mitk::ContourModel::Pointer mitk::ContourUtils::BackProjectContourFrom2DSlice(const Geometry3D* sliceGeometry, ContourModel* contourIn2D, bool itkNotUsed( correctionForIpSegmentation ) )
{
if ( !sliceGeometry || !contourIn2D ) return NULL;
ContourModel::Pointer worldContour = ContourModel::New();
worldContour->Initialize(*contourIn2D);
int numberOfTimesteps = contourIn2D->GetTimeGeometry()->CountTimeSteps();
for(int currentTimestep = 0; currentTimestep < numberOfTimesteps; currentTimestep++)
{
ContourModel::VertexIterator iter = contourIn2D->Begin(currentTimestep);
ContourModel::VertexIterator end = contourIn2D->End(currentTimestep);
while( iter != end)
{
Point3D currentPointIn2D = (*iter)->Coordinates;
Point3D worldPointIn3D;
worldPointIn3D.Fill(0.0);
sliceGeometry->IndexToWorld( currentPointIn2D, worldPointIn3D );
//MITK_INFO << "index " << currentPointIn2D << " world " << worldPointIn3D << std::endl;
worldContour->AddVertex( worldPointIn3D, currentTimestep );
iter++;
}
}
return worldContour;
}
mitk::ContourModel::Pointer mitk::ContourUtils::ProjectContourTo2DSlice(Image* slice, ContourModel* contourIn3D, bool itkNotUsed( correctionForIpSegmentation ), bool constrainToInside)
{
if ( !slice || !contourIn3D ) return NULL;
ContourModel::Pointer projectedContour = ContourModel::New();
projectedContour->Initialize(*contourIn3D);
const Geometry3D* sliceGeometry = slice->GetGeometry();
int numberOfTimesteps = contourIn3D->GetTimeGeometry()->CountTimeSteps();
for(int currentTimestep = 0; currentTimestep < numberOfTimesteps; currentTimestep++)
{
ContourModel::VertexIterator iter = contourIn3D->Begin(currentTimestep);
ContourModel::VertexIterator end = contourIn3D->End(currentTimestep);
while( iter != end)
{
Point3D currentPointIn3D = (*iter)->Coordinates;
Point3D projectedPointIn2D;
projectedPointIn2D.Fill(0.0);
sliceGeometry->WorldToIndex( currentPointIn3D, projectedPointIn2D );
// MITK_INFO << "world point " << currentPointIn3D << " in index is " << projectedPointIn2D;
if ( !sliceGeometry->IsIndexInside( projectedPointIn2D ) && constrainToInside )
{
MITK_INFO << "**" << currentPointIn3D << " is " << projectedPointIn2D << " --> correct it (TODO)" << std::endl;
}
projectedContour->AddVertex( projectedPointIn2D, currentTimestep );
iter++;
}
}
return projectedContour;
}
/**
Uses ipSegmentation algorithms to do the actual region growing. The result (binary image) is first smoothed by a 5x5 circle mask, then
its contour is extracted and converted to MITK coordinates.
*/
mitkIpPicDescriptor* mitk::RegionGrowingTool::PerformRegionGrowingAndUpdateContour(int timestep)
{
// 1. m_OriginalPicSlice and m_SeedPointMemoryOffset are set to sensitive values, as well as m_LowerThreshold and m_UpperThreshold
assert (m_OriginalPicSlice);
if (m_OriginalPicSlice->n[0] != 256 || m_OriginalPicSlice->n[1] != 256) // ???
assert( (m_SeedPointMemoryOffset < static_cast<int>( m_OriginalPicSlice->n[0] * m_OriginalPicSlice->n[1] )) && (m_SeedPointMemoryOffset >= 0) ); // inside the image
// 2. ipSegmentation is used to perform region growing
float ignored;
int oneContourOffset( 0 );
mitkIpPicDescriptor* regionGrowerResult = ipMITKSegmentationGrowRegion4N( m_OriginalPicSlice,
m_SeedPointMemoryOffset, // seed point
true, // grayvalue interval relative to seed point gray value?
m_LowerThreshold,
m_UpperThreshold,
0, // continue until done (maxIterations == 0)
NULL, // allocate new memory (only this time, on mouse move we'll reuse the old buffer)
oneContourOffset, // a pixel that is near the resulting contour
ignored // ignored by us
);
if (!regionGrowerResult || oneContourOffset == -1)
{
ContourModel::Pointer dummyContour = ContourModel::New();
dummyContour->Initialize();
FeedbackContourTool::SetFeedbackContour( *dummyContour );
if (regionGrowerResult) ipMITKSegmentationFree(regionGrowerResult);
return NULL;
}
// 3. We smooth the result a little to reduce contour complexity
bool smoothResult( true ); // currently fixed, perhaps remove else block
mitkIpPicDescriptor* smoothedRegionGrowerResult;
if (smoothResult)
{
// Smooth the result (otherwise very detailed contour)
smoothedRegionGrowerResult = SmoothIPPicBinaryImage( regionGrowerResult, oneContourOffset );
ipMITKSegmentationFree( regionGrowerResult );
}
else
{
smoothedRegionGrowerResult = regionGrowerResult;
}
// 4. convert the result of region growing into a mitk::Contour
// At this point oneContourOffset could be useless, if smoothing destroyed a thin bridge. In these
// cases, we have two or more unconnected segmentation regions, and we don't know, which one is touched by oneContourOffset.
// In the bad case, the contour is not the one around our seedpoint, so the result looks very strange to the user.
// -> we remove the point where the contour started so far. Then we look from the bottom of the image for the first segmentation pixel
// and start another contour extraction from there. This is done, until the seedpoint is inside the contour
int numberOfContourPoints( 0 );
int newBufferSize( 0 );
float* contourPoints = ipMITKSegmentationGetContour8N( smoothedRegionGrowerResult, oneContourOffset, numberOfContourPoints, newBufferSize ); // memory allocated with malloc
if (contourPoints)
{
while ( !ipMITKSegmentationIsInsideContour( contourPoints, // contour
numberOfContourPoints, // points in contour
m_SeedPointMemoryOffset % smoothedRegionGrowerResult->n[0], // test point x
m_SeedPointMemoryOffset / smoothedRegionGrowerResult->n[0] // test point y
) )
{
// we decide that this cannot be part of the segmentation because the seedpoint is not contained in the contour (fill the 4-neighborhood with 0)
ipMITKSegmentationReplaceRegion4N( smoothedRegionGrowerResult, oneContourOffset, 0 );
// move the contour offset to the last row (x position of the seed point)
int rowLength = smoothedRegionGrowerResult->n[0]; // number of pixels in a row
oneContourOffset = m_SeedPointMemoryOffset % smoothedRegionGrowerResult->n[0] // x of seed point
+ rowLength*(smoothedRegionGrowerResult->n[1]-1); // y of last row
while ( oneContourOffset >=0
&& (*(static_cast<ipMITKSegmentationTYPE*>(smoothedRegionGrowerResult->data) + oneContourOffset) == 0) )
{
oneContourOffset -= rowLength; // if pixel at data+oneContourOffset is 0, then move up one row
}
if ( oneContourOffset < 0 )
{
break; // just use the last contour we found
}
free(contourPoints); // release contour memory
contourPoints = ipMITKSegmentationGetContour8N( smoothedRegionGrowerResult, oneContourOffset, numberOfContourPoints, newBufferSize ); // memory allocated with malloc
}
// copy point from float* to mitk::Contour
ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New();
contourInImageIndexCoordinates->Expand(timestep + 1);
contourInImageIndexCoordinates->SetClosed(true, timestep);
Point3D newPoint;
for (int index = 0; index < numberOfContourPoints; ++index)
{
newPoint[0] = contourPoints[ 2 * index + 0 ] - 0.5;//correction is needed because the output of the algorithm is center based
newPoint[1] = contourPoints[ 2 * index + 1 ] - 0.5;//and we want our contour displayed corner based.
newPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex( newPoint, timestep );
}
free(contourPoints);
ContourModel::Pointer contourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( m_ReferenceSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true: sub 0.5 for ipSegmentation correctio
FeedbackContourTool::SetFeedbackContour( *contourInWorldCoordinates );
}
// 5. Result HAS TO BE freed by caller, contains the binary region growing result
return smoothedRegionGrowerResult;
}
/**
Insert the point to the feedback contour,finish to build the contour and at the same time the painting function
*/
bool mitk::PaintbrushTool::MouseMoved(mitk::InteractionEvent* interactionEvent, bool leftMouseButtonPressed)
{
if ( SegTool2D::CanHandleEvent(interactionEvent) < 1.0 )
return false;
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
//const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
CheckIfCurrentSliceHasChanged( positionEvent );
if ( m_LastContourSize != m_Size )
{
UpdateContour( positionEvent );
m_LastContourSize = m_Size;
}
// stateEvent->GetId() == 530
// || stateEvent->GetId() == 534
// || stateEvent->GetId() == 1
// || stateEvent->GetId() == 5
// );
Point3D worldCoordinates = positionEvent->GetPositionInWorld();
Point3D indexCoordinates;
m_WorkingSlice->GetGeometry()->WorldToIndex( worldCoordinates, indexCoordinates );
MITK_DEBUG << "Mouse at W " << worldCoordinates << std::endl;
MITK_DEBUG << "Mouse at I " << indexCoordinates << std::endl;
// round to nearest voxel center (abort if this hasn't changed)
if ( m_Size % 2 == 0 ) // even
{
indexCoordinates[0] = ROUND( indexCoordinates[0]);// /*+ 0.5*/) + 0.5;
indexCoordinates[1] = ROUND( indexCoordinates[1]);// /*+ 0.5*/ ) + 0.5;
}
else // odd
{
indexCoordinates[0] = ROUND( indexCoordinates[0] ) ;
indexCoordinates[1] = ROUND( indexCoordinates[1] ) ;
}
static Point3D lastPos; // uninitialized: if somebody finds out how this can be initialized in a one-liner, tell me
if ( fabs(indexCoordinates[0] - lastPos[0]) > mitk::eps ||
fabs(indexCoordinates[1] - lastPos[1]) > mitk::eps ||
fabs(indexCoordinates[2] - lastPos[2]) > mitk::eps ||
leftMouseButtonPressed
)
{
lastPos = indexCoordinates;
}
else
{
MITK_DEBUG << "." << std::flush;
return false;
}
MITK_DEBUG << "Mouse at C " << indexCoordinates;
int timestep = positionEvent->GetSender()->GetTimeStep();
ContourModel::Pointer contour = ContourModel::New();
contour->Expand(timestep + 1);
contour->SetClosed(true, timestep);
ContourModel::VertexIterator it = m_MasterContour->Begin();
ContourModel::VertexIterator end = m_MasterContour->End();
while(it != end)
{
Point3D point = (*it)->Coordinates;
point[0] += indexCoordinates[ 0 ];
point[1] += indexCoordinates[ 1 ];
contour->AddVertex( point, timestep );
it++;
}
if (leftMouseButtonPressed)
{
FeedbackContourTool::FillContourInSlice( contour, timestep, m_WorkingSlice, m_PaintingPixelValue );
m_WorkingNode->SetData(m_WorkingSlice);
m_WorkingNode->Modified();
}
// visualize contour
ContourModel::Pointer displayContour = ContourModel::New();
displayContour->Initialize();
//for (unsigned int index = 0; index < contour->GetNumberOfPoints(); ++index)
//{
// Point3D point = contour->GetPoints()->ElementAt(index);
// if ( m_Size % 2 == 0 ) // even
// {
// point[0] += 0.5;
// point[1] += 0.5;
// }
// displayContour->AddVertex( point );
//}
displayContour = FeedbackContourTool::BackProjectContourFrom2DSlice( m_WorkingSlice->GetGeometry(), /*displayContour*/contour );
SetFeedbackContour( *displayContour );
assert( positionEvent->GetSender()->GetRenderWindow() );
RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
return true;
}