masklinresampler_d.h

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#include <aims/resampling/masklinresampler.h>
 
#include <cmath>
#include <iomanip>
#include <iostream>
#include <limits>
#include <stdexcept>
 
#include <aims/vector/vector.h>
#include <aims/transformation/affinetransformation3d.h>
 
 
namespace {
  template <class T>
  void _sliceResamp( const carto::Volume<T>& input_data,
                     carto::Volume<T> & resamp,
                     const T&background, T* out,
                     const Point3df& start,
                     int t, const carto::Volume<float>& Rinv );
} // anonymous namespace
 
namespace aims
{
 
template <class T>
void MaskLinearResampler<T>::
doResample( const carto::Volume<T> &input_data,
            const soma::Transformation3d &inverse_transform,
            const T &background,
            const Point3df& output_location,
            T &output_value, int t ) const
{
  const Point3df input_location = inverse_transform.transform(output_location);
 
  float xf = std::floor(input_location[0]);
  float yf = std::floor(input_location[1]);
  float zf = std::floor(input_location[2]);
 
  std::vector<int> dims = input_data.getSize();
 
  // The test is done using floating-point so that NaN values are excluded (the
  // background value is returned if the transformation yields NaN)
  if ( ( xf >= 0 ) && ( xf < dims[0] ) &&
       ( yf >= 0 ) && ( yf < dims[1] ) &&
       ( zf >= 0 ) && ( zf < dims[2] ) )
  {
    int x = static_cast<int>(xf);
    int y = static_cast<int>(yf);
    int z = static_cast<int>(zf);
 
    if (input_data.at(x,     y,     z, t) == -32768 ||
        input_data.at(x + 1, y,     z, t) == -32768 ||
        input_data.at(x,     y + 1, z, t) == -32768 ||
        input_data.at(x + 1, y + 1, z, t) == -32768 ||
        input_data.at(x,     y,     z + 1, t) == -32768 ||
        input_data.at(x + 1, y,     z + 1, t) == -32768 ||
        input_data.at(x,     y + 1, z + 1, t) == -32768 ||
        input_data.at(x + 1, y + 1, z + 1, t) == -32768)
    {
      output_value = -32768;
    } else {
      // Normal linear interpolation
      _linearresampler.resample_inv_to_vox(input_data, inverse_transform,
                                           background, output_location,
                                           output_value, t);
    }
  } else {
    output_value = background;
  }
}
 
 
template <class T>
void MaskLinearResampler<T>::resample( const carto::Volume< T >& input_data,
                                       const aims::AffineTransformation3d&
                                         motion,
                                       const T& background,
                                       carto::Volume< T > & thing,
                                       bool verbose ) const
{
  int dimt = thing.getSizeT();
  ASSERT( thing.getSizeT() == input_data.getSizeT()
          && thing.refVolume().isNull() );
 
  aims::AffineTransformation3d dirMotion = motion;
  std::unique_ptr<aims::AffineTransformation3d> invMotion = motion.inverse();
  
  // scale motion
  Point3df sizeFrom( input_data.getVoxelSize() );
  Point3df sizeTo( thing.getVoxelSize() );
  dirMotion.scale( sizeFrom, sizeTo );
  invMotion->scale( sizeTo, sizeFrom );
 
  //
  Point3df start;
  T* it = &thing.at( 0 );
  int dimz = thing.getSizeZ();
 
  if(verbose) {
    std::cout << "Resampling volume [  1] / slice [  1]" << std::flush;
  }
 
  for (int t = 1; t <= dimt; t++ )
  {
    start = invMotion->translation();
    for ( int s = 1; s <= dimz; s++ )
    {
      if(verbose) {
        std::cout << "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b"
                  << std::setw( 3 ) << t << "] / slice ["
                  << std::setw( 3 ) << s << "]" << std::flush;
      }
 
      _sliceResamp( input_data, thing, background, it, start, t - 1,
                    invMotion->rotation() );
      it = &thing.at( 0, 0, s, t - 1 );
      start[ 0 ] += invMotion->rotation()( 0, 2 );
      start[ 1 ] += invMotion->rotation()( 1, 2 );
      start[ 2 ] += invMotion->rotation()( 2, 2 );
    }
  }
  if(verbose) {
    std::cout << std::endl;
  }
}
 
} // namespace aims
 
 
namespace {
 
template <class T>
void _sliceResamp( const carto::Volume<T>& input_data,
                   carto::Volume<T> & resamp,
                   const T& background, T* out,
                   const Point3df& start, int t,
                   const carto::Volume<float>& Rinv )
{
  static_assert(std::numeric_limits<int>::digits >= 31,
                "the optimizations need at least 32-bit int");
 
  const T* pOrig = &input_data.at( 0, 0, 0, t );
 
  int dimX1 = input_data.getSizeX();
  int dimX2 = resamp.getSizeX();
  int dimY2 = resamp.getSizeY();
 
  const int SIXTEEN = 16;
  const int TWO_THEN_SIXTEEN = 65536;
 
  int maxX = TWO_THEN_SIXTEEN * ( dimX1 - 1 );
  int maxY = TWO_THEN_SIXTEEN * ( input_data.getSizeY() - 1 );
  int maxZ = TWO_THEN_SIXTEEN * ( input_data.getSizeZ() - 1 );
 
  int xLinCurrent = ( int )( 65536.0 * start[ 0 ] );
  int yLinCurrent = ( int )( 65536.0 * start[ 1 ] );
  int zLinCurrent = ( int )( 65536.0 * start[ 2 ] );
 
  int xu = ( int )( 65536.0 * Rinv( 0, 0 ) );
  int yu = ( int )( 65536.0 * Rinv( 1, 0 ) );
  int zu = ( int )( 65536.0 * Rinv( 2, 0 ) );
  int xv = ( int )( 65536.0 * Rinv( 0, 1 ) );
  int yv = ( int )( 65536.0 * Rinv( 1, 1 ) );
  int zv = ( int )( 65536.0 * Rinv( 2, 1 ) );
 
  int xCurrent, yCurrent, zCurrent;
  int dx, dy, dz;
  const T* it;
  long   incr_vois[8] = {
    0,
    1,
    &input_data.at( 0, 1, 0 ) - &input_data.at( 0 ),
    &input_data.at( 0, 1, 0 ) - &input_data.at( 0 ),
    &input_data.at( 0, 0, 1 ) - &input_data.at( 0 ),
    &input_data.at( 1, 0, 1 ) - &input_data.at( 0 ),
    &input_data.at( 1, 1, 1 ) - &input_data.at( 0 ),
    &input_data.at( 0, 1, 1 ) - &input_data.at( 0 )
  };
float stock1, stock2, stock3;
  for ( int v = dimY2; v--; )
  {
    xCurrent = xLinCurrent;
    yCurrent = yLinCurrent;
    zCurrent = zLinCurrent;
 
    for ( int u = dimX2; u--; )
    {
      if ( xCurrent >= 0 && xCurrent < maxX &&
           yCurrent >= 0 && yCurrent < maxY &&
           zCurrent >= 0 && zCurrent < maxZ   )
      {
        dx = xCurrent & 0xffff;
        dy = yCurrent & 0xffff;
        dz = zCurrent & 0xffff;
 
        it = pOrig + ( zCurrent >> SIXTEEN ) * incr_vois[4]
                   + ( yCurrent >> SIXTEEN ) * dimX1
                   + ( xCurrent >> SIXTEEN );
 
        if (*(it + incr_vois[0]) == -32768 ||
            *(it + incr_vois[1]) == -32768 ||
            *(it + incr_vois[2]) == -32768 ||
            *(it + incr_vois[3]) == -32768 ||
            *(it + incr_vois[4]) == -32768 ||
            *(it + incr_vois[5]) == -32768 ||
            *(it + incr_vois[6]) == -32768 ||
            *(it + incr_vois[7]) == -32768 )
          {
            *out++ = -32768;
          }
        else
          {
 
          
            stock1 = *it * ( TWO_THEN_SIXTEEN - dx );
            stock1 += *(++it) * dx;
            stock1 /= TWO_THEN_SIXTEEN;
 
            it += dimX1;
            stock2 = *it * dx;
            stock2 += *(--it) * ( TWO_THEN_SIXTEEN - dx );
            stock2 /= TWO_THEN_SIXTEEN;
 
            stock1 *= ( TWO_THEN_SIXTEEN - dy );
            stock1 += stock2 * dy;
            stock1 /= TWO_THEN_SIXTEEN;
 
            it += incr_vois[4] - dimX1;
            stock2 = *it * ( TWO_THEN_SIXTEEN - dx );
            stock2 += *(++it) * dx;
            stock2 /= TWO_THEN_SIXTEEN;
 
            it += dimX1;
            stock3 = *it * dx;
            stock3 += *(--it) * ( TWO_THEN_SIXTEEN - dx );
            stock3 /= TWO_THEN_SIXTEEN;
 
            stock2 *= TWO_THEN_SIXTEEN - dy;
            stock2 += stock3 * dy;
            stock2 /= TWO_THEN_SIXTEEN;
 
            stock1 *= ( TWO_THEN_SIXTEEN - dz );
            stock1 += stock2 * dz;
 
            *out++ = static_cast<T>( stock1 / TWO_THEN_SIXTEEN );
          }
      }
      else
        *out++ = background;
 
      xCurrent += xu;
      yCurrent += yu;
      zCurrent += zu;
    }
    xLinCurrent += xv;
    yLinCurrent += yv;
    zLinCurrent += zv;
  }
}
 
} // anonymous namespace