Rejection (opt[i][0], list.get_rng());
list.add (seed);
}
opt = get_options ("seed_gmwmi");
if (opt.size()) {
App::Options opt_act = get_options ("act");
if (!opt_act.size())
throw Exception ("Cannot perform GM-WM Interface seeding without ACT segmented tissue image");
for (size_t i = 0; i < opt.size(); ++i) {
GMWMI* seed = new GMWMI (opt[i][0], list.get_rng(), str(opt_act[0][0]));
list.add (seed);
}
}
// Can't instantiate the dynamic seeder here; internal FMLS segmenter has to use the same Directions::Set as TrackMapperDixel
opt = get_options ("seed_dynamic");
if (opt.size()) {
if (list.num_seeds())
throw Exception ("If performing dynamic streamline seeding, cannot specify any other type of seed!");
properties["seed_dynamic"] = str(opt[0][0]);
} else if (!list.num_seeds()) {
throw Exception ("Must provide at least one source of streamline seeds!");
}
opt = get_options ("max_seed_attempts");
if (opt.size()) properties["max_seed_attempts"] = std::string (opt[0][0]);
opt = get_options ("output_seeds");
if (opt.size()) properties["seed_output"] = std::string (opt[0][0]);
}