void run()
{
auto input_image = Image<float>::open (argument[0]);
Eigen::MatrixXd grad = DWI::get_valid_DW_scheme (input_image);
// 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<int> volumes;
bool bzero = get_options ("bzero").size();
auto 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 (const auto v : shells[s].get_volumes())
volumes.push_back (v);
}
bzero = (shells.count() == 1 && shells[0].is_bzero());
} else {
const float bzero_threshold = File::Config::get_float ("BValueThreshold", 10.0);
for (ssize_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()) {
auto type = (bzero) ? "b=0" : "dwi";
throw Exception ("No " + str(type) + " volumes present");
}
std::sort (volumes.begin(), volumes.end());
Header header (input_image);
Stride::set_from_command_line (header);
header.size (3) = volumes.size();
Eigen::MatrixXd new_grad (volumes.size(), grad.cols());
for (size_t i = 0; i < volumes.size(); i++)
new_grad.row (i) = grad.row (volumes[i]);
header.set_DW_scheme (new_grad);
auto output_image = Image<float>::create (argument[1], header);
auto input_volumes = Adapter::make<Adapter::Extract1D> (input_image, 3, volumes);
threaded_copy_with_progress_message ("extracting volumes", input_volumes, output_image);
}
void run ()
{
try {
auto directions = DWI::Directions::load_cartesian (argument[0]);
report (argument[0], directions);
}
catch (Exception& E) {
auto directions = load_matrix<double> (argument[0]);
DWI::normalise_grad (directions);
if (directions.cols() < 3)
throw Exception ("unexpected matrix size for DW scheme \"" + str(argument[0]) + "\"");
print (str(argument[0]) + " [ " + str(directions.rows()) + " volumes ]\n");
DWI::Shells shells (directions);
for (size_t n = 0; n < shells.count(); ++n) {
Eigen::MatrixXd subset (shells[n].count(), 3);
for (ssize_t i = 0; i < subset.rows(); ++i)
subset.row(i) = directions.row(shells[n].get_volumes()[i]).head(3);
report ("\nb = " + str(shells[n].get_mean(), precision), subset);
}
}
}
void run ()
{
try {
Math::Matrix<value_type> directions = DWI::Directions::load_cartesian<value_type> (argument[0]);
report (str(argument[0]), directions);
}
catch (Exception& E) {
Math::Matrix<value_type> directions (str(argument[0]));
DWI::normalise_grad (directions);
if (directions.columns() < 3)
throw Exception ("unexpected matrix size for DW scheme \"" + str(argument[0]) + "\"");
print (str(argument[0]) + " [ " + str(directions.rows()) + " volumes ]\n");
DWI::Shells shells (directions);
for (size_t n = 0; n < shells.count(); ++n) {
Math::Matrix<value_type> subset (shells[n].count(), 3);
for (size_t i = 0; i < subset.rows(); ++i)
subset.row(i) = directions.row(shells[n].get_volumes()[i]).sub(0,3);
report ("\nb = " + str(shells[n].get_mean()), subset);
}
}
}
void run() {
auto input_image = Image<float>::open (argument[0]).with_direct_io (3);
Eigen::MatrixXd grad = DWI::get_valid_DW_scheme (input_image);
// 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();
auto 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 (ssize_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()) {
auto type = (bzero) ? "b=0" : "dwi";
throw Exception ("No " + str(type) + " volumes present");
}
std::sort (volumes.begin(), volumes.end());
Header header (input_image);
if (volumes.size() == 1)
header.set_ndim (3);
else
header.size (3) = volumes.size();
Eigen::MatrixXd new_grad (volumes.size(), grad.cols());
for (size_t i = 0; i < volumes.size(); i++)
new_grad.row (i) = grad.row (volumes[i]);
header.set_DW_scheme (new_grad);
auto output_image = Image<float>::create (argument[1], header);
auto outer = Loop ("extracting volumes", input_image, 0, 3);
if (output_image.ndim() == 4) {
for (auto i = outer (output_image, input_image); i; ++i) {
for (size_t i = 0; i < volumes.size(); i++) {
input_image.index(3) = volumes[i];
output_image.index(3) = i;
output_image.value() = input_image.value();
}
}
} else {
const size_t volume = volumes[0];
for (auto i = outer (output_image, input_image); i; ++i) {
input_image.index(3) = volume;
output_image.value() = input_image.value();
}
}
}
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();
}
}
}