diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp index d2b15a1fb7..b989877725 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp @@ -1,362 +1,362 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkTrackingHandlerTensor.h" namespace mitk { TrackingHandlerTensor::TrackingHandlerTensor() : m_InterpolateTensors(true) , m_FaThreshold(0.1) { } TrackingHandlerTensor::~TrackingHandlerTensor() { } void TrackingHandlerTensor::InitForTracking() { MITK_INFO << "Initializing tensor tracker."; if (m_NeedsDataInit) { m_NumberOfInputs = m_TensorImages.size(); for (int i=0; iSetSpacing( m_TensorImages.at(0)->GetSpacing() ); pdImage->SetOrigin( m_TensorImages.at(0)->GetOrigin() ); pdImage->SetDirection( m_TensorImages.at(0)->GetDirection() ); pdImage->SetRegions( m_TensorImages.at(0)->GetLargestPossibleRegion() ); pdImage->Allocate(); m_PdImage.push_back(pdImage); ItkDoubleImgType::Pointer emaxImage = ItkDoubleImgType::New(); emaxImage->SetSpacing( m_TensorImages.at(0)->GetSpacing() ); emaxImage->SetOrigin( m_TensorImages.at(0)->GetOrigin() ); emaxImage->SetDirection( m_TensorImages.at(0)->GetDirection() ); emaxImage->SetRegions( m_TensorImages.at(0)->GetLargestPossibleRegion() ); emaxImage->Allocate(); emaxImage->FillBuffer(1.0); m_EmaxImage.push_back(emaxImage); } bool useUserFaImage = true; if (m_FaImage.IsNull()) { m_FaImage = ItkFloatImgType::New(); m_FaImage->SetSpacing( m_TensorImages.at(0)->GetSpacing() ); m_FaImage->SetOrigin( m_TensorImages.at(0)->GetOrigin() ); m_FaImage->SetDirection( m_TensorImages.at(0)->GetDirection() ); m_FaImage->SetRegions( m_TensorImages.at(0)->GetLargestPossibleRegion() ); m_FaImage->Allocate(); m_FaImage->FillBuffer(0.0); useUserFaImage = false; } typedef itk::DiffusionTensor3D TensorType; TensorType::EigenValuesArrayType eigenvalues; TensorType::EigenVectorsMatrixType eigenvectors; #ifdef WIN32 #pragma omp parallel for #else #pragma omp parallel for collapse(3) #endif - for (unsigned int x=0; xGetLargestPossibleRegion().GetSize()[0]; x++) - for (unsigned int y=0; yGetLargestPossibleRegion().GetSize()[1]; y++) - for (unsigned int z=0; zGetLargestPossibleRegion().GetSize()[2]; z++) + for (int x=0; xGetLargestPossibleRegion().GetSize()[0]; x++) + for (int y=0; yGetLargestPossibleRegion().GetSize()[1]; y++) + for (int z=0; zGetLargestPossibleRegion().GetSize()[2]; z++) { ItkTensorImageType::IndexType index; index[0] = x; index[1] = y; index[2] = z; for (int i=0; iGetPixel(index); vnl_vector_fixed dir; tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); if (dir.magnitude()>mitk::eps) dir.normalize(); else dir.fill(0.0); #pragma omp critical { m_PdImage.at(i)->SetPixel(index, dir); if (!useUserFaImage) m_FaImage->SetPixel(index, m_FaImage->GetPixel(index)+tensor.GetFractionalAnisotropy()); m_EmaxImage.at(i)->SetPixel(index, 2/eigenvalues[2]); } } if (!useUserFaImage) { #pragma omp critical m_FaImage->SetPixel(index, m_FaImage->GetPixel(index)/m_NumberOfInputs); } } m_NeedsDataInit = false; } if (m_F+m_G>1.0) { float temp = m_F+m_G; m_F /= temp; m_G /= temp; } } vnl_vector_fixed TrackingHandlerTensor::GetMatchingDirection(itk::Index<3> idx, vnl_vector_fixed& oldDir, int& image_num) { vnl_vector_fixed out_dir; out_dir.fill(0); float angle = 0; float mag = oldDir.magnitude(); if (magGetPixel(idx); if (out_dir.magnitude()>0.5) { image_num = i; oldDir[0] = out_dir[0]; oldDir[1] = out_dir[1]; oldDir[2] = out_dir[2]; break; } } } else { for (unsigned int i=0; i dir = m_PdImage.at(i)->GetPixel(idx); float a = dot_product(dir, oldDir); if (fabs(a)>angle) { image_num = i; angle = fabs(a); if (a<0) out_dir = -dir; else out_dir = dir; out_dir *= angle; // shrink contribution of direction if is less parallel to previous direction } } } return out_dir; } vnl_vector_fixed TrackingHandlerTensor::GetDirection(itk::Point itkP, vnl_vector_fixed oldDir, TensorType& tensor) { // transform physical point to index coordinates itk::Index<3> idx; itk::ContinuousIndex< float, 3> cIdx; m_FaImage->TransformPhysicalPointToIndex(itkP, idx); m_FaImage->TransformPhysicalPointToContinuousIndex(itkP, cIdx); vnl_vector_fixed dir; dir.fill(0.0); if ( !m_FaImage->GetLargestPossibleRegion().IsInside(idx) ) return dir; int image_num = -1; if (!m_Interpolate) { dir = GetMatchingDirection(idx, oldDir, image_num); if (image_num>=0) tensor = m_TensorImages[image_num]->GetPixel(idx) * m_EmaxImage[image_num]->GetPixel(idx); } else { float frac_x = cIdx[0] - idx[0]; float frac_y = cIdx[1] - idx[1]; float frac_z = cIdx[2] - idx[2]; if (frac_x<0) { idx[0] -= 1; frac_x += 1; } if (frac_y<0) { idx[1] -= 1; frac_y += 1; } if (frac_z<0) { idx[2] -= 1; frac_z += 1; } frac_x = 1-frac_x; frac_y = 1-frac_y; frac_z = 1-frac_z; // int coordinates inside image? if (idx[0] >= 0 && idx[0] < static_cast(m_FaImage->GetLargestPossibleRegion().GetSize(0) - 1) && idx[1] >= 0 && idx[1] < static_cast(m_FaImage->GetLargestPossibleRegion().GetSize(1) - 1) && idx[2] >= 0 && idx[2] < static_cast(m_FaImage->GetLargestPossibleRegion().GetSize(2) - 1)) { // trilinear interpolation vnl_vector_fixed interpWeights; interpWeights[0] = ( frac_x)*( frac_y)*( frac_z); interpWeights[1] = (1-frac_x)*( frac_y)*( frac_z); interpWeights[2] = ( frac_x)*(1-frac_y)*( frac_z); interpWeights[3] = ( frac_x)*( frac_y)*(1-frac_z); interpWeights[4] = (1-frac_x)*(1-frac_y)*( frac_z); interpWeights[5] = ( frac_x)*(1-frac_y)*(1-frac_z); interpWeights[6] = (1-frac_x)*( frac_y)*(1-frac_z); interpWeights[7] = (1-frac_x)*(1-frac_y)*(1-frac_z); dir = GetMatchingDirection(idx, oldDir, image_num) * interpWeights[0]; if (image_num>=0) tensor += m_TensorImages[image_num]->GetPixel(idx) * m_EmaxImage[image_num]->GetPixel(idx) * interpWeights[0]; itk::Index<3> tmpIdx = idx; tmpIdx[0]++; dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[1]; if (image_num>=0) tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[1]; tmpIdx = idx; tmpIdx[1]++; dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[2]; if (image_num>=0) tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[2]; tmpIdx = idx; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[3]; if (image_num>=0) tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[3]; tmpIdx = idx; tmpIdx[0]++; tmpIdx[1]++; dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[4]; if (image_num>=0) tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[4]; tmpIdx = idx; tmpIdx[1]++; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[5]; if (image_num>=0) tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[5]; tmpIdx = idx; tmpIdx[2]++; tmpIdx[0]++; dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[6]; if (image_num>=0) tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[6]; tmpIdx = idx; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[7]; if (image_num>=0) tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[7]; } } return dir; } vnl_vector_fixed TrackingHandlerTensor::GetLargestEigenvector(TensorType& tensor) { vnl_vector_fixed dir; TensorType::EigenValuesArrayType eigenvalues; TensorType::EigenVectorsMatrixType eigenvectors; tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); if (dir.magnitude() TrackingHandlerTensor::ProposeDirection(const itk::Point& pos, std::deque >& olddirs, itk::Index<3>& oldIndex) { vnl_vector_fixed output_direction; output_direction.fill(0); TensorType tensor; tensor.Fill(0); try { itk::Index<3> index; m_TensorImages.at(0)->TransformPhysicalPointToIndex(pos, index); float fa = GetImageValue(pos, m_FaImage, m_Interpolate); if (fa oldDir = olddirs.back(); if (m_FlipX) oldDir[0] *= -1; if (m_FlipY) oldDir[1] *= -1; if (m_FlipZ) oldDir[2] *= -1; float old_mag = oldDir.magnitude(); if (!m_Interpolate && oldIndex==index) return oldDir; output_direction = GetDirection(pos, oldDir, tensor); float mag = output_direction.magnitude(); if (mag>=mitk::eps) { output_direction.normalize(); if (old_mag>0.5 && m_G>mitk::eps) // TEND tracking { output_direction[0] = m_F*output_direction[0] + (1-m_F)*( (1-m_G)*oldDir[0] + m_G*(tensor[0]*oldDir[0] + tensor[1]*oldDir[1] + tensor[2]*oldDir[2])); output_direction[1] = m_F*output_direction[1] + (1-m_F)*( (1-m_G)*oldDir[1] + m_G*(tensor[1]*oldDir[0] + tensor[3]*oldDir[1] + tensor[4]*oldDir[2])); output_direction[2] = m_F*output_direction[2] + (1-m_F)*( (1-m_G)*oldDir[2] + m_G*(tensor[2]*oldDir[0] + tensor[4]*oldDir[1] + tensor[5]*oldDir[2])); output_direction.normalize(); } float a = 1; if (old_mag>0.5) a = dot_product(output_direction, oldDir); if (a>=m_AngularThreshold) output_direction *= mag; else output_direction.fill(0); } else output_direction.fill(0); } catch(...) { } if (m_FlipX) output_direction[0] *= -1; if (m_FlipY) output_direction[1] *= -1; if (m_FlipZ) output_direction[2] *= -1; return output_direction; } }