/* 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/.
 */

#ifndef __registration_transform_initialiser_h__
#define __registration_transform_initialiser_h__

#include "image.h"
#include "transform.h"
#include "registration/transform/base.h"
#include "registration/transform/initialiser_helpers.h"

namespace MR
{
  namespace Registration
  {
    namespace Transform
    {
      namespace Init
      {
        enum InitType {set_centre_mass, set_centre_geometric, mass, geometric, moments, rot_search, none};
        struct LinearInitialisationParams { MEMALIGN(LinearInitialisationParams)
          struct TranslationInit { MEMALIGN(TranslationInit)
            bool unmasked1;
            bool unmasked2;
            TranslationInit () :
              unmasked1 (false),
              unmasked2 (false) {} // TODO config parsing
          };

          struct RotationInit { MEMALIGN(RotationInit)
            bool unmasked1;
            bool unmasked2;
            struct rot_search { MEMALIGN(rot_search)
              vector<default_type> angles;
              default_type scale;
              size_t directions;
              bool run_global;
              double translation_extent;
              struct global_search { MEMALIGN(global_search)
                size_t iterations;
                global_search () :
                  iterations (10000) {}
              };
              global_search global;
              rot_search () :
                angles (5),
                scale (0.15),
                directions (250),
                run_global (false),
                translation_extent (0.05) {
                  angles[0] =  2.0 / 180.0 * Math::pi;
                  angles[1] =  5.0 / 180.0 * Math::pi;
                  angles[2] = 10.0 / 180.0 * Math::pi;
                  angles[3] = 15.0 / 180.0 * Math::pi;
                  angles[4] = 20.0 / 180.0 * Math::pi;
                }
            };
            rot_search search;
            RotationInit () :
              unmasked1 (false),
              unmasked2 (false) {    } // TODO config parsing
          };
          TranslationInit init_translation;
          RotationInit init_rotation;
        };

        extern void set_centre_via_mass (
          Image<default_type>& im1,
          Image<default_type>& im2,
          Image<default_type>& mask1,
          Image<default_type>& mask2,
          Registration::Transform::Base& transform,
          Registration::Transform::Init::LinearInitialisationParams& init,
          const vector<MultiContrastSetting>& contrast_settings);

        extern void set_centre_via_image_centres (
          const Image<default_type>& im1,
          const Image<default_type>& im2,
          const Image<default_type>& mask1,
          const Image<default_type>& mask2,
          Registration::Transform::Base& transform,
          Registration::Transform::Init::LinearInitialisationParams& init);

        extern void initialise_using_image_centres (
          const Image<default_type>& im1,
          const Image<default_type>& im2,
          const Image<default_type>& mask1,
          const Image<default_type>& mask2,
          Registration::Transform::Base& transform,
          Registration::Transform::Init::LinearInitialisationParams& init);

        extern void initialise_using_image_moments (
          Image<default_type>& im1,
          Image<default_type>& im2,
          Image<default_type>& mask1,
          Image<default_type>& mask2,
          Registration::Transform::Base& transform,
          Registration::Transform::Init::LinearInitialisationParams& init,
          const vector<MultiContrastSetting>& contrast_settings);

        extern void initialise_using_FOD (
          Image<default_type>& im1,
          Image<default_type>& im2,
          Image<default_type>& mask1,
          Image<default_type>& mask2,
          Registration::Transform::Base& transform,
          Registration::Transform::Init::LinearInitialisationParams& init);


        extern void initialise_using_rotation_search (
          Image<default_type>& im1,
          Image<default_type>& im2,
          Image<default_type>& mask1,
          Image<default_type>& mask2,
          Registration::Transform::Base& transform,
          Registration::Transform::Init::LinearInitialisationParams& init,
          const vector<MultiContrastSetting>& contrast_settings);

        extern void initialise_using_image_mass (
          Image<default_type>& im1,
          Image<default_type>& im2,
          Image<default_type>& mask1,
          Image<default_type>& mask2,
          Registration::Transform::Base& transform,
          Registration::Transform::Init::LinearInitialisationParams& init,
          const vector<MultiContrastSetting>& contrast_settings);
      }
    }
  }
}

#endif
