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/* Copyright (c) 2008-2025 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#include "command.h"
#include "progressbar.h"
#include "math/rng.h"
#include "math/SH.h"
#include "file/utils.h"
#include "thread.h"
#include "dwi/directions/file.h"
constexpr size_t default_permutations = 1e8;
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";
SYNOPSIS = "Invert the polarity of individual directions so as to optimise a unipolar electrostatic repulsion model";
DESCRIPTION
+ "The orientations themselves are not affected, only their "
"polarity; this is necessary to ensure near-optimal distribution of DW "
"directions for eddy-current correction.";
ARGUMENTS
+ Argument ("in", "the input files for the directions.").type_file_in()
+ Argument ("out", "the output files for the directions.").type_file_out();
OPTIONS
+ Option ("permutations", "number of permutations to try (default: " + str(default_permutations) + ")")
+ Argument ("num").type_integer (1)
+ Option ("cartesian", "Output the directions in Cartesian coordinates [x y z] instead of [az el].");
}
using value_type = double;
using vector3_type = Eigen::Vector3d;
class Shared { MEMALIGN(Shared)
public:
Shared (const Eigen::MatrixXd& directions, size_t target_num_permutations) :
directions (directions), target_num_permutations (target_num_permutations), num_permutations(0),
progress ("optimising directions for eddy-currents", target_num_permutations),
best_signs (directions.rows(), 1), best_eddy (std::numeric_limits<value_type>::max()) { }
bool update (value_type eddy, const vector<int>& signs)
{
std::lock_guard<std::mutex> lock (mutex);
if (eddy < best_eddy) {
best_eddy = eddy;
best_signs = signs;
progress.set_text ("optimising directions for eddy-currents (current best configuration: energy = " + str(best_eddy) + ")");
}
++num_permutations;
++progress;
return num_permutations < target_num_permutations;
}
value_type eddy (size_t i, size_t j, const vector<int>& signs) const {
vector3_type a = { directions(i,0), directions(i,1), directions(i,2) };
vector3_type b = { directions(j,0), directions(j,1), directions(j,2) };
if (signs[i] < 0) a = -a;
if (signs[j] < 0) b = -b;
return 1.0 / (a-b).norm();
}
vector<int> get_init_signs () const { return vector<int> (directions.rows(), 1); }
const vector<int>& get_best_signs () const { return best_signs; }
protected:
const Eigen::MatrixXd& directions;
const size_t target_num_permutations;
size_t num_permutations;
ProgressBar progress;
vector<int> best_signs;
value_type best_eddy;
std::mutex mutex;
};
class Processor { MEMALIGN(Processor)
public:
Processor (Shared& shared) :
shared (shared),
signs (shared.get_init_signs()),
uniform (0, signs.size()-1) { }
void execute () {
while (eval());
}
void next_permutation ()
{
signs[uniform(rng)] *= -1;
}
bool eval ()
{
next_permutation();
value_type eddy = 0.0;
for (size_t i = 0; i < signs.size(); ++i)
for (size_t j = i+1; j < signs.size(); ++j)
eddy += shared.eddy (i, j, signs);
return shared.update (eddy, signs);
}
protected:
Shared& shared;
vector<int> signs;
Math::RNG rng;
std::uniform_int_distribution<int> uniform;
};
void run ()
{
auto directions = DWI::Directions::load_cartesian (argument[0]);
size_t num_permutations = get_option_value<size_t> ("permutations", default_permutations);
vector<int> signs;
{
Shared eddy_shared (directions, num_permutations);
Thread::run (Thread::multi (Processor (eddy_shared)), "eval thread");
signs = eddy_shared.get_best_signs();
}
for (ssize_t n = 0; n < directions.rows(); ++n)
if (signs[n] < 0)
directions.row(n) *= -1.0;
bool cartesian = get_options("cartesian").size();
DWI::Directions::save (directions, argument[1], cartesian);
}
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