stos.hxx

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// File         : stos.hxx
// Author       : Pavel A. Koshevoy
// Created      : 2006/06/23 13:40
// Copyright    : (C) 2004-2008 University of Utah
// Description  : Slice to slice registration container class.

#ifndef STOS_HXX_
#define STOS_HXX_

// system includes:
#include <iostream>
#include <iomanip>
#include <fstream>
#include <string>

// boost:
#include <boost/filesystem.hpp>

// local includes:
#include <Core/ITKCommon/common.hxx>
#include <Core/ITKCommon/the_utils.hxx>

#include <Core/Utils/Exception.h>
#include <Core/Utils/Log.h>

namespace bfs=boost::filesystem;

//----------------------------------------------------------------
// stos_t
//
template <typename TImage = image_t>
class stos_t
{
public:
  stos_t() {}
  
  stos_t(const bfs::path & fn_s0,
         const bfs::path & fn_s1,
         const bfs::path & fn_mask_s0,
         const bfs::path & fn_mask_s1,
         const bool & flipped_0,
         const bool & flipped_1,
         const TImage * s0,
         const TImage * s1,
         const unsigned int & shrink_factor,
         const base_transform_t * t01) : t01_(t01)
  {
    fn_[0] = fn_s0;
    fn_[1] = fn_s1;
    
    fn_mask_[0] = fn_mask_s0;
    fn_mask_[1] = fn_mask_s1;
    
    flipped_[0] = flipped_0;
    flipped_[1] = flipped_1;
    
    sp_[0] = s0->GetSpacing();
    sp_[1] = s1->GetSpacing();
    
    sz_[0] = s0->GetLargestPossibleRegion().GetSize();
    sz_[1] = s1->GetLargestPossibleRegion().GetSize();
    
    sp_[0][0] /= shrink_factor;
    sp_[0][1] /= shrink_factor;
    sp_[1][0] /= shrink_factor;
    sp_[1][1] /= shrink_factor;
    
    sz_[0][0] *= shrink_factor;
    sz_[0][1] *= shrink_factor;
    sz_[1][0] *= shrink_factor;
    sz_[1][1] *= shrink_factor;
  }
  
  stos_t(const bfs::path & fn_s0,
         const bfs::path & fn_s1,
         const bfs::path & fn_mask_s0,
         const bfs::path & fn_mask_s1,
         const bool & flipped_0,
         const bool & flipped_1,
         const double spacing_x0,
         const double spacing_y0,
         const double spacing_x1,
         const double spacing_y1,
         const unsigned int size_x0,
         const unsigned int size_y0,
         const unsigned int size_x1,
         const unsigned int size_y1,
         const base_transform_t * t01) : t01_(t01)
  {
    fn_[0] = fn_s0;
    fn_[1] = fn_s1;
    
    fn_mask_[0] = fn_mask_s0;
    fn_mask_[1] = fn_mask_s1;
    
    flipped_[0] = flipped_0;
    flipped_[1] = flipped_1;
    
    sp_[0][0] = spacing_x0;
    sp_[0][1] = spacing_y0;
    sp_[1][0] = spacing_x1;
    sp_[1][1] = spacing_y1;
    
    sz_[0][0] = size_x0;
    sz_[0][1] = size_y0;
    sz_[1][0] = size_x1;
    sz_[1][1] = size_y1;
  }
  
  stos_t(const bfs::path & fn_load,
         const bfs::path & override_slice0_path = "",
         const bfs::path & override_slice1_path = "")
  {
    if (! load(fn_load, override_slice0_path, override_slice1_path) )
    {
      std::ostringstream oss;
      oss << "Loading stos file " << fn_load << " (with slice path overrides "
      << override_slice0_path << " and " << override_slice1_path << ") failed.";
      CORE_THROW_EXCEPTION(oss.str());
    }
  }
  
  // load the filenames of the slices and the corresponding transform:
  bool load(const bfs::path & fn_load,
            const bfs::path & slice0_path = "",
            const bfs::path & slice1_path = "",
            const bool blab = false)
  {
    std::fstream si;
    the::open_utf8(si, fn_load.string().c_str(), std::ios::in);
    if (!si.is_open())
    {
      std::ostringstream oss;
      oss << "Could not open " << fn_load << " for reading, skipping....";
      CORE_LOG_WARNING(oss.str());
      return false;
    }
    
    fn_load_ = fn_load;
    if (blab) std::cout << "stos_t loading " << fn_load_.string() << std::endl;
    
    bool ok = load(si, slice0_path, slice1_path);
    si.close();
    
    return ok;
  }
  
  bool load(std::istream & si,
            const bfs::path & override_slice0_path = "",
            const bfs::path & override_slice1_path = "")
  {
    std::string f[2];
    std::getline(si, f[0]);
    std::getline(si, f[1]);
    
    // Setup slice paths...
    bfs::path corrected_path[2];
    corrected_path[0] = override_slice0_path;
    corrected_path[1] = override_slice1_path;
    
    // Override if needed.
    for (int i = 0; i < 2; i++)
    {
      if (! corrected_path[i].empty() )
      {
        bfs::path mosaicPath(f[i]);
        bfs::path p = corrected_path[i] / mosaicPath.filename();
        if ( bfs::exists(p) )
        {
          fn_[i] = p;
        }
        else
        {
          std::ostringstream oss;
          oss << "Overridden file path " << p << " does not exist. Ignoring path override.";
          CORE_LOG_WARNING(oss.str());

          fn_[i] = f[i];
        }
      }
      else
      {
        if ( bfs::exists(f[i]) )
        {
          fn_[i] = f[i];
        }
        else
        {
          std::ostringstream oss;
          oss << "File path " << f[i] << " does not exist.";
          CORE_LOG_ERROR(oss.str());
          return false;
        }
      }
    }

    std::string line;
    {
      std::getline(si, line);
      std::istringstream iss(line);
      iss >> flipped_[0];
      line.clear();
    }

    {
      std::getline(si, line);
      std::istringstream iss(line);
      iss >> flipped_[1];
      line.clear();
    }

    {
      std::getline(si, line);
      std::istringstream iss(line);
      iss >> sp_[0][0] >> sp_[0][1] >> sz_[0][0] >> sz_[0][1];
      line.clear();
    }
    
    {
      std::getline(si, line);
      std::istringstream iss(line);
      iss >> sp_[1][0] >> sp_[1][1] >> sz_[1][0] >> sz_[1][1];
      line.clear();
    }
    
    itk::TransformBase::Pointer tmp = load_transform(si);
    
    t01_ = dynamic_cast<base_transform_t *>(tmp.GetPointer());
    bool ok = t01_.GetPointer() != NULL;
    
    fn_mask_[0].clear();
    fn_mask_[1].clear();
    
    // skip to the next line (by skipping white space):
    si >> std::ws;
    
    std::string optional;
    std::getline(si, optional);
    if (optional == "two_user_supplied_masks:")
    {
      std::string tmp;
      std::getline(si, tmp);
      if ( bfs::exists(bfs::path(tmp)) )
      {
        fn_mask_[0] = tmp;
      }
      tmp.clear();
      std::getline(si, tmp);
      if ( bfs::exists(bfs::path(tmp)) )
      {
        fn_mask_[1] = tmp;
      }
    }
    
    return ok;
  }
  
  // save this slice-to-slice registration:
  bool save(const bfs::path & fn_save, const bool blab = false) const
  {
    std::fstream so;
    the::open_utf8(so, fn_save.string().c_str(), std::ios::out);
    if (!so.is_open())
    {
      std::ostringstream oss;
      oss << "Could not open " << fn_save << " for writing, skipping....";
      CORE_LOG_WARNING(oss.str());
      return false;
    }
    if (blab) std::cout << "saving " << fn_save << std::endl;
    
    save(so);
    so.close();
    
    // FIXME: not sure if this is useful/necessary:
    fn_load_ = fn_save;
    
    return true;
  }
  
  void save(std::ostream & so) const
  {
    std::ios::fmtflags old_flags = so.setf(std::ios::scientific);
    int old_precision = so.precision();
    so.precision(12);
    
    so << fn_[0].string() << std::endl
    << fn_[1].string() << std::endl
    << flipped_[0] << std::endl
    << flipped_[1] << std::endl
    << sp_[0][0] << '\t'
    << sp_[0][1] << '\t'
    << static_cast<int>(sz_[0][0]) << '\t'
    << static_cast<int>(sz_[0][1]) << std::endl
    << sp_[1][0] << '\t'
    << sp_[1][1] << '\t'
    << static_cast<int>(sz_[1][0]) << '\t'
    << static_cast<int>(sz_[1][1]) << std::endl;
    
    save_transform(so, t01_);
    so << std::endl;
    
    if (!fn_mask_[0].empty() && !fn_mask_[1].empty())
    {
      so << "two_user_supplied_masks:" << std::endl
      << fn_mask_[0].string() << std::endl
      << fn_mask_[1].string() << std::endl;
    }
    
    so.setf(old_flags);
    so.precision(old_precision);
  }
  
  // convenience functions:
  inline pnt2d_t tile_min(unsigned int /* i */) const
  { return pnt2d(0, 0); }
  
  inline pnt2d_t tile_max(unsigned int i) const
  {
    return pnt2d(sp_[i][0] * static_cast<double>(sz_[i][0]),
                 sp_[i][1] * static_cast<double>(sz_[i][1]));
  }
  
  inline pnt2d_t tile_center(unsigned int i) const
  {
    pnt2d_t min = tile_min(i);
    pnt2d_t max = tile_max(i);
    return min + (max - min) * 0.5;
  }
  
  // datamembers:
  mutable bfs::path fn_load_;
  bfs::path fn_[2]; // filenames of the fixed/moving slices
  bfs::path image_dirs_[2];
  bfs::path fn_mask_[2]; // filenames of slice masks, optional
  bool flipped_[2];
  typename TImage::SpacingType sp_[2];
  typename TImage::RegionType::SizeType sz_[2];
  base_transform_t::ConstPointer t01_;
};

//----------------------------------------------------------------
// operator <<
// 
template <typename TImage>
inline static std::ostream &
operator << (std::ostream & so, const stos_t<TImage> & stos)
{
  stos.save(so);
  return so;
}

//----------------------------------------------------------------
// save_stos
//
template <typename TImage>
inline static bool
save_stos(const bfs::path & fn_save,
          const bfs::path & fn_s0,
          const bfs::path & fn_s1,
          const bfs::path & fn_mask_s0,
          const bfs::path & fn_mask_s1,
          const bool & flipped_0,
          const bool & flipped_1,
          const TImage * s0,
          const TImage * s1,
          const unsigned int & shrink_factor,
          const base_transform_t * transform,
          const bool blab = false)
{
  stos_t<TImage> stos(fn_s0,
                      fn_s1,
                      fn_mask_s0,
                      fn_mask_s1,
                      flipped_0,
                      flipped_1,
                      s0,
                      s1,
                      shrink_factor,
                      transform);
  return stos.save(fn_save, blab);
}


#endif // STOS_HXX_