shared.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_tracking_shared_h__
#define __dwi_tractography_tracking_shared_h__
 
#include <atomic>
 
#include "header.h"
#include "image.h"
#include "memory.h"
#include "transform.h"
#include "dwi/tractography/properties.h"
#include "dwi/tractography/roi.h"
#include "dwi/tractography/ACT/shared.h"
#include "dwi/tractography/resampling/downsampler.h"
#include "dwi/tractography/tracking/types.h"
#include "dwi/tractography/tracking/tractography.h"
 
 
// If this is enabled, images will be output in the current directory showing the density of streamline terminations due to different termination mechanisms throughout the brain
//#define DEBUG_TERMINATIONS
 
 
 
namespace MR
{
  namespace DWI
  {
    namespace Tractography
    {
      namespace Tracking
      {
 
 
 
        class SharedBase { MEMALIGN(SharedBase)
 
          public:
 
            SharedBase (const std::string& diff_path, Properties& property_set);
 
            virtual ~SharedBase();
 
 
            Image<float> source;
            Properties& properties;
            Eigen::Vector3f init_dir;
            size_t max_num_tracks, max_num_seeds;
            size_t min_num_points_preds, max_num_points_preds;
            size_t min_num_points_postds, max_num_points_postds;
            float min_dist, max_dist;
            // Different variables for 1st-order integration vs. higher-order integration
            float max_angle_1o, max_angle_ho, cos_max_angle_1o, cos_max_angle_ho;
            float step_size, min_radius, threshold, init_threshold;
            size_t max_seed_attempts;
            bool unidirectional, rk4, stop_on_all_include, implicit_max_num_seeds;
            DWI::Tractography::Resampling::Downsampler downsampler;
 
            // Additional members for ACT
            bool is_act() const { return bool (act_shared_additions); }
            const ACT::ACT_Shared_additions& act() const { return *act_shared_additions; }
 
            float vox () const
            {
              return std::pow (source.spacing(0)*source.spacing(1)*source.spacing(2), float (1.0/3.0));
            }
 
            void set_step_and_angle (const float stepsize, const float angle, bool is_higher_order);
            void set_num_points();
            void set_num_points (const float angle_minradius_preds, const float max_step_postds);
            void set_cutoff (float cutoff);
 
            // This gets overloaded for iFOD2, as each sample is output rather than just each step, and there are
            //   multiple samples per step
            // (Only utilised for Exec::satisfy_wm_requirement())
            virtual float internal_step_size() const { return step_size; }
 
 
            void add_termination (const term_t i)   const { terminations[i].fetch_add (1, std::memory_order_relaxed); }
            void add_rejection   (const reject_t i) const { rejections[i]  .fetch_add (1, std::memory_order_relaxed); }
 
 
#ifdef DEBUG_TERMINATIONS
            void add_termination (const term_t i, const Eigen::Vector3f& p) const;
#endif
 
 
          private:
            mutable std::atomic<size_t> terminations[TERMINATION_REASON_COUNT];
            mutable std::atomic<size_t> rejections  [REJECTION_REASON_COUNT];
 
            std::unique_ptr<ACT::ACT_Shared_additions> act_shared_additions;
 
#ifdef DEBUG_TERMINATIONS
            Header debug_header;
            Image<uint32_t>* debug_images[TERMINATION_REASON_COUNT];
            const Transform transform;
#endif
 
        };
 
 
 
      }
    }
  }
}
 
#endif