/**
 *  \file DensityHeader.cpp
 *  \brief Metadata for a density file.
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#include <IMP/em/DensityHeader.h>

IMPEM_BEGIN_NAMESPACE


namespace {
  template <class T>
   void initialize(T &t) {
     if (std::numeric_limits<T>::has_signaling_NaN) {
       t= std::numeric_limits<T>::signaling_NaN();
     } else if (std::numeric_limits<T>::has_quiet_NaN) {
       t= std::numeric_limits<T>::quiet_NaN();
     } else if (std::numeric_limits<T>::has_infinity) {
       t= std::numeric_limits<T>::infinity();
     } else {
       // numerical limits for int and double have completely
       // different meanings of max/min
       t= -std::numeric_limits<T>::max();
     }
  }
}
DensityHeader::DensityHeader() {
 initialize(nx_);
  initialize(ny_);
  initialize(nz_);
  initialize(data_type_);
  initialize(nxstart);
  initialize(nystart);
  initialize(nzstart);
  initialize(mx);
  initialize(my);
  initialize(mz);
  initialize(xlen);
  initialize(ylen);
  initialize(zlen);
  initialize(alpha);
   initialize(beta);
   initialize(gamma);
   initialize(mapc); initialize(mapr); initialize(maps);
   initialize(dmin); initialize(dmax); initialize(dmean);
   initialize(ispg);
   initialize(nsymbt);
   user[0]=0;
   map[0]=0;
   initialize(machinestamp);
   initialize(rms);
   initialize(nlabl);
   for (unsigned int i=0; i< COMMENT_FIELD_NUM_OF; ++i) {
       comments[i][0]=0;
     }
   initialize(magic);
   initialize(voltage);
   initialize(Cs);  //Cs of microscope
   initialize(Aperture);  //Aperture used
   initialize(Magnification);  //Magnification
   initialize(Postmagnification); //Postmagnification (of energy filter)
   initialize(Exposuretime); //Exposuretime
   initialize(Microscope);  //Microscope
   initialize(Pixelsize); //Pixelsize - used for the microscope CCD camera
   initialize(CCDArea);  //CCDArea
   initialize(Defocus);  //Defocus
   initialize(Astigmatism);//Astigmatism
   initialize(AstigmatismAngle); //Astigmatism Angle
   initialize(FocusIncrement);//Focus-Increment
   initialize(CountsPerElectron);//Counts/Electron
   initialize(Intensity);//Intensity
   initialize(EnergySlitwidth);//Energy slitwidth of energy filter
   initialize(EnergyOffset); //Energy offset of Energy filter
   initialize(Tiltangle);//Tiltangle of stage
   initialize(Tiltaxis);//Tiltaxis
   initialize(MarkerX);//Marker_X coordinate
   initialize(MarkerY);//Marker_Y coordinate
   initialize(lswap);
   initialize(Objectpixelsize_); //this is the actual pixelsize
   initialize(xtop_);
   initialize(ytop_);
   initialize(ztop_); // The upper bound for the x,y and z grid.
   initialize(xorigin_);
   initialize(yorigin_);
   initialize(zorigin_); //Origin used for transforms
   top_calculated_=false;
   initialize(resolution_);
   is_resolution_set_= false;
   top_calculated_ = false;
   // Initialize some of the parameters of the header
   nx_=0;ny_=0;nz_=0;
   data_type_=5;
   nxstart=1; nystart=1; nzstart=1;
   mx = nxstart + nx_ - 1; my = nystart + ny_ - 1; mz = nzstart + nz_ - 1;
  xorigin_ = yorigin_ = zorigin_ = 0.0;
  alpha=90. ; beta=90. ; gamma=90.;
  mapc =1; mapr=2; maps=3;
  ispg=0;
  nsymbt=0;
  Objectpixelsize_=1.0;
  machinestamp = 0;
  nlabl=0;
  strcpy(map,"MAP\0");
  magic=6;
}

void DensityHeader::compute_xyz_top(bool force)
{
  if (top_calculated_ && !force)
    return;
  xtop_ = xorigin_ + Objectpixelsize_*nx_;
  ytop_ = yorigin_ + Objectpixelsize_*ny_;
  ztop_ = zorigin_ + Objectpixelsize_*nz_;
  top_calculated_ = true;
}

void DensityHeader::update_map_dimensions(int nnx,int nny,int nnz) {
  nx_=nnx;
  ny_=nny;
  nz_=nnz;
  mx = nx_;
  my = ny_;
  mz = nz_;
  top_calculated_ = false;
  compute_xyz_top();
  update_cell_dimensions();
}

void DensityHeader::update_cell_dimensions() {
  xlen=nx_*Objectpixelsize_;
  ylen=ny_*Objectpixelsize_;
  zlen=nz_*Objectpixelsize_;
}

DensityHeader create_density_header(const algebra::BoundingBoxD<3> &bb,
                                    float spacing) {
  DensityHeader header;
  algebra::Vector3D origin=bb.get_corner(0);
  algebra::Vector3D top=bb.get_corner(1);
  header.set_xorigin(origin[0]);
  header.set_yorigin(origin[1]);
  header.set_zorigin(origin[2]);
  header.Objectpixelsize_=spacing;
  //calculate the extent of the map
  int extent[3];
  for(int i=0;i<3;i++) {
    extent[i]=ceil((top[i]-origin[i])/spacing);
  }
  header.update_map_dimensions(extent[0],extent[1],extent[2]);
  header.compute_xyz_top(true);
  return header;
}
void DensityHeader::show(std::ostream& out) const {
    out<< "nx: " << nx_ << " ny: " << ny_ << " nz: " << nz_ << std::endl;
    out<<"data_type: " << data_type_ << std::endl;
    out<<"nxstart: " << nxstart << " nystart: " << nystart <<" nzstart: "
      << nzstart << std::endl;
    out<<"mx: "<< mx <<" my:" << my << " mz: " << mz << std::endl;
    out<< "xlen: " << xlen <<" ylen: " << ylen <<" zlen: " << zlen
      << std::endl;
    out<<"alpha : " << alpha << " beta: " << beta <<" gamma: "<< gamma
      << std::endl;
    out<< "mapc : " << mapc << " mapr: " << mapr <<" maps: " << maps
      << std::endl;
    out<< "dmin: " << dmin << " dmax: " << dmax << " dmean: " << dmean
      << std::endl;
    out<<"ispg: " << ispg << std::endl;
    out<<"nsymbt: " << nsymbt << std::endl;
    out<< "user: " << user << std::endl;
    out<<"xorigin: " << xorigin_ << " yorigin: "<< yorigin_ <<" zorigin: "
       << zorigin_ << std::endl;
    out<<"map: " << map << std::endl;
    out<< "Objectpixelsize: " << Objectpixelsize_ << std::endl;
    out<< "Resolution: " << resolution_ << std::endl;
    out<< "machinestamp: " << machinestamp << std::endl;
    out<<"rms: " << rms << std::endl;
    out<<"nlabl: " << nlabl <<std::endl;
    for(int i=0;i<nlabl;i++)
      out<< "comments[" << i << "] = ->" <<  comments[i] << "<-" << std::endl;
  }
IMPEM_END_NAMESPACE