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, 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::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;
}
}
}
}
