propagate_along_field.tcc

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/*
Copyright CEA (2014).
Copyright Université Paris XI (2014).
 
Contributor: Yann Leprince <yann.leprince@ylep.fr>.
 
This file is part of highres-cortex, a collection of software designed
to process high-resolution magnetic resonance images of the cerebral
cortex.
 
This software is governed by the CeCILL licence under French law and
abiding by the rules of distribution of free software. You can use,
modify and/or redistribute the software under the terms of the CeCILL
licence as circulated by CEA, CNRS and INRIA at the following URL:
<http://www.cecill.info/>.
 
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the licence, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
 
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of scientific
software, that may mean that it is complicated to manipulate, and that
also therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
 
The fact that you are presently reading this means that you have had
knowledge of the CeCILL licence and that you accept its terms.
*/
 
#include "propagate_along_field.hh"
 
#include <cassert>
#include <cmath>
#include <iostream>
#include <stdexcept>
 
#include <boost/shared_ptr.hpp>
#include <boost/tuple/tuple.hpp>
 
namespace
{
 
using carto::VolumeRef;
using std::clog;
using std::endl;
using std::flush;
 
template <typename Tlabel>
struct SeedValueAscensionResult
{
  typedef Tlabel result_type;
  Tlabel operator()(const Tlabel& label, const Point3df& /*point*/, float /*distance*/) const
  {
    return label;
  };
  static const Tlabel& failure_result()
  {
    static const Tlabel failure_res = 0;
    return failure_res;
  };
};
template <typename Tlabel>
struct SeedAndPointAscensionResult
{
  typedef std::pair<Tlabel, Point3df> result_type;
  std::pair<Tlabel, Point3df>
  operator()(const Tlabel& label, const Point3df& point, float /*distance*/) const
  {
    return std::make_pair(label, point);
  };
  static const std::pair<Tlabel, Point3df>& failure_result()
  {
    static const std::pair<Tlabel, Point3df> failure_res
      = std::make_pair(0, Point3df(-1, -1, -1));
    return failure_res;
  }
};
 
template <typename Tlabel>
struct SeedPointDistAscensionResult
{
  typedef boost::tuple<Tlabel, Point3df, float> result_type;
 
  result_type
  operator()(const Tlabel& label, const Point3df& point, float distance) const
  {
    return boost::make_tuple(label, point, distance);
  };
  static const result_type& failure_result()
  {
    static const result_type failure_res
      = boost::make_tuple(0, Point3df(-1, -1, -1), 0.0f);
    return failure_res;
  }
};
 
 
} // end of anonymous namespace
 
template <template <typename> class ResultChooserTemplate, typename Tlabel>
typename ResultChooserTemplate<Tlabel>::result_type
inline
yl::PropagateAlongField::
internal_ascension(const Point3df &start_point,
                   const VolumeRef<Tlabel> &seeds,
                   const Tlabel ignore_label,
                   const ResultChooserTemplate<Tlabel>& result_chooser) const
{
  return internal_ascension<ResultChooserTemplate<Tlabel> >
           (start_point, seeds, ignore_label, result_chooser);
}
 
template <class ResultChooser, typename Tlabel>
typename ResultChooser::result_type
yl::PropagateAlongField::
internal_ascension(const Point3df &start_point,
                   const VolumeRef<Tlabel> &seeds,
                   const Tlabel ignore_label,
                   const ResultChooser& result_chooser) const
{
  if(debug_output >= 3 && m_verbose >= 3) {
    clog << "    ascension at " << start_point << endl;
  }
 
  const std::vector<float> voxel_size = seeds->getVoxelSize();
  const float voxel_size_x = voxel_size[0];
  const float voxel_size_y = voxel_size[1];
  const float voxel_size_z = voxel_size[2];
  const float invsize_x = 1.0f / voxel_size_x;
  const float invsize_y = 1.0f / voxel_size_y;
  const float invsize_z = 1.0f / voxel_size_z;
  if(!std::isnormal(voxel_size_x) ||
     !std::isnormal(voxel_size_y) ||
     !std::isnormal(voxel_size_z)) {
    throw std::runtime_error("inconsistent voxel_size value");
  }
 
  Point3df current_point = start_point;
 
  const int size_x = seeds.getSizeX();
  const int size_y = seeds.getSizeY();
  const int size_z = seeds.getSizeZ();
 
  unsigned int iter;
  for(iter = 0; iter < m_max_iter ; ++iter) {
    const float xp = current_point[0],
      yp = current_point[1], zp = current_point[2];
 
    const int ix = lround(xp * invsize_x);
    if(ix < 0 || ix >= size_x) break;
    const int iy = lround(yp * invsize_y);
    if(iy < 0 || iy >= size_y) break;
    const int iz = lround(zp * invsize_z);
    if(iz < 0 || iz >= size_z) break;
 
    const Tlabel seed_value = seeds(ix, iy, iz);
    if(debug_output >= 4 && m_verbose >= 4) {
      clog << "      iteration " << iter << " at " << current_point
           << ", seed_value = " << seed_value << endl;
    }
    if(seed_value != 0 && seed_value != ignore_label) {
      return result_chooser(seed_value, current_point, std::abs(m_step * iter));
    }
 
    // Move along the field
    Point3df local_field;
    float& gx = local_field[0], gy = local_field[1], gz = local_field[2];
    try {
      m_vector_field->evaluate(current_point, local_field);
    } catch(const Field::UndefinedField&) {
      if(m_verbose >= 2) {
        clog << "    ascension at " << start_point << " aborted after "
             << iter << " iterations: vector field is undefined at ("
             << gx << ", " << gy << ", " << gz << ")" << endl;
      }
      return ResultChooser::failure_result();
    }
 
    // Normalize the field, stop if too small or infinite or NaN.
    const float gn = std::sqrt(gx*gx + gy*gy + gz*gz);
    if(!std::isnormal(gn)) break;
    gx /= gn; gy /= gn; gz /= gn;
 
    current_point[0] = xp + m_step * gx;
    current_point[1] = yp + m_step * gy;
    current_point[2] = zp + m_step * gz;
  }
 
  if(m_verbose >= 2) {
    clog << "    ascension at " << start_point << " aborted after "
         << iter << " iterations" << endl;
  }
  return ResultChooser::failure_result();
}
 
 
class ScalarFieldSumVisitor
{
public:
  explicit ScalarFieldSumVisitor(const boost::shared_ptr<yl::ScalarField>& field)
    : m_field(field), m_sum(0.f) {};
 
  void init(const Point3df& /*start_point*/) {};
  void visit(const Point3df& point)
  {
    m_sum += m_field->evaluate(point);
  };
 
  float sum() const
  { return m_sum; };
private:
  boost::shared_ptr<yl::ScalarField> m_field;
  float m_sum;
};
 
template <typename Tlabel>
float yl::PropagateAlongField::
integrate_field_along_advection(const Point3df& start_point,
                                const VolumeRef<Tlabel>& seeds,
                                const boost::shared_ptr<yl::ScalarField>& field,
                                const Tlabel ignore_label) const
{
  ScalarFieldSumVisitor visitor(field);
  if(visitor_ascension(start_point, seeds, ignore_label, visitor)) {
    return m_step * visitor.sum();
  }
  throw AbortedAdvection();
}
 
template <class TVisitor, typename Tlabel>
bool
yl::PropagateAlongField::
visitor_ascension(const Point3df& start_point,
                  const VolumeRef<Tlabel>& seeds,
                  const Tlabel ignore_label,
                  TVisitor& visitor) const
{
  if(debug_output >= 3 && m_verbose >= 3) {
    clog << "    ascension at " << start_point << endl;
  }
 
  const std::vector<float> voxel_size = seeds->getVoxelSize();
  const float voxel_size_x = voxel_size[0];
  const float voxel_size_y = voxel_size[1];
  const float voxel_size_z = voxel_size[2];
  const float invsize_x = 1.0f / voxel_size_x;
  const float invsize_y = 1.0f / voxel_size_y;
  const float invsize_z = 1.0f / voxel_size_z;
  if(!std::isnormal(voxel_size_x) ||
     !std::isnormal(voxel_size_y) ||
     !std::isnormal(voxel_size_z)) {
    throw std::runtime_error("inconsistent voxel_size value");
  }
 
  Point3df current_point = start_point;
  visitor.init(start_point);
 
  const int size_x = seeds.getSizeX();
  const int size_y = seeds.getSizeY();
  const int size_z = seeds.getSizeZ();
 
  unsigned int iter;
  for(iter = 0; iter < m_max_iter ; ++iter) {
    const float xp = current_point[0],
      yp = current_point[1], zp = current_point[2];
 
    const int ix = lround(xp * invsize_x);
    if(ix < 0 || ix >= size_x) break;
    const int iy = lround(yp * invsize_y);
    if(iy < 0 || iy >= size_y) break;
    const int iz = lround(zp * invsize_z);
    if(iz < 0 || iz >= size_z) break;
 
    const Tlabel seed_value = seeds(ix, iy, iz);
    if(debug_output >= 4 && m_verbose >= 4) {
      clog << "      iteration " << iter << " at " << current_point
           << ", seed_value = " << seed_value << endl;
    }
    visitor.visit(current_point);
    if(seed_value != 0 && seed_value != ignore_label) {
      return true;
    }
 
    // Move along the field
    Point3df local_field;
    float& gx = local_field[0], gy = local_field[1], gz = local_field[2];
    try {
      m_vector_field->evaluate(current_point, local_field);
    } catch(const Field::UndefinedField&) {
      if(m_verbose >= 2) {
        clog << "    ascension at " << start_point << " aborted after "
             << iter << " iterations: vector field is undefined at ("
             << gx << ", " << gy << ", " << gz << ")" << endl;
      }
      return false;
    }
 
    // Normalize the field, stop if too small or infinite or NaN.
    const float gn = std::sqrt(gx*gx + gy*gy + gz*gz);
    if(!std::isnormal(gn)) break;
    gx /= gn; gy /= gn; gz /= gn;
 
    current_point[0] = xp + m_step * gx;
    current_point[1] = yp + m_step * gy;
    current_point[2] = zp + m_step * gz;
  }
 
  if(m_verbose >= 2) {
    clog << "    ascension at " << start_point << " aborted after "
         << iter << " iterations" << endl;
  }
  return false;
}
 
 
template <typename Tlabel>
Tlabel
yl::PropagateAlongField::
ascend_until_nonzero(const Point3df &start_point,
                     const VolumeRef<Tlabel> &seeds,
                     const Tlabel ignore_label) const
{
  return internal_ascension(start_point, seeds, ignore_label,
                            SeedValueAscensionResult<Tlabel>());
}
 
 
namespace {
 
template <typename Tlabel>
class SeedValueRecorder
{
public:
  explicit SeedValueRecorder(const VolumeRef<Tlabel>& seeds)
    : m_seed_values(new carto::Volume<Tlabel>(*seeds)) {};
 
  void record(const int x, const int y, const int z,
              const std::pair<Tlabel, Point3df>& value)
  {
    m_seed_values(x, y, z) = value.first;
  };
 
  VolumeRef<Tlabel> result() const {return m_seed_values;};
 
private:
  VolumeRef<Tlabel> m_seed_values;
};
 
template <typename Tlabel>
class SeedValueAndPointRecorder
{
public:
  explicit SeedValueAndPointRecorder(const VolumeRef<Tlabel>& seeds)
    : m_seed_values(new carto::Volume<Tlabel>(*seeds)),
      m_points(seeds.getSizeX(), seeds.getSizeY(), seeds.getSizeZ(), 3)
  {
    m_points->copyHeaderFrom(seeds.header());
    m_points.fill(-1);
    assert(m_points.getSizeT() == 3);
  };
 
  void record(const int x, const int y, const int z,
              const std::pair<Tlabel, Point3df>& value)
  {
    m_seed_values(x, y, z) = value.first;
    const Point3df& point = value.second;
    m_points(x, y, z, 0) = point[0];
    m_points(x, y, z, 1) = point[1];
    m_points(x, y, z, 2) = point[2];
  };
 
  std::pair<VolumeRef<Tlabel>, VolumeRef<float> >
  result() const {return std::make_pair(m_seed_values, m_points);};
 
private:
  VolumeRef<Tlabel> m_seed_values;
  VolumeRef<float> m_points;
};
 
} // end of anonymous namespace
 
 
template<typename Tlabel>
carto::VolumeRef<Tlabel>
yl::PropagateAlongField::
propagate_regions(const carto::VolumeRef<Tlabel> &seeds,
                  const Tlabel target_label) const
{
  SeedValueRecorder<Tlabel> result_recorder(seeds);
  internal_propagation(seeds, target_label, result_recorder);
  return result_recorder.result();
}
 
template<typename Tlabel>
std::pair<carto::VolumeRef<Tlabel>, carto::VolumeRef<float> >
yl::PropagateAlongField::
propagate_regions_keeping_dests(const carto::VolumeRef<Tlabel> &seeds,
                                const Tlabel target_label) const
{
  SeedValueAndPointRecorder<Tlabel> result_recorder(seeds);
  internal_propagation(seeds, target_label, result_recorder);
  return result_recorder.result();
}
 
template<class ResultRecorder, typename Tlabel>
void
yl::PropagateAlongField::
internal_propagation(const carto::VolumeRef<Tlabel> &seeds,
                     const Tlabel target_label,
                     ResultRecorder& result_recorder) const
{
  SeedAndPointAscensionResult<Tlabel> ascension_result_chooser;
 
  const int size_x = seeds.getSizeX();
  const int size_y = seeds.getSizeY();
  const int size_z = seeds.getSizeZ();
 
  const std::vector<float> voxel_size = seeds->getVoxelSize();
  const float voxel_size_x = voxel_size[0];
  const float voxel_size_y = voxel_size[1];
  const float voxel_size_z = voxel_size[2];
 
  if(m_verbose) {
    std::clog << "yl::PropagateAlongField::propagate_regions:\n"
                 "  maximum propagation distance: "
              << std::abs(m_step * m_max_iter) << " mm." << std::endl;
  }
 
  unsigned int n_propagated = 0, n_dead_end = 0, n_lost = 0;
 
  int slices_done = 0;
  #pragma omp parallel for schedule(dynamic)
  for(int z = 0; z < size_z; ++z)
  {
    for(int y = 0; y < size_y; ++y)
    for(int x = 0; x < size_x; ++x)
    {
      if(seeds(x, y, z) == target_label) {
        const Point3df point(x * voxel_size_x,
                             y * voxel_size_y,
                             z * voxel_size_z);
 
        std::pair<Tlabel, Point3df> result
          = internal_ascension(point, seeds, target_label,
                               ascension_result_chooser);
        const Tlabel& result_label = result.first;
 
        if(result_label > 0) {
          result_recorder.record(x, y, z, result);
          #pragma omp atomic
          ++n_propagated;
        } else if(result_label < 0) {
          #pragma omp atomic
          ++n_dead_end;
        } else {  // result_label == 0
          #pragma omp atomic
          ++n_lost;
        }
      }
    }
 
    #pragma omp atomic
    ++slices_done;
 
    if(m_verbose) {
      #pragma omp critical(print_stderr)
      std::clog << "\r  " << slices_done << " / "
                << size_z << " slices processed. "
                << n_propagated << " voxels propagated, "
                << n_dead_end << " dead-end, "
                << n_lost << " lost..." << std::flush;
    }
  }
 
  if(m_verbose) {
    std::clog << "\nyl::PropagateAlongField::propagate_regions: "
              << n_propagated << " propagated, "
              << n_dead_end << " dead-end, "
              << n_lost << " lost." << std::endl;
  }
}