void mitk::ConnectomicsNetworkCreator::CreateNetworkFromFibersAndSegmentation()
{
//empty graph
m_ConNetwork->clear();
m_LabelToVertexMap.clear();
m_LabelToNodePropertyMap.clear();
vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
vtkSmartPointer<vtkCellArray> vLines = fiberPolyData->GetLines();
vLines->InitTraversal();
int numFibers = m_FiberBundle->GetNumFibers();
for( int fiberID( 0 ); fiberID < numFibers; fiberID++ )
{
vtkIdType numPointsInCell(0);
vtkIdType* pointsInCell(NULL);
vLines->GetNextCell ( numPointsInCell, pointsInCell );
TractType::Pointer singleTract = TractType::New();
for( int pointInCellID( 0 ); pointInCellID < numPointsInCell ; pointInCellID++)
{
// push back point
PointType point = GetItkPoint( fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] ) );
singleTract->InsertElement( singleTract->Size(), point );
}
//MappingStrategy strategy = EndElementPosition;
//MappingStrategy strategy = JustEndPointVerticesNoLabel;
MappingStrategy strategy = EndElementPositionAvoidingWhiteMatter;
if ( singleTract && ( singleTract->Size() > 0 ) )
{
AddConnectionToNetwork(
ReturnAssociatedVertexPairForLabelPair(
ReturnLabelForFiberTract( singleTract, strategy )
)
);
}
}
// Prune unconnected nodes
m_ConNetwork->PruneUnconnectedSingleNodes();
// provide network with geometry
m_ConNetwork->SetGeometry( m_Segmentation->GetGeometry() );
m_ConNetwork->UpdateBounds();
m_ConNetwork->SetIsModified( true );
MBI_INFO << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_INFO_NETWORK_CREATED;
}
void mitk::ConnectomicsNetworkCreator::CreateNetworkFromFibersAndSegmentation()
{
//empty graph
m_ConNetwork = mitk::ConnectomicsNetwork::New();
m_LabelToVertexMap.clear();
m_LabelToNodePropertyMap.clear();
idCounter = 0;
vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
int numFibers = m_FiberBundle->GetNumFibers();
for( int fiberID( 0 ); fiberID < numFibers; fiberID++ )
{
vtkCell* cell = fiberPolyData->GetCell(fiberID);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
TractType::Pointer singleTract = TractType::New();
for( int pointInCellID( 0 ); pointInCellID < numPoints ; pointInCellID++)
{
// push back point
PointType point = GetItkPoint( points->GetPoint( pointInCellID ) );
singleTract->InsertElement( singleTract->Size(), point );
}
if ( singleTract && ( singleTract->Size() > 0 ) )
{
AddConnectionToNetwork(
ReturnAssociatedVertexPairForLabelPair(
ReturnLabelForFiberTract( singleTract, m_MappingStrategy )
)
);
m_AbortConnection = false;
}
}
// Prune unconnected nodes
//m_ConNetwork->PruneUnconnectedSingleNodes();
// provide network with geometry
m_ConNetwork->SetGeometry( dynamic_cast<mitk::BaseGeometry*>(m_Segmentation->GetGeometry()->Clone().GetPointer()) );
m_ConNetwork->UpdateBounds();
m_ConNetwork->SetIsModified( true );
MBI_INFO << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_INFO_NETWORK_CREATED;
}
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;
itk::Index<3> firstElementSegIndex, lastElementSegIndex;
if( singleTract->front().Size() != 3 )
{
MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
}
for( unsigned 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
CreateNewNode( firstLabel, firstElementSegIndex, m_UseCoMCoordinates );
CreateNewNode( lastLabel, lastElementSegIndex, m_UseCoMCoordinates );
}
return labelpair;
}
void mitk::ConnectomicsNetworkCreator::RetractionUntilBrainMatter( bool retractFront, TractType::Pointer singleTract,
int & label, itk::Index<3> & mitkIndex )
{
int retractionStartIndex( singleTract->Size() - 1 );
int retractionStepIndexSize( -1 );
int retractionTerminationIndex( 0 );
if( retractFront )
{
retractionStartIndex = 0;
retractionStepIndexSize = 1;
retractionTerminationIndex = singleTract->Size() - 1;
}
int currentRetractionIndex = retractionStartIndex;
bool keepRetracting( true );
mitk::Point3D currentPoint, nextPoint;
std::vector< double > differenceVector;
differenceVector.resize( singleTract->front().Size() );
while( keepRetracting && ( currentRetractionIndex != retractionTerminationIndex ) )
{
// convert to segmentation coords
mitk::Point3D currentPointFiberCoord, nextPointFiberCoord;
for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
{
currentPointFiberCoord.SetElement( index, singleTract->GetElement( currentRetractionIndex ).GetElement( index ) );
nextPointFiberCoord.SetElement( index, singleTract->GetElement( currentRetractionIndex + retractionStepIndexSize ).GetElement( index ) );
}
FiberToSegmentationCoords( currentPointFiberCoord, currentPoint );
FiberToSegmentationCoords( nextPointFiberCoord, nextPoint );
// calculate straight line
for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
{
differenceVector[ index ] = nextPoint.GetElement( index ) - currentPoint.GetElement( index );
}
// calculate length of direction vector
double length( 0.0 );
double sum( 0.0 );
for( unsigned int index = 0; index < differenceVector.size() ; index++ )
{
sum = sum + differenceVector[ index ] * differenceVector[ index ];
}
length = std::sqrt( sum );
// retract
itk::Index<3> tempIndex;
int tempLabel( label );
for( int parameter( 0 ) ; parameter < length ; parameter++ )
{
for( int index( 0 ); index < 3; index++ )
{
tempIndex.SetElement( index,
currentPoint.GetElement( index ) + ( 1.0 + parameter ) / ( 1.0 + length ) * differenceVector[ index ] );
}
tempLabel = m_SegmentationItk->GetPixel( tempIndex );
if( !IsBackgroundLabel( tempLabel ) )
{
// check whether result is within the search space
{
mitk::Point3D endPoint, foundPointSegmentation, foundPointFiber;
for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
{
// this is in fiber (world) coordinates
endPoint.SetElement( index, singleTract->GetElement( retractionStartIndex ).GetElement( index ) );
}
for( int index( 0 ); index < 3; index++ )
{
foundPointSegmentation.SetElement( index,
currentPoint.GetElement( index ) + ( 1.0 + parameter ) / ( 1.0 + length ) * differenceVector[ index ] );
}
SegmentationToFiberCoords( foundPointSegmentation, foundPointFiber );
std::vector< double > finalDistance;
finalDistance.resize( singleTract->front().Size() );
for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
{
finalDistance[ index ] = foundPointFiber.GetElement( index ) - endPoint.GetElement( index );
}
// calculate length of direction vector
double finalLength( 0.0 );
double finalSum( 0.0 );
for( unsigned int index = 0; index < finalDistance.size() ; index++ )
{
finalSum = finalSum + finalDistance[ index ] * finalDistance[ index ];
}
finalLength = std::sqrt( finalSum );
if( finalLength > m_EndPointSearchRadius )
{
// the found point was not within the search space
return;
}
}
label = tempLabel;
mitkIndex = tempIndex;
return;
}
// hit next point without finding brain matter
currentRetractionIndex = currentRetractionIndex + retractionStepIndexSize;
if( ( currentRetractionIndex < 1 ) || ( (unsigned int)currentRetractionIndex > ( singleTract->Size() - 2 ) ) )
{
keepRetracting = false;
}
}
}
}
void mitk::ConnectomicsNetworkCreator::LinearExtensionUntilGreyMatter(
std::vector<int> & indexVectorOfPointsToUse,
TractType::Pointer singleTract,
int & label,
itk::Index<3> & mitkIndex )
{
if( indexVectorOfPointsToUse.size() > singleTract->Size() )
{
MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_MORE_POINTS_THAN_PRESENT;
return;
}
if( indexVectorOfPointsToUse.size() < 2 )
{
MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_LESS_THAN_2;
return;
}
for( unsigned int index( 0 ); index < indexVectorOfPointsToUse.size(); index++ )
{
if( indexVectorOfPointsToUse[ index ] < 0 )
{
MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_BEYOND_START;
return;
}
if( (unsigned int)indexVectorOfPointsToUse[ index ] > singleTract->Size() )
{
MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_BEYOND_END;
return;
}
}
mitk::Point3D startPoint, endPoint;
std::vector< double > differenceVector;
differenceVector.resize( singleTract->front().Size() );
{
// which points to use, currently only last two //TODO correct using all points
int endPointIndex = indexVectorOfPointsToUse.size() - 1;
int startPointIndex = indexVectorOfPointsToUse.size() - 2;
// convert to segmentation coords
mitk::Point3D startFiber, endFiber;
for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
{
endFiber.SetElement( index, singleTract->GetElement( indexVectorOfPointsToUse[ endPointIndex ] ).GetElement( index ) );
startFiber.SetElement( index, singleTract->GetElement( indexVectorOfPointsToUse[ startPointIndex ] ).GetElement( index ) );
}
FiberToSegmentationCoords( endFiber, endPoint );
FiberToSegmentationCoords( startFiber, startPoint );
// calculate straight line
for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
{
differenceVector[ index ] = endPoint.GetElement( index ) - startPoint.GetElement( index );
}
// normalizing direction vector
double length( 0.0 );
double sum( 0.0 );
for( unsigned int index = 0; index < differenceVector.size() ; index++ )
{
sum = sum + differenceVector[ index ] * differenceVector[ index ];
}
length = std::sqrt( sum );
for( unsigned int index = 0; index < differenceVector.size() ; index++ )
{
differenceVector[ index ] = differenceVector[ index ] / length;
}
// follow line until first non white matter label
itk::Index<3> tempIndex;
int tempLabel( label );
bool keepOn( true );
itk::ImageRegion<3> itkRegion = m_SegmentationItk->GetLargestPossibleRegion();
for( int parameter( 0 ) ; keepOn ; parameter++ )
{
if( parameter > 1000 )
{
MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_DID_NOT_FIND_WHITE;
break;
}
for( int index( 0 ); index < 3; index++ )
{
tempIndex.SetElement( index, endPoint.GetElement( index ) + parameter * differenceVector[ index ] );
}
if( itkRegion.IsInside( tempIndex ) )
{
tempLabel = m_SegmentationItk->GetPixel( tempIndex );
}
else
{
tempLabel = -1;
}
if( IsNonWhiteMatterLabel( tempLabel ) )
{
if( tempLabel < 1 )
{
keepOn = false;
//MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_NOT_EXTEND_TO_WHITE;
}
else
{
label = tempLabel;
mitkIndex = tempIndex;
keepOn = false;
}
}
}
}
}
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;
itk::Index<3> firstElementSegIndex, lastElementSegIndex;
if( singleTract->front().Size() != 3 )
{
MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
}
for( unsigned 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_SegmentationItk->GetPixel(firstElementSegIndex);
int lastLabel = m_SegmentationItk->GetPixel(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 );
itk::Index<3> 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 );
itk::Index<3> tempIndex = lastElementSegIndex;
LinearExtensionUntilGreyMatter( indexVectorOfPointsToUse, singleTract, tempLabel, tempIndex );
lastLabel = tempLabel;
lastElementSegIndex = tempIndex;
}
if ( retractFront )
{
// label and coordinate temp storage
int tempLabel( firstLabel );
itk::Index<3> tempIndex = firstElementSegIndex;
RetractionUntilBrainMatter( true, singleTract, tempLabel, tempIndex );
firstLabel = tempLabel;
firstElementSegIndex = tempIndex;
}
if ( retractEnd )
{
// label and coordinate temp storage
int tempLabel( lastLabel );
itk::Index<3> 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
CreateNewNode( firstLabel, firstElementSegIndex, m_UseCoMCoordinates );
CreateNewNode( lastLabel, lastElementSegIndex, m_UseCoMCoordinates );
}
return labelpair;
}
void mitk::ConnectomicsNetworkCreator::RetractionUntilBrainMatter( bool retractFront, TractType::Pointer singleTract,
int & label, mitk::Index3D & mitkIndex )
{
int retractionStartIndex( singleTract->Size() - 1 );
int retractionStepIndexSize( -1 );
int retractionTerminationIndex( 0 );
if( retractFront )
{
retractionStartIndex = 0;
retractionStepIndexSize = 1;
retractionTerminationIndex = singleTract->Size() - 1;
}
int currentRetractionIndex = retractionStartIndex;
bool keepRetracting( true );
mitk::Point3D currentPoint, nextPoint;
std::vector< double > differenceVector;
differenceVector.resize( singleTract->front().Size() );
while( keepRetracting && ( currentRetractionIndex != retractionTerminationIndex ) )
{
// convert to segmentation coords
mitk::Point3D currentPointFiberCoord, nextPointFiberCoord;
for( int index = 0; index < singleTract->front().Size(); index++ )
{
currentPointFiberCoord.SetElement( index, singleTract->GetElement( currentRetractionIndex ).GetElement( index ) );
nextPointFiberCoord.SetElement( index, singleTract->GetElement( currentRetractionIndex + retractionStepIndexSize ).GetElement( index ) );
}
FiberToSegmentationCoords( currentPointFiberCoord, currentPoint );
FiberToSegmentationCoords( nextPointFiberCoord, nextPoint );
// calculate straight line
for( int index = 0; index < singleTract->front().Size(); index++ )
{
differenceVector[ index ] = nextPoint.GetElement( index ) - currentPoint.GetElement( index );
}
// calculate length of direction vector
double length( 0.0 );
double sum( 0.0 );
for( int index = 0; index < differenceVector.size() ; index++ )
{
sum = sum + differenceVector[ index ] * differenceVector[ index ];
}
length = std::sqrt( sum );
// retract
mitk::Index3D tempIndex;
int tempLabel( label );
for( int parameter( 0 ) ; parameter < length ; parameter++ )
{
for( int index( 0 ); index < 3; index++ )
{
tempIndex.SetElement( index,
currentPoint.GetElement( index ) + ( 1.0 + parameter ) / ( 1.0 + length ) * differenceVector[ index ] );
}
tempLabel = m_Segmentation->GetPixelValueByIndex( tempIndex );
if( !IsBackgroundLabel( tempLabel ) )
{
label = tempLabel;
mitkIndex = tempIndex;
return;
}
// hit next point without finding brain matter
currentRetractionIndex = currentRetractionIndex + retractionStepIndexSize;
if( ( currentRetractionIndex < 1 ) || ( currentRetractionIndex > ( singleTract->Size() - 2 ) ) )
{
keepRetracting = false;
}
}
}
}
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;
}