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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 "image.h"
#include "algo/loop.h"
#include "fixel/helpers.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";
SYNOPSIS = "Extract amplitudes from a peak directions image";
ARGUMENTS
+ Argument ("directions", "the input directions image. Each volume corresponds to the x, y & z "
"component of each direction vector in turn.").type_image_in ()
+ Argument ("amplitudes", "the output amplitudes image.").type_image_out ();
}
void run ()
{
Header H_in = Header::open (argument[0]);
Peaks::check (H_in);
auto dir = H_in.get_image<float>();
Header header (dir);
header.size(3) = header.size(3)/3;
auto amp = Image<float>::create (argument[1], header);
auto loop = Loop("converting directions to amplitudes", 0, 3);
for (auto i = loop (dir, amp); i; ++i) {
Eigen::Vector3f n;
dir.index(3) = 0;
amp.index(3) = 0;
while (dir.index(3) < dir.size(3)) {
n[0] = dir.value(); ++dir.index(3);
n[1] = dir.value(); ++dir.index(3);
n[2] = dir.value(); ++dir.index(3);
float amplitude = 0.0;
if (std::isfinite (n[0]) && std::isfinite (n[1]) && std::isfinite (n[2]))
amplitude = n.norm();
amp.value() = amplitude;
++amp.index(3);
}
}
}
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