component_d.h

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/* This software and supporting documentation are distributed by
 *     Institut Federatif de Recherche 49
 *     CEA/NeuroSpin, Batiment 145,
 *     91191 Gif-sur-Yvette cedex
 *     France
 *
 * This software is governed by the CeCILL-B license 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-B license as circulated by CEA, CNRS
 * and INRIA at the following URL "http://www.cecill.info".
 *
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 * modify and redistribute granted by the license, users are provided only
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 * economic rights,  and the successive licensors  have only  limited
 * liability.
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 * In this respect, the user's attention is drawn to the risks associated
 * with loading,  using,  modifying and/or developing or reproducing the
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 */
 
/*
 *  Connected components
 */
#ifndef AIMS_CONNECTIVITY_COMPONENT_D_H
#define AIMS_CONNECTIVITY_COMPONENT_D_H
 
#include <aims/connectivity/component.h>
#include <aims/bucket/bucket.h>
#include <cartobase/containers/nditerator.h>
#include <map>
#include <queue>
#include <iostream>
#include <iomanip>
 
namespace aims
{
 
 
  template<typename T, typename O>
  void ConnectedComponentEngine<carto::VolumeRef<T>,
                                carto::VolumeRef<O> >::filterInFrame(
    const carto::VolumeRef<T> & cc,
    carto::VolumeRef<O> out,
    std::map<O, size_t>& valids,
    int t,
    bool verbose )
  {
    int x = 0, y = 0, z = 0;
    
    if( verbose )
      std::cout << "filtering...\n";
 
    out->fill( 0 );
 
    typename std::map<O, size_t>::iterator  is, es = valids.end();
 
    carto::const_line_NDIterator<T> it( &cc->at( 0 ), cc->getSize(),
                                        cc->getStrides() );
    carto::line_NDIterator<O> oit( &out->at( 0, 0, 0, t ), out->getSize(),
                                   out->getStrides() );
    const T *p, *pn;
    O* o;
 
    for( ; !it.ended(); ++it, ++oit )
    {
      p = &*it;
      o = &*oit;
      for( pn=p + it.line_length(); p!=pn;
           it.inc_line_ptr( p ), oit.inc_line_ptr( o ) )
      {
        is = valids.find( (O) *p );
        if( is != es )
          *o = (O) is->second; // RISK OF OVERFLOW on char types
      }
    }
  }
 
 
  template<typename T, typename O>
  void ConnectedComponentEngine<carto::VolumeRef<T>,
                                carto::VolumeRef<O> >::connectedInFrame(
    const carto::VolumeRef<T>& data,
    carto::VolumeRef<O> out,
    Connectivity::Type connectivity,
    std::multimap<size_t, O>& compSizes,
    int t,
    const T & backg,
    bool bin,
    bool verbose )
  {
    int x = 0, y = 0, z = 0, n = 0;
    std::vector<int> dims = data->getSize();
    int dimX = dims[0];
    int dimY = dims[1];
    int dimZ = dims[2];
 
    out->fill( 0 );
 
    //
    // boolean volume to say if a voxel is already used
    //
 
    carto::Volume<byte> flag( dimX, dimY, dimZ );
 
    flag.fill( false );
    carto::line_NDIterator<byte> bit( &flag.at(0), flag.getSize(),
                                      flag.getStrides() );
    carto::const_line_NDIterator<T> it( &data->at( 0, 0, 0, t ),
                                        data->getSize(),
                                        data->getStrides() );
 
    byte *bp, *bpn;
    const T *p;
 
    for( ; !bit.ended(); ++bit, ++it )
    {
      bp = &*bit;
      p = &*it;
      for( bpn=bp + bit.line_length(); bp!=bpn;
          bit.inc_line_ptr( bp ), it.inc_line_ptr( p ) )
        if( *p == backg )
          *bp = true;
    }
 
    Connectivity cd( data->getStrides()[1], data->getStrides()[2],
                     connectivity );
 
    O    label = 1;
    Point3dl   pos, newpos;
    std::queue<Point3dl> que;
    T     val;
    size_t    sz;
 
    //
    // track connected components
    //
    for ( z = 0; z < dimZ; ++z )
    {
      if( verbose )
        std::cout << "\rz: " << z << std::flush;
 
      for ( y = 0; y < dimY; ++y )
        for ( x = 0; x < dimX; ++x )
          if( !flag( x, y, z ) )
          {
            val = data( x, y, z, t );
            que.push( Point3dl( x, y, z ) );
            flag( x, y, z ) = true;
            sz = 0;
            while ( !que.empty() )
            {
              pos = que.front();
              que.pop();
              out( pos ) = label; // RISK of overflow in char types
              ++sz;
              for ( n = 0; n < cd.nbNeighbors(); n++ )
              {
                newpos = pos + Point3dl(cd.xyzOffset( n )[0],
                                        cd.xyzOffset( n )[1],
                                        cd.xyzOffset( n )[2]);
                
                if ( newpos[0] >= 0   &&
                     newpos[0] < dimX &&
                     newpos[1] >= 0   &&
                     newpos[1] < dimY &&
                     newpos[2] >= 0   &&
                     newpos[2] < dimZ   )
            
                  if ( !flag( newpos ) 
                        && ( bin || data( newpos[0], newpos[1], newpos[2], t ) == val ) )
                  {
                    flag( newpos ) = true;
                    que.push( newpos );
                  }
              }
            }
            /* std::cout << "comp. " << label << ", val: " << val << " ("
              << sz << " voxels)\n"; */
 
            compSizes.insert( std::pair<size_t, O>( sz, label ) );
            ++label;
          }
    }
 
    if( verbose )
    {
      std::cout << std::endl;
      std::cout << label << " components" << std::endl;
    } 
  }
 
 
  template<typename T, typename O>
  void ConnectedComponentEngine<carto::VolumeRef<T>,
                                carto::VolumeRef<O> >::connected(
    const carto::VolumeRef<T>& data,
    carto::VolumeRef<O> out,
    Connectivity::Type connectivity,
    std::map<O, size_t>& valids,
    const T & backg, bool bin, 
    size_t minSize, size_t maxSize,
    size_t numMax, bool verbose )
  {
    std::multimap<size_t, size_t> compSizes;
    int t=0;
    int dimX = data->getSizeX();
    int dimY = data->getSizeY();
    int dimZ = data->getSizeZ();
    int dimT = data->getSizeT() ;
 
    for( t = 0 ; t < dimT ; ++t )
    {
      // Get Volume of size_t to avoid risk of overflow in char types
      // before filtering
      carto::VolumeRef<size_t> cc( dimX, dimY, dimZ );
 
      ConnectedComponentEngine<carto::VolumeRef<T>, carto::VolumeRef<size_t> >
        ::connectedInFrame( data, 
                            cc,
                            connectivity, 
                            compSizes,
                            t,
                            backg,
                            bin,
                            verbose );
 
      // Filter small comps
      std::multimap<size_t, size_t>::reverse_iterator 
        im, em = compSizes.rend();
 
      O label = 1;
 
      for( im = compSizes.rbegin(); 
           im != em && ( numMax == 0 || static_cast<size_t>(label) <= numMax ); ++im )
      {
        if ((minSize ==0 || im->first >= minSize) && (maxSize == 0 || im->first <= maxSize))
        {
            if( verbose )
            std::cout << "component " << std::setw( 4 ) << im->second 
                        << " : " << std::setw( 8 ) << im->first 
                        << " points" << std::endl;
            valids[ im->second ] = static_cast<size_t>( label++ );
        }
      }
 
      ConnectedComponentEngine<carto::VolumeRef<size_t>, carto::VolumeRef<O> >
        ::filterInFrame( cc, out, valids, t, verbose );
 
      if( verbose )
        std::cout << "after filtering: " << valids.size() << " components\n";
 
    }
  }
  
  template <typename T> 
  void AimsConnectedComponent( AimsBucket<Void>& components,
                               const carto::VolumeRef<T>& data,
                               Connectivity::Type connectivity, 
                               const T & backgrnd, bool bin, 
                               size_t minsize, size_t maxsize,
                               size_t maxcomp, bool verbose )
  {
    AimsBucket<Void>                    *cbk;
    std::unique_ptr<AimsBucket<Void> >  abk;
    if( minsize == 0 && maxsize == 0 && maxcomp == 0 )
      cbk = &components;
    else
    {
 
      abk.reset( new AimsBucket<Void> );
      cbk = abk.get();
    }
    AimsBucket<Void>    & component = *cbk;
 
    int x=0, y=0, z=0, t=0, n=0;
 
    int dimX = data->getSizeX();
    int dimY = data->getSizeY();
    int dimZ = data->getSizeZ();
    int dimT = data->getSizeT();
 
 
    //
    // boolean volume to say if a voxel is already used
    //
 
    for( t = 0 ; t < dimT ; ++t )
    {
      carto::VolumeRef<byte> flag( dimX, dimY, dimZ );
      flag->fill( false );
      carto::line_NDIterator<byte> bit( &flag->at( 0 ), flag->getSize(),
                                        flag->getStrides() );
      carto::const_line_NDIterator<T> it( &data->at( 0, 0, 0, t ),
                                          data->getSize(),
                                          data->getStrides() );
      byte *bp;
      const T *p, *pn;
 
      for( ; !bit.ended(); ++bit, ++it )
      {
        p = &*it;
        bp = &*bit;
        for( pn=p + it.line_length(); p!=pn;
            it.inc_line_ptr( p ), bit.inc_line_ptr( bp ) )
          if( *p == backgrnd )
            *bp = true;
      }
 
      Connectivity cd( data->getStrides()[1], data->getStrides()[2],
                       connectivity );
      //Connectivity cf( flag.oLine(), flag.oSlice(), connectivity );
      size_t                                    label = 1;
      AimsBucketItem<Void>              item,newItem;
      std::queue< AimsBucketItem< Void > >      que;
      T                                         val;
 
 
      //
      // track connected components
      //
      for ( z = 0; z < dimZ; ++z )
      {
        if( verbose )
          std::cout << "\rz: " << z << std::flush;
        for ( y = 0; y < dimY; ++y )
          for ( x = 0; x < dimX; ++x )
            {
              if( !flag( x, y, z ) )
                {
   
                  val = data( x, y, z );
                  item.location() = Point3d( x, y, z );
                  que.push( item );
                  flag( x, y, z ) = true;
                  std::list<AimsBucketItem<Void> > & bk = component[ label ];
                  while ( !que.empty() )
                    {
                      item.location() = que.front().location();
                      que.pop();
                      bk.push_back( item );
                      for ( n = 0; n < cd.nbNeighbors(); n++ )
                        {
                          newItem.location() = item.location() 
                            + cd.xyzOffset( n );
                          if ( newItem.location().item( 0 ) >= 0   &&
                               newItem.location().item( 0 ) < dimX &&
                               newItem.location().item( 1 ) >= 0   &&
                               newItem.location().item( 1 ) < dimY &&
                               newItem.location().item( 2 ) >= 0   &&
                               newItem.location().item( 2 ) < dimZ   )
                   
                            if ( flag( newItem.location() ) == false 
                                 && ( bin || data( newItem.location() ) 
                                      == val ) )
                              {
                                flag( newItem.location() ) = true;
                                que.push( newItem );
                              }
                        }
                    }
                  ++label;
                }
            }
      }
      if( verbose )
        std::cout << std::endl;
 
      // filtering
      if( minsize == 0 && maxsize == 0 && maxcomp == 0 )
        return;
 
      AimsBucket<Void>::iterator        i, e = component.end();
      std::multimap<unsigned, std::list<AimsBucketItem<Void> > *>       comps;
      for( i=component.begin(); i!=e; ++i )
        if(( minsize == 0 || i->second.size() >= minsize ) && ( maxsize == 0 || i->second.size() <= maxsize ))
          comps.insert( std::pair<unsigned, std::list<AimsBucketItem<Void> > *>
                      ( i->second.size(),&i->second ) );
      std::multimap<unsigned, 
        std::list<AimsBucketItem<Void> > *>::reverse_iterator 
        im, em = comps.rend();
      label = 0;
      for( im=comps.rbegin(); im!=em && label < maxcomp; ++im )
        components[ label++ ] = *im->second;
    }
  }
 
  namespace internal
  {
 
    template <typename T> inline 
    bool _nulltesttemplate_iseq( const T & x, const T & val )
    {
      return x == val;
    }
 
    template<> inline 
    bool _nulltesttemplate_iseq( const Void &, const Void & )
    {
      return false;
    }
 
  }
 
 
  template <typename T>
  void AimsConnectedComponent( AimsBucket<Void>& components,
                               const BucketMap<T>& data,
                               Connectivity::Type connectivity, 
                               const T & backg, bool bin, 
                               size_t minsize, size_t maxsize,
                               size_t maxcomp, bool )
  {
    AimsBucket<Void>                    *cbk;
    std::unique_ptr<AimsBucket<Void> >  abk;
    if( minsize == 0 && maxsize == 0 && maxcomp == 0 )
      cbk = &components;
    else
      {
        abk.reset( new AimsBucket<Void> );
        cbk = abk.get();
      }
    AimsBucket<Void>    & component = *cbk;
 
 
    //
    // boolean bucket to say if a voxel is already used
    //
    BucketMap<byte>                             flags;
    BucketMap<byte>::Bucket                     & flag = flags[0];
    BucketMap<byte>::Bucket::iterator           ifl, efl = flag.end();
    const typename  BucketMap<T>::Bucket        & b = data.begin()->second;
    typename BucketMap<T>::Bucket::const_iterator       ib, eb = b.end();
    int                                         n;
 
    for( ib=b.begin(); ib!=eb; ++ib )
      flag[ ib->first ] 
        = internal::_nulltesttemplate_iseq( ib->second, backg );
 
    Connectivity cd( 0, 0, connectivity );
    //Connectivity cf( flag.oLine(), flag.oSlice(), connectivity );
    size_t                                      label = 1;
    AimsBucketItem<Void>                        item,newItem;
    std::queue< AimsBucketItem< Void > >        que;
    T                                           val;
 
    //
    // track connected components
    //
    for( ib=b.begin(); ib!=eb; ++ib )
      {
        ifl = flag.find( ib->first );
        if( !ifl->second )
          {
            val = ib->second;
            item.location() = ib->first;
            que.push( item );
            ifl->second = true;
//             cout << "comp. " << label << ", val: " << val << std::endl;
            std::list<AimsBucketItem<Void> >    & bk = component[ label ];
            while ( !que.empty() )
              {
                item.location() = que.front().location();
                que.pop();
                bk.push_back( item );
                for ( n = 0; n < cd.nbNeighbors(); n++ )
                  {
                    newItem.location() = item.location() + cd.xyzOffset( n );
                    ifl = flag.find( newItem.location() );
                    if( ifl != efl && ifl->second == false 
                        && ( bin 
                             || b.find( newItem.location() )->second == val ) )
                      {
                        ifl->second = true;
                        que.push( newItem );
                      }
                  }
              }
            //std::cout << "(" << bk.size() << " voxels)\n";
            ++label;
          }
      }
 
    // filtering
    if( minsize == 0 && maxcomp == 0 )
      return;
 
    AimsBucket<Void>::iterator  i, e = component.end();
    std::multimap<unsigned, std::list<AimsBucketItem<Void> > *> comps;
    for( i=component.begin(); i!=e; ++i )
      if(( minsize == 0 || i->second.size() >= minsize ) && ( maxsize == 0 || i->second.size() <= maxsize ))
        comps.insert( std::pair<unsigned, std::list<AimsBucketItem<Void> > *>
                      ( i->second.size(),&i->second ) );
    std::multimap<unsigned, 
      std::list<AimsBucketItem<Void> > *>::reverse_iterator 
      im, em = comps.rend();
    label = 0;
    for( im=comps.rbegin(); im!=em && label<maxcomp; ++im )
      components[ label++ ] = *im->second;
  }
 
 
  template <typename T>
  void AimsConnectedComponent( BucketMap<T>& data,
                               Connectivity::Type connectivity,
                               const T & backgrnd, bool bin,
                               size_t minsize, size_t maxsize,
                               size_t maxcomp,
                               bool verbose )
  {
    AimsBucket<Void>    comps;
    AimsConnectedComponent( comps, data, connectivity, backgrnd, bin, minsize, maxsize,
                            maxcomp, verbose );
    AimsBucket<Void>::iterator                  i, e = comps.end();
    std::list<AimsBucketItem<Void> >::iterator  ic, ec;
    typename BucketMap<T>::iterator             ib, eb = data.end();
    typename BucketMap<T>::Bucket::iterator     ibb, ebb;
 
    // clear input bucket
    for( ib=data.begin(); ib!=eb; ++ib )
      for( ibb=ib->second.begin(), ebb=ib->second.end(); ibb!=ebb; ++ibb )
        ibb->second = 0;
    // fill it
    typename BucketMap<T>::Bucket       & bk = data.begin()->second;
    for( i=comps.begin(); i!=e; ++i )
      for( ic=i->second.begin(), ec=i->second.end(); ic!=ec; ++ic )
        bk[ ic->location() ] = i->first + 1;
  }
 
 
  template <typename T> 
  carto::VolumeRef<int16_t> AimsLabeledConnectedComponent(
    AimsBucket<Void>& components,
    const carto::VolumeRef<T>& data,
    Connectivity::Type connectivity,
    const T & backgrnd, bool bin,
    size_t minsize, size_t maxsize,
    size_t maxcomp, bool verbose )
  {
    AimsBucket<Void>      *cbk;
    // added to return the labels image
    carto::VolumeRef<int16_t> labelImage( data->getSizeX(), data->getSizeY(),
                                          data->getSizeZ(), data->getSizeT() );
    labelImage->fill( 0 );
    std::unique_ptr<AimsBucket<Void> >  abk;
    if( minsize == 0 && maxsize == 0 && maxcomp == 0 )
      cbk = &components;
    else
    {
 
      abk.reset( new AimsBucket<Void> );
      cbk = abk.get();
    }
    AimsBucket<Void>  & component = *cbk;
 
    int x=0, y=0, z=0, t=0, n=0;
 
    int dimX = data->getSizeX();
    int dimY = data->getSizeY();
    int dimZ = data->getSizeZ();
    int dimT = data->getSizeT();
 
    
    //     boolean volume to say if a voxel is already used
    
 
    for( t = 0 ; t < dimT ; ++t )
    {
      carto::VolumeRef<byte> flag( dimX, dimY, dimZ );
      flag->fill( false );
      carto::line_NDIterator<byte> bit( &flag->at( 0 ), flag->getSize(),
                                        flag->getStrides() );
      carto::const_line_NDIterator<T> it( &data->at( 0, 0, 0, t ),
                                          data->getSize(),
                                          data->getStrides() );
      byte *bp;
      const T *p, *pn;
      for( ; !bit.ended(); ++it, ++bit )
      {
        p = &*it;
        bp = &*bit;
        for( pn=p + it.line_length(); p!=pn;
            it.inc_line_ptr( p ), bit.inc_line_ptr( bp ) )
          if( *p == backgrnd )
            *bp = true;
      }
 
      Connectivity cd( data->getStrides()[1], data->getStrides()[2],
                       connectivity );
      Connectivity cf( flag->getStrides()[1], flag->getStrides()[2],
                       connectivity );
      size_t          label = 1;
      AimsBucketItem<Void>      item,newItem;
      std::queue< AimsBucketItem< Void > >  que;
      T           val;
 
 
//       track connected components
      
      for ( z = 0; z < dimZ; ++z )
      {
        if( verbose )
          std::cout << "\rz: " << z << std::flush;
        for ( y = 0; y < dimY; ++y )
          for ( x = 0; x < dimX; ++x )
        {
 
          if( !flag( x, y, z ) )
          {
 
            val = data( x, y, z );
            item.location() = Point3d( x, y, z );
 
            labelImage (x, y, z) = label;
            que.push( item );
            flag( x, y, z ) = true;
//                   std::cout << "comp. " << lcbkabel << ", val: " << val 
//                   << std::endl;
            std::list<AimsBucketItem<Void> > & bk = component[ label ];
            while ( !que.empty() )
            {
              item.location() = que.front().location();
              que.pop();
              bk.push_back( item );
              labelImage (item.location()) =label;
              for ( n = 0; n < cd.nbNeighbors(); n++ )
              {
                newItem.location() = item.location() 
                    + cd.xyzOffset( n );
                if ( newItem.location().item( 0 ) >= 0   &&
                     newItem.location().item( 0 ) < dimX &&
                     newItem.location().item( 1 ) >= 0   &&
                     newItem.location().item( 1 ) < dimY &&
                     newItem.location().item( 2 ) >= 0   &&
                     newItem.location().item( 2 ) < dimZ   )
                   
                  if ( flag( newItem.location() ) == false 
                       && ( bin || data( newItem.location() ) 
                       == val ) )
                {
                  flag( newItem.location() ) = true;
                  que.push( newItem );
                  labelImage (newItem.location()) = label;
                }
              }
            }
//                   std::cout << "(" << bk.size() << " voxels)\n";
            ++label;
          }
        }
      }
      if( verbose )
        std::cout << std::endl;
 
//       filtering probleme filtrage
      if( minsize == 0 && maxsize == 0 && maxcomp == 0 )
        return labelImage;
 
      AimsBucket<Void>::iterator  i, e = component.end();
      std::multimap<unsigned, std::list<AimsBucketItem<Void> > *> comps;
      for( i=component.begin(); i!=e; ++i )
        if(( minsize == 0 || i->second.size() >= minsize ) && (maxsize == 0 || i->second.size() <= maxsize ))
          comps.insert( std::pair<unsigned, std::list<AimsBucketItem<Void> > *>
              ( i->second.size(),&i->second ) );
      
      std::multimap<unsigned, 
      std::list<AimsBucketItem<Void> > *>::reverse_iterator 
          im, em = comps.rend();
      label = 0;
      labelImage = 0;
      for( im=comps.rbegin(); im!=em && (label < maxcomp || maxcomp == 0); ++im ){
          std::list<AimsBucketItem<Void> > bucket = *im->second;
          std::list<AimsBucketItem<Void> >::iterator ite, iteend = bucket.end();
          for (ite = bucket.begin(); ite != iteend ; ite ++ ) {
              labelImage ((*ite).location()) = label;
          }
        components[ label++ ] = *im->second;
      }
    }
    return labelImage;
  }
 
}
 
#endif