void save_bvecs_bvals (const Image::Header& header, const std::string& path)
{
std::string bvecs_path, bvals_path;
if (path.size() >= 5 && path.substr (path.size() - 5, path.size()) == "bvecs") {
bvecs_path = path;
bvals_path = path.substr (0, path.size() - 5) + "bvals";
} else if (path.size() >= 5 && path.substr (path.size() - 5, path.size()) == "bvals") {
bvecs_path = path.substr (0, path.size() - 5) + "bvecs";
bvals_path = path;
} else {
bvecs_path = path + "bvecs";
bvals_path = path + "bvals";
}
const Math::Matrix<float>& grad (header.DW_scheme());
Math::Matrix<float> G (grad.rows(), 3);
// rotate vectors from scanner space to image space
Math::Matrix<float> D (header.transform());
Math::Permutation p (4);
int signum;
Math::LU::decomp (D, p, signum);
Math::Matrix<float> image2scanner (4,4);
Math::LU::inv (image2scanner, D, p);
Math::Matrix<float> rotation = image2scanner.sub (0,3,0,3);
Math::Matrix<float> grad_G = grad.sub (0, grad.rows(), 0, 3);
Math::mult (G, float(0.0), float(1.0), CblasNoTrans, grad_G, CblasTrans, rotation);
// deal with FSL requiring gradient directions to coincide with data strides
// also transpose matrices in preparation for file output
std::vector<size_t> order = Image::Stride::order (header, 0, 3);
Math::Matrix<float> bvecs (3, grad.rows());
Math::Matrix<float> bvals (1, grad.rows());
for (size_t n = 0; n < G.rows(); ++n) {
bvecs(0,n) = header.stride(order[0]) > 0 ? G(n,order[0]) : -G(n,order[0]);
bvecs(1,n) = header.stride(order[1]) > 0 ? G(n,order[1]) : -G(n,order[1]);
bvecs(2,n) = header.stride(order[2]) > 0 ? G(n,order[2]) : -G(n,order[2]);
bvals(0,n) = grad(n,3);
}
bvecs.save (bvecs_path);
bvals.save (bvals_path);
}
void run () {
Point<> p[3];
for (size_t arg = 0; arg < 3; ++arg) {
std::vector<float> V = argument[arg];
if (V.size() != 3)
throw Exception ("coordinates must contain 3 elements");
p[arg][0] = V[0];
p[arg][1] = V[1];
p[arg][2] = V[2];
}
Image::Header header (argument[3]);
float vox = Math::pow (header.vox(0)*header.vox(1)*header.vox(2), 1.0f/3.0f);
Options opt = get_options ("vox");
if (opt.size())
vox = opt[0][0];
Point<> d1 = p[1] - p[0];
Point<> d2 = p[2] - p[0];
d1.normalise();
d2.normalise();
d2 = d2 - d1 * d1.dot(d2);
d2.normalise();
Point<> d3 = d1.cross(d2);
float min1 = std::numeric_limits<float>::infinity();
float min2 = std::numeric_limits<float>::infinity();
float max1 = -std::numeric_limits<float>::infinity();
float max2 = -std::numeric_limits<float>::infinity();
update_bounds (min1, min2, max1, max2, header, Point<int>(0,0,0), 0, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(0,0,0), 1, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(0,0,0), 2, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(1,0,0), 1, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(1,0,0), 2, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(0,1,0), 0, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(0,1,0), 2, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(0,0,1), 0, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(0,0,1), 1, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(1,1,0), 2, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(1,0,1), 1, p[0], d1, d2);
update_bounds (min1, min2, max1, max2, header, Point<int>(0,1,1), 0, p[0], d1, d2);
Point<> translation (p[0] + min1*d1 + min2*d2);
header.transform()(0,0) = d1[0];
header.transform()(1,0) = d1[1];
header.transform()(2,0) = d1[2];
header.transform()(0,1) = d2[0];
header.transform()(1,1) = d2[1];
header.transform()(2,1) = d2[2];
header.transform()(0,2) = d3[0];
header.transform()(1,2) = d3[1];
header.transform()(2,2) = d3[2];
header.transform()(0,3) = translation[0];
header.transform()(1,3) = translation[1];
header.transform()(2,3) = translation[2];
header.set_ndim (3);
header.dim (0) = (max1-min1) / vox;
header.dim (1) = (max2-min2) / vox;
header.dim (2) = 1;
header.vox(0) = header.vox(1) = header.vox(2) = vox;
header.datatype() = DataType::Bit;
header.DW_scheme().clear();
Image::Buffer<bool> roi_buffer (argument[4], header);
Image::Buffer<bool>::voxel_type roi (roi_buffer);
Image::LoopInOrder loop (roi);
for (loop.start (roi); loop.ok(); loop.next (roi))
roi.value() = true;
}
void run ()
{
if (get_options ("norealign").size())
Image::Header::do_not_realign_transform = true;
const bool format = get_options("format") .size();
const bool ndim = get_options("ndim") .size();
const bool dimensions = get_options("dimensions") .size();
const bool vox = get_options("vox") .size();
const bool dt_long = get_options("datatype_long") .size();
const bool dt_short = get_options("datatype_short").size();
const bool stride = get_options("stride") .size();
const bool offset = get_options("offset") .size();
const bool multiplier = get_options("multiplier") .size();
const bool comments = get_options("comments") .size();
const bool properties = get_options("properties") .size();
const bool transform = get_options("transform") .size();
const bool dwgrad = get_options("dwgrad") .size();
Options opt = get_options ("export_grad_mrtrix");
const std::string dw_out_mrtrix = opt.size() ? opt[0][0] : std::string();
opt = get_options ("export_grad_fsl");
std::string dw_out_fsl_bvecs, dw_out_fsl_bvals;
if (opt.size()) {
dw_out_fsl_bvecs = str(opt[0][0]);
dw_out_fsl_bvals = str(opt[0][1]);
}
if ((dw_out_mrtrix.size() || dw_out_fsl_bvecs.size()) && (argument.size() > 1))
throw Exception ("Can only export gradient table information to file if a single input image is provided");
const bool print_full_header = (!(format || ndim || dimensions || vox || dt_long || dt_short || stride
|| offset || multiplier || comments || properties || transform || dwgrad)
&& dw_out_mrtrix.empty() && dw_out_fsl_bvecs.empty());
for (size_t i = 0; i < argument.size(); ++i) {
Image::Header header (argument[i]);
if (format) std::cout << header.format() << "\n";
if (ndim) std::cout << header.ndim() << "\n";
if (dimensions) print_dimensions (header);
if (vox) print_vox (header);
if (dt_long) std::cout << (header.datatype().description() ? header.datatype().description() : "invalid") << "\n";
if (dt_short) std::cout << (header.datatype().specifier() ? header.datatype().specifier() : "invalid") << "\n";
if (stride) print_strides (header);
if (offset) std::cout << header.intensity_offset() << "\n";
if (multiplier) std::cout << header.intensity_scale() << "\n";
if (comments) print_comments (header);
if (properties) print_properties (header);
if (transform) std::cout << header.transform();
if (dwgrad) std::cout << header.DW_scheme();
if (dw_out_mrtrix.size()) {
if (!header.DW_scheme().is_set())
throw Exception ("no gradient information found within image \"" + header.name() + "\"");
header.DW_scheme().save (dw_out_mrtrix);
}
if (dw_out_fsl_bvecs.size()) {
if (!header.DW_scheme().is_set())
throw Exception ("no gradient information found within image \"" + header.name() + "\"");
DWI::save_bvecs_bvals (header, dw_out_fsl_bvecs, dw_out_fsl_bvals);
}
if (print_full_header)
std::cout << header.description();
}
}
void run() {
Image::BufferPreload<float> data_in (argument[0], Image::Stride::contiguous_along_axis (3));
auto voxel_in = data_in.voxel();
Math::Matrix<value_type> grad (DWI::get_valid_DW_scheme<float> (data_in));
// Want to support non-shell-like data if it's just a straight extraction
// of all dwis or all bzeros i.e. don't initialise the Shells class
std::vector<size_t> volumes;
bool bzero = get_options ("bzero").size();
Options opt = get_options ("shell");
if (opt.size()) {
DWI::Shells shells (grad);
shells.select_shells (false, false);
for (size_t s = 0; s != shells.count(); ++s) {
DEBUG ("Including data from shell b=" + str(shells[s].get_mean()) + " +- " + str(shells[s].get_stdev()));
for (std::vector<size_t>::const_iterator v = shells[s].get_volumes().begin(); v != shells[s].get_volumes().end(); ++v)
volumes.push_back (*v);
}
// Remove DW information from header if b=0 is the only 'shell' selected
bzero = (shells.count() == 1 && shells[0].is_bzero());
} else {
const float bzero_threshold = File::Config::get_float ("BValueThreshold", 10.0);
for (size_t row = 0; row != grad.rows(); ++row) {
if ((bzero && (grad (row, 3) < bzero_threshold)) || (!bzero && (grad (row, 3) > bzero_threshold)))
volumes.push_back (row);
}
}
if (volumes.empty())
throw Exception ("No " + str(bzero ? "b=0" : "dwi") + " volumes present");
std::sort (volumes.begin(), volumes.end());
Image::Header header (data_in);
if (volumes.size() == 1)
header.set_ndim (3);
else
header.dim (3) = volumes.size();
Math::Matrix<value_type> new_grad (volumes.size(), grad.columns());
for (size_t i = 0; i < volumes.size(); i++)
new_grad.row (i) = grad.row (volumes[i]);
header.DW_scheme() = new_grad;
Image::Buffer<value_type> data_out (argument[1], header);
auto voxel_out = data_out.voxel();
Image::Loop outer ("extracting volumes...", 0, 3);
if (voxel_out.ndim() == 4) {
for (auto i = outer (voxel_out, voxel_in); i; ++i) {
for (size_t i = 0; i < volumes.size(); i++) {
voxel_in[3] = volumes[i];
voxel_out[3] = i;
voxel_out.value() = voxel_in.value();
}
}
} else {
const size_t volume = volumes[0];
for (auto i = outer (voxel_out, voxel_in); i; ++i) {
voxel_in[3] = volume;
voxel_out.value() = voxel_in.value();
}
}
}