libminc-dev 2.3.00-2build1 / usr / include / minc_1_simple.h

/* ----------------------------- MNI Header -----------------------------------
@NAME       : 
@DESCRIPTION: Simplified interator-based access to minc files, using minc_1_rw interface
@COPYRIGHT  :
              Copyright 2007 Vladimir Fonov, McConnell Brain Imaging Centre, 
              Montreal Neurological Institute, McGill University.
              Permission to use, copy, modify, and distribute this
              software and its documentation for any purpose and without
              fee is hereby granted, provided that the above copyright
              notice appear in all copies.  The author and McGill University
              make no representations about the suitability of this
              software for any purpose.  It is provided "as is" without
              express or implied warranty.
---------------------------------------------------------------------------- */
#ifndef MINC_1_SIMPLE_H
#define MINC_1_SIMPLE_H

#include "minc_1_rw.h"

namespace minc
{
  
  template <class T> class minc_input_iterator
  {
    protected:
      mutable minc_1_reader* _rw;
      std::vector<T> _buf;
      std::vector<long> _cur;
      bool _last;
      size_t _count;
    public:
      
    const std::vector<long>& cur(void) const
    {
      return _cur;
    }
    
    
    minc_input_iterator(const minc_input_iterator<T>& a):_rw(a._rw),_cur(a._cur),_last(a._last),_count(a._count)
    {
    }
    
    minc_input_iterator(minc_1_reader& rw):_rw(&rw),_last(false),_count(0)
    {
    }
    
    minc_input_iterator():_rw(NULL),_last(false),_count(0)
    {
    }
    
    void attach(minc_1_reader& rw)
    {
      _rw=&rw;
      _last=false;
      _count=0;
    }
    
    bool next(void)
    {
      if(_last) return false;
      _count++;
      for(size_t i=static_cast<size_t>(_rw->dim_no()-1);
          i>static_cast<size_t>(_rw->dim_no()-_rw->slice_dimensions()-1);i--)
      {
        _cur[i]++;
        if(_cur[i]<static_cast<long>(_rw->dim(i).length))
          break;
        if(i>static_cast<size_t>(_rw->dim_no()-_rw->slice_dimensions())) 
          _cur[i]=0;
        else
        {
          //move to next slice 
          if(i==0) // the case when slice_dimensions==dim_no
          {
            _last=true;
            _count=0;
            break;
          }
          if(!_rw->next_slice())
          {
            _last=true;
            break;
          }
          _rw->read(&_buf[0]);
          _cur=_rw->current_slice();
          _count=0;
          break;
        }
      }
      return !_last;
    }
    
    bool last(void)
    {
      return _last;
    }
    
    void begin(void)
    {
      _cur.resize(MAX_VAR_DIMS,0);
      _buf.resize(_rw->slice_len());
      _count=0;
      _rw->begin();
      _rw->read(&_buf[0]);
      _cur=_rw->current_slice();
    }
    
    const T& value(void) const
    {
      return _buf[_count];
    }
  };
  
  template <class T> class minc_output_iterator
  {
    protected:
      mutable minc_1_writer* _rw;
      std::vector<T> _buf;
      std::vector<long> _cur;
      bool _last;
      size_t _count;
    public:
    const std::vector<long>& cur(void) const
    {
      return _cur;
    }
    
    minc_output_iterator(const minc_output_iterator<T>& a):_rw(a._rw),_cur(a._cur),_last(a._last),_count(a._count)
    {
    }
    
    minc_output_iterator(minc_1_writer& rw):_rw(&rw),_last(false),_count(0)
    {
      _buf.resize(rw.slice_len()); 
    }
    
    minc_output_iterator():_rw(NULL),_last(false),_count(0)
    {
    }
    
    void attach(minc_1_writer& rw)
    {
      _rw=&rw;
      _last=false;
      _count=0;
    }
    
    ~minc_output_iterator()
    {
      if(_count && !_last)
        _rw->write(&_buf[0]);
    }
    
    bool next(void)
    {
      if(_last) return false;
      _count++;
      for(int i=_rw->dim_no()-1;i>(_rw->dim_no()-_rw->slice_dimensions()-1);i--)
      {
        _cur[i]++;
        if(_cur[i]<static_cast<long>(_rw->dim(i).length))
          break;
        if(i>(_rw->dim_no()-_rw->slice_dimensions())) 
          _cur[i]=0;
        else
        {
          //write slice into minc file
          _rw->write(&_buf[0]);
          _count=0;
          //move to next slice 
          if(i==0) // the case when slice_dimensions==dim_no
          {
            _last=true;
            return false;
          }
          if(!_rw->next_slice())
          {
            _last=true;
            break;
          }
          _cur=_rw->current_slice();
          break;
        }
      }
      return !_last;
    }
    
    bool last(void)
    {
      return _last;
    }
    
    void begin(void)
    {
      _buf.resize(_rw->slice_len());
      _cur.resize(MAX_VAR_DIMS,0);
      _count=0;
      _rw->begin();
      _cur=_rw->current_slice();
    }
    
    void value(const T& v) 
    {
      _buf[_count]=v;
    }
  };
  
  //! will attempt to laod the whole volume in T Z Y X V order into buffer, file should be prepared (setup_read_XXXX)
  template<class T> void load_standard_volume(minc_1_reader& rw, T* volume)
  {
    std::vector<size_t> strides(MAX_VAR_DIMS,0);
    size_t str=1;
    for(size_t i=0;i<5;i++)
    {      
      if(rw.map_space(i)<0) continue;
      strides[rw.map_space(i)]=str;
      str*=rw.ndim(i);
    }

    minc_input_iterator<T> in(rw);
    for(in.begin();!in.last();in.next())
    {
      size_t address=0;
      for(size_t i=0;i<static_cast<size_t>(rw.dim_no());i++)
        address+=in.cur()[i]*strides[i];
        
      volume[address]=in.value();
    }
  }
  
  //! will attempt to save the whole volume in T Z Y X V order from buffer, file should be prepared (setup_read_XXXX)
  template<class T> void save_standard_volume(minc_1_writer& rw, const T* volume)
  {
    std::vector<size_t> strides(MAX_VAR_DIMS,0);
    size_t str=1;
    for(size_t i=0;i<5;i++)
    {      
      if(rw.map_space(i)<0) continue;
      strides[rw.map_space(i)]=str;
      str*=rw.ndim(i);
    }
    
    minc_output_iterator<T> out(rw);
    for(out.begin();!out.last();out.next())
    {
      size_t address=0;
      for(size_t i=0;i<static_cast<size_t>(rw.dim_no());i++)
        address+=out.cur()[i]*strides[i];
        
      out.value(volume[address]);
    }
  }

  //! will attempt to load the whole volume in Z Y X T V  order into buffer, file should be prepared (setup_read_XXXX)
  template<class T> void load_non_standard_volume(minc_1_reader& rw, T* volume)
  {
    std::vector<size_t> strides(MAX_VAR_DIMS,0);
    size_t str=1;
    const size_t dimorder[]={0,4,1,2,3};
    for(size_t i=0;i<5;i++)
    {
      if(rw.map_space(dimorder[i])<0|| !rw.ndim(dimorder[i]) ) continue;
      strides[rw.map_space(dimorder[i])]=str;
      str*=rw.ndim(dimorder[i]);
    }
    
    minc_input_iterator<T> in(rw);
    for(in.begin();!in.last();in.next())
    {
      size_t address=0;
      for(int i=0;i<rw.dim_no();i++)
        address+=in.cur()[i]*strides[i];
      
      volume[address]=in.value();
    }
  }
  
  //! will attempt to save the whole volume in V T Z Y X order from buffer, file should be prepared (setup_read_XXXX)
  template<class T> void save_non_standard_volume(minc_1_writer& rw, const T* volume)
  {
    std::vector<size_t> strides(MAX_VAR_DIMS,0);
    size_t str=1;
    const size_t dimorder[]={0,4,1,2,3};
    for(size_t i=0;i<5;i++)
    {
      if(rw.map_space(dimorder[i])<0 || !rw.ndim(dimorder[i]) ) continue;
      strides[rw.map_space(dimorder[i])]=str;
      str*=rw.ndim(dimorder[i]);
    }
    minc_output_iterator<T> out(rw);
    for(out.begin();!out.last();out.next())
    {
      size_t address=0;
      for(int i=0;i<rw.dim_no();i++)
        address+=out.cur()[i]*strides[i];

      out.value(volume[address]);
    }
  }
  
  
}//minc

#endif //MINC_1_SIMPLE_H