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/* Copyright (c) 2008-2022 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 "axes.h"
#include "exception.h"
#include "mrtrix.h"
namespace MR
{
namespace Axes
{
std::string dir2id (const Eigen::Vector3d& axis)
{
if (axis[0] == -1) {
assert (!axis[1]); assert (!axis[2]); return "i-";
} else if (axis[0] == 1) {
assert (!axis[1]); assert (!axis[2]); return "i";
} else if (axis[1] == -1) {
assert (!axis[0]); assert (!axis[2]); return "j-";
} else if (axis[1] == 1) {
assert (!axis[0]); assert (!axis[2]); return "j";
} else if (axis[2] == -1) {
assert (!axis[0]); assert (!axis[1]); return "k-";
} else if (axis[2] == 1) {
assert (!axis[0]); assert (!axis[1]); return "k";
} else {
throw Exception ("Malformed axis direction: \"" + str(axis.transpose()) + "\"");
}
}
Eigen::Vector3d id2dir (const std::string& id)
{
if (id == "i-")
return { -1, 0, 0 };
else if (id == "i")
return { 1, 0, 0 };
else if (id == "j-")
return { 0, -1, 0 };
else if (id == "j")
return { 0, 1, 0 };
else if (id == "k-")
return { 0, 0, -1 };
else if (id == "k")
return { 0, 0, 1 };
else
throw Exception ("Malformed image axis identifier: \"" + id + "\"");
}
void get_permutation_to_make_axial (const transform_type& T, std::array<size_t, 3>& perm, std::array<bool, 3>& flip)
{
// Find which row of the transform is closest to each scanner axis
decltype(T.matrix().topLeftCorner<3,3>())::Index index;
T.matrix().topLeftCorner<3,3>().row(0).cwiseAbs().maxCoeff (&index); perm[0] = index;
T.matrix().topLeftCorner<3,3>().row(1).cwiseAbs().maxCoeff (&index); perm[1] = index;
T.matrix().topLeftCorner<3,3>().row(2).cwiseAbs().maxCoeff (&index); perm[2] = index;
// Disambiguate permutations
auto not_any_of = [] (size_t a, size_t b) -> size_t
{
for (size_t i = 0; i < 3; ++i) {
if (a == i || b == i)
continue;
return i;
}
assert (0);
return std::numeric_limits<size_t>::max();
};
if (perm[0] == perm[1])
perm[1] = not_any_of (perm[0], perm[2]);
if (perm[0] == perm[2])
perm[2] = not_any_of (perm[0], perm[1]);
if (perm[1] == perm[2])
perm[2] = not_any_of (perm[0], perm[1]);
assert (perm[0] != perm[1] && perm[1] != perm[2] && perm[2] != perm[0]);
// Figure out whether any of the rows of the transform point in the
// opposite direction to the MRtrix convention
flip[perm[0]] = T(0,perm[0]) < 0.0;
flip[perm[1]] = T(1,perm[1]) < 0.0;
flip[perm[2]] = T(2,perm[2]) < 0.0;
}
}
}
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