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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/.
*/
#ifndef __image_adapter_jacobian_h__
#define __image_adapter_jacobian_h__
#include "adapter/base.h"
#include "adapter/gradient1D.h"
#include "transform.h"
namespace MR
{
namespace Adapter
{
template <class WarpType>
class Jacobian :
public Base<Jacobian<WarpType>,WarpType>
{ MEMALIGN (Jacobian<WarpType>)
public:
using base_type = Base<Jacobian<WarpType>, WarpType>;
using value_type = Eigen::Matrix<typename WarpType::value_type, 3, 3>;
using base_type::name;
using base_type::size;
using base_type::spacing;
using base_type::index;
Jacobian (const WarpType& parent, bool wrt_scanner = true) :
base_type (parent),
gradient1D (parent, 0, wrt_scanner),
transform (parent),
wrt_scanner (wrt_scanner) { }
value_type value ()
{
for (size_t dim = 0; dim < 3; ++dim)
gradient1D.index(dim) = index(dim);
for (size_t i = 0; i < 3; ++i) {
gradient1D.index(3) = i;
for (size_t j = 0; j < 3; ++j) {
gradient1D.set_axis(j);
jacobian (i, j) = gradient1D.value();
}
}
if (wrt_scanner)
jacobian = jacobian * transform.scanner2image.linear().template cast<typename WarpType::value_type>();
return jacobian;
}
protected:
value_type jacobian;
Gradient1D<WarpType> gradient1D;
Transform transform;
const bool wrt_scanner;
};
}
}
#endif
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