proc_mask.h

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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 __dwi_tractography_sift_proc_mask_h__
#define __dwi_tractography_sift_proc_mask_h__
 
#include "cmdline_option.h"
#include "image.h"
 
#include "algo/iterator.h"
#include "interp/linear.h"
 
#include "dwi/tractography/ACT/act.h"
#include "dwi/tractography/ACT/tissues.h"
 
 
 
namespace MR
{
  namespace DWI
  {
    namespace Tractography
    {
      namespace SIFT
      {
 
 
        extern const App::OptionGroup SIFTModelProcMaskOption;
 
 
        void initialise_processing_mask (Image<float>&, Image<float>&, Image<float>&);
 
 
        // Private functor for performing ACT image regridding
        class ResampleFunctor
        { MEMALIGN(ResampleFunctor)
 
            using transform_type = Eigen::Transform<float, 3, Eigen::AffineCompact>;
 
          public:
            ResampleFunctor (Image<float>&, Image<float>&, Image<float>&);
            ResampleFunctor (const ResampleFunctor&);
 
            void operator() (const Iterator&);
 
          private:
            Image<float> dwi;
            std::shared_ptr<transform_type> voxel2scanner;
            Interp::Linear<Image<float>> interp_anat;
            Image<float> out;
 
            // Helper function for doing the regridding
            ACT::Tissues ACT2pve (const Iterator&);
        };
 
 
 
      }
    }
  }
}
 
 
#endif