void run() {
Image::Header input_SH_header (argument[0]);
if (input_SH_header.ndim() != 4)
throw Exception ("input SH image should contain 4 dimensions");
std::vector<ssize_t> strides (4, 0);
strides[3] = 1;
Image::BufferPreload<value_type> input_buf (input_SH_header, strides);
Math::Vector<value_type> responseSH;
responseSH.load (argument[1]);
Math::Vector<value_type> responseRH;
Math::SH::SH2RH (responseRH, responseSH);
Ptr<Image::Buffer<bool> > mask_buf;
Options opt = get_options ("mask");
if (opt.size()) {
mask_buf = new Image::Buffer<bool> (opt[0][0]);
Image::check_dimensions (*mask_buf, input_buf, 0, 3);
}
Image::Header output_SH_header (input_SH_header);
Image::Stride::set_from_command_line (output_SH_header, Image::Stride::contiguous_along_axis (3));
Image::Buffer<value_type> output_SH_buf (argument[2], output_SH_header);
SDeconvFunctor sconv (input_buf, output_SH_buf, mask_buf, responseRH);
Image::ThreadedLoop loop ("performing convolution...", input_buf, 2, 0, 3);
loop.run (sconv);
}
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());
}