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/*
//
// Copyright 1997-2010 Torsten Rohlfing
//
// Copyright 2011, 2014 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit is free software: you can
// redistribute it and/or modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation, either version 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit is distributed in the hope that it
// will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include "cmtkDataGridMorphologicalOperators.h"
#include <Base/cmtkUnionFind.h>
#include <map>
#include <vector>
#include <list>
cmtk::TypedArray::SmartPtr
cmtk::DataGridMorphologicalOperators::GetBinaryConnectedComponents() const
{
const size_t numberOfPixels = this->m_DataGrid->GetNumberOfPixels();
// this vector will hold the component index per pixel; since we move strictly forward and only look back in the algorithm below,
// there is no need to initialize the vector elements.
std::vector<int> result( numberOfPixels);
const DataGrid::IndexType& dims = this->m_DataGrid->GetDims();
DataGrid::IndexType relative;
relative[0] = this->m_DataGrid->GetNextI();
relative[1] = this->m_DataGrid->GetNextJ();
relative[2] = this->m_DataGrid->GetNextK();
UnionFind<int> connected;
int nextComponent = 1;
DataGrid::IndexType index;
size_t offset = 0;
for ( index[2] = 0; index[2] < dims[2]; ++index[2] )
{
for ( index[1] = 0; index[1] < dims[1]; ++index[1] )
{
for ( index[0] = 0; index[0] < dims[0]; ++index[0], ++offset )
{
// initialize as "background"
int component = 0;
// foreground pixel?
if ( this->m_DataGrid->GetDataAt( offset ) != 0 )
{
// loop over x,y,z neighbor
for ( int dim = 2; dim >= 0; --dim )
{
// is there a preceding neighbor in this direction?
if ( index[dim] )
{
// get component ID for that neighbor
const int existing = result[offset - relative[dim]];
// is there something there?
if ( existing )
{
// did we already get a different component ID from another neighbor?
if ( component && (component != existing) ) // note: this implies "component != 0" because "existing" is at least 1 in this branch.
{
// link old and new component via this pixel
connected.Union( connected.Find( component ), connected.Find( existing ) );
}
// mark current pixel as belonging to the same component
component = existing;
}
}
}
// none of the neighbors is foreground, so use next available component ID.
if ( !component )
{
component = nextComponent++;
connected.Insert( component );
}
}
// set component result for this pixel
result[offset] = component;
}
}
}
// now collapse all component indexes into their unique representative
std::map<int,int> linkMap;
for ( int component = 1; component < nextComponent; ++component )
{
linkMap[component] = connected.FindKey( component );
}
// re-number components
TypedArray::SmartPtr resultArray( TypedArray::Create( TYPE_INT, numberOfPixels ) );
#pragma omp parallel for
for ( int px = 0; px < static_cast<int>( numberOfPixels ); ++px )
{
resultArray->Set( linkMap[result[px]], px );
}
resultArray->SetDataClass( DATACLASS_LABEL );
return resultArray;
}
cmtk::TypedArray::SmartPtr
cmtk::DataGridMorphologicalOperators::GetRegionsRenumberedBySize() const
{
const size_t numberOfPixels = this->m_DataGrid->GetNumberOfPixels();
// first, count pixels in each region
std::map<int,int> regionSizeMap;
for ( size_t px = 0; px < numberOfPixels; ++px )
{
const int value = static_cast<int>( this->m_DataGrid->GetDataAt( px ) );
if ( value )
++regionSizeMap[value];
}
// now create list sorted by region size
std::list< std::pair<const int,int> > sortedList;
for ( std::map<int,int>::const_iterator it = regionSizeMap.begin(); it != regionSizeMap.end(); ++it )
{
std::list< std::pair<const int,int> >::iterator ins = sortedList.begin();
while ( (ins != sortedList.end()) && (ins->second >= it->second) )
++ins;
sortedList.insert( ins, *it ); // need to explicitly create new pair because some STL implementation have it->first as "const".
}
// create renumbering lookup map
std::map<int,int> renumberMap;
int component = 1;
for ( std::list< std::pair<const int,int> >::iterator it = sortedList.begin(); it != sortedList.end(); ++it )
{
renumberMap[it->first] = component++;
}
// re-number components
TypedArray::SmartPtr resultArray( TypedArray::Create( TYPE_INT, numberOfPixels ) );
for ( size_t px = 0; px < numberOfPixels; ++px )
{
resultArray->Set( renumberMap[static_cast<int>( this->m_DataGrid->GetDataAt( px ) )], px );
}
resultArray->SetDataClass( DATACLASS_LABEL );
return resultArray;
}
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