void run ()
{
Header H = Header::open (argument[0]);
Math::SH::check (H);
auto fod_data = H.get_image<float>();
Segmented_FOD_receiver receiver (H);
auto
opt = get_options ("afd"); if (opt.size()) receiver.set_afd_output (opt[0][0]);
opt = get_options ("peak"); if (opt.size()) receiver.set_peak_output (opt[0][0]);
opt = get_options ("disp"); if (opt.size()) receiver.set_disp_output (opt[0][0]);
if (!receiver.num_outputs())
throw Exception ("Nothing to do; please specify at least one output image type");
opt = get_options ("mask");
Image<float> mask;
if (opt.size()) {
mask = Image<float>::open (std::string (opt[0][0]));
if (!dimensions_match (fod_data, mask, 0, 3))
throw Exception ("Cannot use image \"" + str(opt[0][0]) + "\" as mask image; dimensions do not match FOD image");
}
FMLS::FODQueueWriter writer (fod_data, mask);
const DWI::Directions::Set dirs (1281);
Segmenter fmls (dirs, Math::SH::LforN (H.size(3)));
load_fmls_thresholds (fmls);
Thread::run_queue (writer, Thread::batch (SH_coefs()), Thread::multi (fmls), Thread::batch (FOD_lobes()), receiver);
}
void run ()
{
Image::Header H (argument[0]);
Image::Buffer<float> fod_data (H);
if (fod_data.ndim() != 4)
throw Exception ("input FOD image should contain 4 dimensions");
const size_t lmax = Math::SH::LforN (fod_data.dim(3));
if (Math::SH::NforL (lmax) != size_t(fod_data.dim(3)))
throw Exception ("Input image does not appear to contain an SH series per voxel");
const DWI::Directions::Set dirs (1281);
Segmented_FOD_receiver receiver (H, dirs);
size_t output_count = 0;
Options opt = get_options ("afd");
if (opt.size()) {
receiver.set_afd_output (opt[0][0]);
++output_count;
}
opt = get_options ("count");
if (opt.size()) {
receiver.set_count_output (opt[0][0]);
++output_count;
}
opt = get_options ("dec");
if (opt.size()) {
receiver.set_dec_output (opt[0][0]);
++output_count;
}
opt = get_options ("gfa");
if (opt.size()) {
receiver.set_gfa_output (opt[0][0]);
++output_count;
}
opt = get_options ("pseudo_fod");
if (opt.size()) {
receiver.set_pseudo_fod_output (opt[0][0]);
++output_count;
}
opt = get_options ("sf");
if (opt.size()) {
receiver.set_sf_output (opt[0][0]);
++output_count;
}
opt = get_options ("fixel_afd");
if (opt.size()) {
receiver.set_fixel_afd_output (opt[0][0]);
++output_count;
}
opt = get_options ("fixel_peak");
if (opt.size()) {
receiver.set_fixel_peak_output (opt[0][0]);
++output_count;
}
opt = get_options ("fixel_disp");
if (opt.size()) {
receiver.set_fixel_disp_output (opt[0][0]);
++output_count;
}
if (!output_count)
throw Exception ("Nothing to do; please specify at least one output image type");
FMLS::FODQueueWriter<Image::Buffer<float>::voxel_type> writer (fod_data);
opt = get_options ("mask");
Ptr<Image::Buffer<bool> > mask_buffer_ptr;
if (opt.size()) {
mask_buffer_ptr = new Image::Buffer<bool> (std::string (opt[0][0]));
if (!Image::dimensions_match (fod_data, *mask_buffer_ptr, 0, 3))
throw Exception ("Cannot use image \"" + str(opt[0][0]) + "\" as mask image; dimensions do not match FOD image");
writer.set_mask (*mask_buffer_ptr);
}
Segmenter fmls (dirs, lmax);
load_fmls_thresholds (fmls);
Thread::run_queue (writer, SH_coefs(), Thread::multi (fmls), FOD_lobes(), receiver);
}
