void mitk::ConnectomicsNetworkCreator::CreateNewNode( int label, itk::Index<3> index, bool useCoM )
{
// Only create node if it does not exist yet
if( ! ( m_LabelToNodePropertyMap.count( label ) > 0 ) )
{
NetworkNode newNode;
newNode.coordinates.resize( 3 );
if( !useCoM )
{
for( unsigned int loop = 0; loop < newNode.coordinates.size() ; loop++ )
{
newNode.coordinates[ loop ] = index[ loop ] ;
}
}
else
{
std::vector<double> labelCoords = GetCenterOfMass( label );
for( unsigned int loop = 0; loop < newNode.coordinates.size() ; loop++ )
{
newNode.coordinates[ loop ] = labelCoords.at( loop ) ;
}
}
newNode.label = LabelToString( label );
m_LabelToNodePropertyMap.insert( std::pair< ImageLabelType, NetworkNode >( label, newNode ) );
}
}
mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::JustEndPointVerticesNoLabelTest( TractType::Pointer singleTract )
{
ImageLabelPairType labelpair;
{// Note: .fib image tracts are safed using index coordinates
mitk::Point3D firstElementFiberCoord, lastElementFiberCoord;
mitk::Point3D firstElementSegCoord, lastElementSegCoord;
mitk::Index3D firstElementSegIndex, lastElementSegIndex;
if( singleTract->front().Size() != 3 )
{
MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
}
for( int index = 0; index < singleTract->front().Size(); index++ )
{
firstElementFiberCoord.SetElement( index, singleTract->front().GetElement( index ) );
lastElementFiberCoord.SetElement( index, singleTract->back().GetElement( index ) );
}
// convert from fiber index coordinates to segmentation index coordinates
FiberToSegmentationCoords( firstElementFiberCoord, firstElementSegCoord );
FiberToSegmentationCoords( lastElementFiberCoord, lastElementSegCoord );
for( int index = 0; index < 3; index++ )
{
firstElementSegIndex.SetElement( index, firstElementSegCoord.GetElement( index ) );
lastElementSegIndex.SetElement( index, lastElementSegCoord.GetElement( index ) );
}
int firstLabel = 1 * firstElementSegIndex[ 0 ] + 1000 * firstElementSegIndex[ 1 ] + 1000000 * firstElementSegIndex[ 2 ];
int lastLabel = 1 * firstElementSegIndex[ 0 ] + 1000 * firstElementSegIndex[ 1 ] + 1000000 * firstElementSegIndex[ 2 ];
labelpair.first = firstLabel;
labelpair.second = lastLabel;
// Add property to property map
if( ! ( m_LabelToNodePropertyMap.count( firstLabel ) > 0 ) )
{
NetworkNode firstNode;
firstNode.coordinates.resize( 3 );
for( unsigned int index = 0; index < firstNode.coordinates.size() ; index++ )
{
firstNode.coordinates[ index ] = firstElementSegIndex[ index ] ;
}
firstNode.label = LabelToString( firstLabel );
m_LabelToNodePropertyMap.insert( std::pair< ImageLabelType, NetworkNode >( firstLabel, firstNode ) );
}
if( ! ( m_LabelToNodePropertyMap.count( lastLabel ) > 0 ) )
{
NetworkNode lastNode;
lastNode.coordinates.resize( 3 );
for( unsigned int index = 0; index < lastNode.coordinates.size() ; index++ )
{
lastNode.coordinates[ index ] = lastElementSegIndex[ index ] ;
}
lastNode.label = LabelToString( lastLabel );
m_LabelToNodePropertyMap.insert( std::pair< ImageLabelType, NetworkNode >( lastLabel, lastNode ) );
}
}
return labelpair;
}
mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::EndElementPositionLabelAvoidingWhiteMatter( TractType::Pointer singleTract )
{
ImageLabelPairType labelpair;
{// Note: .fib image tracts are safed using index coordinates
mitk::Point3D firstElementFiberCoord, lastElementFiberCoord;
mitk::Point3D firstElementSegCoord, lastElementSegCoord;
mitk::Index3D firstElementSegIndex, lastElementSegIndex;
if( singleTract->front().Size() != 3 )
{
MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
}
for( int index = 0; index < singleTract->front().Size(); index++ )
{
firstElementFiberCoord.SetElement( index, singleTract->front().GetElement( index ) );
lastElementFiberCoord.SetElement( index, singleTract->back().GetElement( index ) );
}
// convert from fiber index coordinates to segmentation index coordinates
FiberToSegmentationCoords( firstElementFiberCoord, firstElementSegCoord );
FiberToSegmentationCoords( lastElementFiberCoord, lastElementSegCoord );
for( int index = 0; index < 3; index++ )
{
firstElementSegIndex.SetElement( index, firstElementSegCoord.GetElement( index ) );
lastElementSegIndex.SetElement( index, lastElementSegCoord.GetElement( index ) );
}
int firstLabel = m_Segmentation->GetPixelValueByIndex( firstElementSegIndex );
int lastLabel = m_Segmentation->GetPixelValueByIndex( lastElementSegIndex );
// Check whether the labels belong to the white matter (which means, that the fibers ended early)
bool extendFront(false), extendEnd(false), retractFront(false), retractEnd(false);
extendFront = !IsNonWhiteMatterLabel( firstLabel );
extendEnd = !IsNonWhiteMatterLabel( lastLabel );
retractFront = IsBackgroundLabel( firstLabel );
retractEnd = IsBackgroundLabel( lastLabel );
//if( extendFront || extendEnd )
//{
//MBI_INFO << "Before Start: " << firstLabel << " at " << firstElementSegIndex[ 0 ] << " " << firstElementSegIndex[ 1 ] << " " << firstElementSegIndex[ 2 ] << " End: " << lastLabel << " at " << lastElementSegIndex[ 0 ] << " " << lastElementSegIndex[ 1 ] << " " << lastElementSegIndex[ 2 ];
//}
if ( extendFront )
{
std::vector< int > indexVectorOfPointsToUse;
//Use first two points for direction
indexVectorOfPointsToUse.push_back( 1 );
indexVectorOfPointsToUse.push_back( 0 );
// label and coordinate temp storage
int tempLabel( firstLabel );
mitk::Index3D tempIndex = firstElementSegIndex;
LinearExtensionUntilGreyMatter( indexVectorOfPointsToUse, singleTract, tempLabel, tempIndex );
firstLabel = tempLabel;
firstElementSegIndex = tempIndex;
}
if ( extendEnd )
{
std::vector< int > indexVectorOfPointsToUse;
//Use last two points for direction
indexVectorOfPointsToUse.push_back( singleTract->Size() - 2 );
indexVectorOfPointsToUse.push_back( singleTract->Size() - 1 );
// label and coordinate temp storage
int tempLabel( lastLabel );
mitk::Index3D tempIndex = lastElementSegIndex;
LinearExtensionUntilGreyMatter( indexVectorOfPointsToUse, singleTract, tempLabel, tempIndex );
lastLabel = tempLabel;
lastElementSegIndex = tempIndex;
}
if ( retractFront )
{
// label and coordinate temp storage
int tempLabel( firstLabel );
mitk::Index3D tempIndex = firstElementSegIndex;
RetractionUntilBrainMatter( true, singleTract, tempLabel, tempIndex );
firstLabel = tempLabel;
firstElementSegIndex = tempIndex;
}
if ( retractEnd )
{
// label and coordinate temp storage
int tempLabel( lastLabel );
mitk::Index3D tempIndex = lastElementSegIndex;
RetractionUntilBrainMatter( false, singleTract, tempLabel, tempIndex );
lastLabel = tempLabel;
lastElementSegIndex = tempIndex;
}
//if( extendFront || extendEnd )
//{
// MBI_INFO << "After Start: " << firstLabel << " at " << firstElementSegIndex[ 0 ] << " " << firstElementSegIndex[ 1 ] << " " << firstElementSegIndex[ 2 ] << " End: " << lastLabel << " at " << lastElementSegIndex[ 0 ] << " " << lastElementSegIndex[ 1 ] << " " << lastElementSegIndex[ 2 ];
//}
labelpair.first = firstLabel;
labelpair.second = lastLabel;
// Add property to property map
if( ! ( m_LabelToNodePropertyMap.count( firstLabel ) > 0 ) )
{
NetworkNode firstNode;
firstNode.coordinates.resize( 3 );
for( unsigned int index = 0; index < firstNode.coordinates.size() ; index++ )
{
firstNode.coordinates[ index ] = firstElementSegIndex[ index ] ;
}
firstNode.label = LabelToString( firstLabel );
m_LabelToNodePropertyMap.insert( std::pair< ImageLabelType, NetworkNode >( firstLabel, firstNode ) );
}
if( ! ( m_LabelToNodePropertyMap.count( lastLabel ) > 0 ) )
{
NetworkNode lastNode;
lastNode.coordinates.resize( 3 );
for( unsigned int index = 0; index < lastNode.coordinates.size() ; index++ )
{
lastNode.coordinates[ index ] = lastElementSegIndex[ index ] ;
}
lastNode.label = LabelToString( lastLabel );
m_LabelToNodePropertyMap.insert( std::pair< ImageLabelType, NetworkNode >( lastLabel, lastNode ) );
}
}
return labelpair;
}
