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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 "exception.h"
#include "image.h"
#include "mrtrix.h"
#include "progressbar.h"
#include "algo/loop.h"
#include "dwi/gradient.h"
#include "dwi/shells.h"
#include "math/math.h"
#include "math/SH.h"
#include "math/ZSH.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";
SYNOPSIS = "Generate an appropriate response function from the image data for spherical deconvolution";
DESCRIPTION
+ Math::SH::encoding_description;
ARGUMENTS
+ Argument ("SH", "the spherical harmonic decomposition of the diffusion-weighted images").type_image_in()
+ Argument ("mask", "the mask containing the voxels from which to estimate the response function").type_image_in()
+ Argument ("directions", "a 4D image containing the direction vectors along which to estimate the response function").type_image_in()
+ Argument ("response", "the output axially-symmetric spherical harmonic coefficients").type_file_out();
OPTIONS
+ Option ("lmax", "specify the maximum harmonic degree of the response function to estimate")
+ Argument ("value").type_integer (0, 20)
+ Option ("dump", "dump the m=0 SH coefficients from all voxels in the mask to the output file, rather than their mean")
+ Argument ("file").type_file_out();
}
using value_type = double;
void run ()
{
auto SH = Image<value_type>::open(argument[0]);
Math::SH::check (SH);
auto mask = Image<bool>::open(argument[1]);
auto dir = Image<value_type>::open(argument[2]).with_direct_io();
int lmax = get_option_value ("lmax", Math::SH::LforN (SH.size(3)));
check_dimensions (SH, mask, 0, 3);
check_dimensions (SH, dir, 0, 3);
if (dir.ndim() != 4)
throw Exception ("input direction image \"" + std::string (argument[2]) + "\" must be a 4D image");
if (dir.size(3) != 3)
throw Exception ("input direction image \"" + std::string (argument[2]) + "\" must contain precisely 3 volumes");
Eigen::VectorXd delta;
Eigen::VectorXd response = Eigen::VectorXd::Zero (Math::ZSH::NforL (lmax));
size_t count = 0;
File::OFStream dump_stream;
auto opt = get_options ("dump");
if (opt.size())
dump_stream.open (opt[0][0]);
Eigen::Matrix<value_type,Eigen::Dynamic,1,0,64> AL (lmax+1);
Math::Legendre::Plm_sph (AL, lmax, 0, value_type (1.0));
auto loop = Loop ("estimating response function", SH, 0, 3);
for (auto l = loop(mask, SH, dir); l; ++l) {
if (!mask.value())
continue;
Eigen::Vector3d d = dir.row(3);
if (!d.allFinite()) {
WARN ("voxel with invalid direction [ " + str(dir.index(0)) + " " + str(dir.index(1)) + " " + str(dir.index(2)) + " ]; skipping");
continue;
}
d.normalize();
// Uncertainty regarding Eigen's behaviour when normalizing a zero vector; may change behaviour between versions
if (!d.allFinite() || !d.squaredNorm()) {
WARN ("voxel with zero direction [ " + str(dir.index(0)) + " " + str(dir.index(1)) + " " + str(dir.index(2)) + " ]; skipping");
continue;
}
Math::SH::delta (delta, d, lmax);
for (int l = 0; l <= lmax; l += 2) {
value_type d_dot_s = 0.0;
value_type d_dot_d = 0.0;
for (int m = -l; m <= l; ++m) {
size_t i = Math::SH::index (l,m);
SH.index(3) = i;
value_type s = SH.value();
// TODO: currently this does NOT handle the non-orthonormal basis
d_dot_s += s*delta[i];
d_dot_d += Math::pow2 (delta[i]);
}
value_type val = AL[l] * d_dot_s / d_dot_d;
response[Math::ZSH::index(l)] += val;
if (dump_stream.is_open())
dump_stream << val << " ";
}
if (dump_stream.is_open())
dump_stream << "\n";
++count;
}
response /= count;
if (std::string(argument[3]) == "-") {
for (ssize_t n = 0; n < response.size(); ++n)
std::cout << response[n] << " ";
std::cout << "\n";
}
else {
save_vector(response, argument[3]);
}
}
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