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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 __misc_voxel2vector_h__
#define __misc_voxel2vector_h__
#include <limits>
#include "exception.h"
#include "header.h"
#include "image.h"
#include "algo/loop.h"
#include "types.h"
#include "adapter/replicate.h"
namespace MR
{
// A class to achieve a mapping from a voxel position in an image
// with any number of axes, to an index within a 1D vector of data.
class Voxel2Vector
{ MEMALIGN(Voxel2Vector)
public:
typedef uint32_t index_t;
static const index_t invalid = std::numeric_limits<index_t>::max();
template <class MaskType>
Voxel2Vector (MaskType& mask, const Header& data);
template <class MaskType>
Voxel2Vector (MaskType& mask) :
Voxel2Vector (mask, Header(mask)) { }
size_t size() const { return reverse.size(); }
const vector<index_t>& operator[] (const size_t index) const {
assert (index < reverse.size());
return reverse[index];
}
template <class PosType>
index_t operator() (const PosType& pos) const {
Image<index_t> temp (forward); // For thread-safety
assign_pos_of (pos).to (temp);
if (is_out_of_bounds (temp))
return invalid;
return temp.value();
}
private:
Image<index_t> forward;
vector< vector<index_t> > reverse;
};
template <class MaskType>
Voxel2Vector::Voxel2Vector (MaskType& mask, const Header& data) :
forward (Image<index_t>::scratch (data, "Voxel to vector index conversion scratch image"))
{
if (!dimensions_match (mask, data, 0, std::min (mask.ndim(), data.ndim())))
throw Exception ("Dimension mismatch between image data and processing mask");
// E.g. Mask may be 3D but data are 4D; for any voxel where the mask is
// true, want to include data from all volumes
Adapter::Replicate<MaskType> r_mask (mask, data);
// Loop in axis order so that those voxels contiguous in memory are still
// contiguous in the vectorised data
index_t counter = 0;
for (auto l = Loop(data) (r_mask, forward); l; ++l) {
if (r_mask.value()) {
forward.value() = counter++;
vector<index_t> pos;
for (size_t index = 0; index != data.ndim(); ++index)
pos.push_back (forward.index(index));
reverse.push_back (pos);
} else {
forward.value() = invalid;
}
}
DEBUG ("Voxel2Vector class has " + str(reverse.size()) + " non-zero entries");
}
}
#endif
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