diff --git a/CMakeExternals/MITKData.cmake b/CMakeExternals/MITKData.cmake index 33c68acf2a..779f547901 100644 --- a/CMakeExternals/MITKData.cmake +++ b/CMakeExternals/MITKData.cmake @@ -1,35 +1,35 @@ #----------------------------------------------------------------------------- # MITK Data #----------------------------------------------------------------------------- # Sanity checks if(DEFINED MITK_DATA_DIR AND NOT EXISTS ${MITK_DATA_DIR}) message(FATAL_ERROR "MITK_DATA_DIR variable is defined but corresponds to non-existing directory") endif() set(proj MITK-Data) set(proj_DEPENDENCIES) set(MITK-Data_DEPENDS ${proj}) if(BUILD_TESTING) - set(revision_tag 3591d110) + set(revision_tag f3670126) # ^^^^^^^^ these are just to check correct length of hash part ExternalProject_Add(${proj} URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/MITK-Data_${revision_tag}.tar.gz UPDATE_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS ${proj_DEPENDENCIES} ) set(MITK_DATA_DIR ${ep_source_dir}/${proj}) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif(BUILD_TESTING) diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.cpp index 930a69efee..c4c8fb3764 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.cpp @@ -1,172 +1,172 @@ /*=================================================================== 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 "mitkEnergyComputer.h" #include #include using namespace mitk; EnergyComputer::EnergyComputer(ItkFloatImageType* mask, ParticleGrid* particleGrid, SphereInterpolator* interpolator, ItkRandGenType* randGen) : m_UseTrilinearInterpolation(true) { m_ParticleGrid = particleGrid; m_RandGen = randGen; //m_Image = qballImage; m_SphereInterpolator = interpolator; m_Mask = mask; m_ParticleLength = m_ParticleGrid->m_ParticleLength; m_SquaredParticleLength = m_ParticleLength*m_ParticleLength; m_Size[0] = mask->GetLargestPossibleRegion().GetSize()[0]; m_Size[1] = mask->GetLargestPossibleRegion().GetSize()[1]; m_Size[2] = mask->GetLargestPossibleRegion().GetSize()[2]; if (m_Size[0]<3 || m_Size[1]<3 || m_Size[2]<3) m_UseTrilinearInterpolation = false; m_Spacing[0] = mask->GetSpacing()[0]; m_Spacing[1] = mask->GetSpacing()[1]; m_Spacing[2] = mask->GetSpacing()[2]; - // calculate rotation matrix + // get rotation matrix vnl_matrix temp = mask->GetDirection().GetVnlMatrix(); vnl_matrix directionMatrix; directionMatrix.set_size(3,3); vnl_copy(temp, directionMatrix); - vnl_vector_fixed d0 = directionMatrix.get_column(0); d0.normalize(); - vnl_vector_fixed d1 = directionMatrix.get_column(1); d1.normalize(); - vnl_vector_fixed d2 = directionMatrix.get_column(2); d2.normalize(); - directionMatrix.set_column(0, d0); - directionMatrix.set_column(1, d1); - directionMatrix.set_column(2, d2); vnl_matrix_fixed I = directionMatrix*directionMatrix.transpose(); - if(!I.is_identity(mitk::eps)) + for (int i = 0; i < 3; i++) + for (int j = 0; j < 3; j++) + I[i][j] = fabs(I[i][j]); + if(!I.is_identity(0.001)) + { fprintf(stderr,"EnergyComputer: image direction is not a rotation matrix. Tracking not possible!\n"); + std::cout << directionMatrix << std::endl; + } m_RotationMatrix = directionMatrix; if (QBALL_ODFSIZE != m_SphereInterpolator->nverts) fprintf(stderr,"EnergyComputer: error during init: data does not match with interpolation scheme\n"); int totsz = m_Size[0]*m_Size[1]*m_Size[2]; m_CumulatedSpatialProbability.resize(totsz + 1, 0.0); m_ActiveIndices.resize(totsz, 0); // calculate active voxels and cumulate probabilities m_NumActiveVoxels = 0; m_CumulatedSpatialProbability[0] = 0; for (int x = 0; x < m_Size[0];x++) for (int y = 0; y < m_Size[1];y++) for (int z = 0; z < m_Size[2];z++) { int idx = x+(y+z*m_Size[1])*m_Size[0]; ItkFloatImageType::IndexType index; index[0] = x; index[1] = y; index[2] = z; if (m_Mask->GetPixel(index) > 0.5) { m_CumulatedSpatialProbability[m_NumActiveVoxels+1] = m_CumulatedSpatialProbability[m_NumActiveVoxels] + m_Mask->GetPixel(index); m_ActiveIndices[m_NumActiveVoxels] = idx; m_NumActiveVoxels++; } } for (int k = 0; k < m_NumActiveVoxels; k++) m_CumulatedSpatialProbability[k] /= m_CumulatedSpatialProbability[m_NumActiveVoxels]; std::cout << "EnergyComputer: " << m_NumActiveVoxels << " active voxels found" << std::endl; } void EnergyComputer::SetParameters(float particleWeight, float particleWidth, float connectionPotential, float curvThres, float inexBalance, float particlePotential) { m_ParticleChemicalPotential = particlePotential; m_ConnectionPotential = connectionPotential; m_ParticleWeight = particleWeight; float bal = 1/(1+exp(-inexBalance)); m_ExtStrength = 2*bal; m_IntStrength = 2*(1-bal)/m_SquaredParticleLength; m_CurvatureThreshold = curvThres; float sigma_s = particleWidth; gamma_s = 1/(sigma_s*sigma_s); gamma_reg_s =1/(m_SquaredParticleLength/4); } // draw random position from active voxels void EnergyComputer::DrawRandomPosition(vnl_vector_fixed& R) { float r = m_RandGen->GetVariate();//m_RandGen->frand(); int j; int rl = 1; int rh = m_NumActiveVoxels; while(rh != rl) { j = rl + (rh-rl)/2; if (r < m_CumulatedSpatialProbability[j]) { rh = j; continue; } if (r > m_CumulatedSpatialProbability[j]) { rl = j+1; continue; } break; } R[0] = m_Spacing[0]*((float)(m_ActiveIndices[rh-1] % m_Size[0]) + m_RandGen->GetVariate()); R[1] = m_Spacing[1]*((float)((m_ActiveIndices[rh-1]/m_Size[0]) % m_Size[1]) + m_RandGen->GetVariate()); R[2] = m_Spacing[2]*((float)(m_ActiveIndices[rh-1]/(m_Size[0]*m_Size[1])) + m_RandGen->GetVariate()); } // return spatial probability of position float EnergyComputer::SpatProb(vnl_vector_fixed pos) { ItkFloatImageType::IndexType index; index[0] = floor(pos[0]/m_Spacing[0]); index[1] = floor(pos[1]/m_Spacing[1]); index[2] = floor(pos[2]/m_Spacing[2]); if (m_Mask->GetLargestPossibleRegion().IsInside(index)) // is inside image? return m_Mask->GetPixel(index); else return 0; } float EnergyComputer::mbesseli0(float x) { // BESSEL_APPROXCOEFF[0] = -0.1714; // BESSEL_APPROXCOEFF[1] = 0.5332; // BESSEL_APPROXCOEFF[2] = -1.4889; // BESSEL_APPROXCOEFF[3] = 2.0389; float y = x*x; float erg = -0.1714; erg += y*0.5332; erg += y*y*-1.4889; erg += y*y*y*2.0389; return erg; } float EnergyComputer::mexp(float x) { return((x>=7.0) ? 0 : ((x>=5.0) ? (-0.0029*x+0.0213) : ((x>=3.0) ? (-0.0215*x+0.1144) : ((x>=2.0) ? (-0.0855*x+0.3064) : ((x>=1.0) ? (-0.2325*x+0.6004) : ((x>=0.5) ? (-0.4773*x+0.8452) : ((x>=0.0) ? (-0.7869*x+1.0000) : 1 ))))))); // return exp(-x); } int EnergyComputer::GetNumActiveVoxels() { return m_NumActiveVoxels; } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.h index 75322cb443..5b6032a038 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.h @@ -1,89 +1,88 @@ /*=================================================================== 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. ===================================================================*/ #ifndef _ENCOMP #define _ENCOMP #include #include #include #include #include using namespace mitk; /** * \brief Calculates internal and external energy of the new particle configuration proposal. */ class FiberTracking_EXPORT EnergyComputer { public: //typedef itk::Vector OdfVectorType; //typedef itk::Image ItkQBallImgType; typedef itk::Image ItkFloatImageType; typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType; EnergyComputer(ItkFloatImageType* mask, ParticleGrid* particleGrid, SphereInterpolator* interpolator, ItkRandGenType* randGen); void SetParameters(float particleWeight, float particleWidth, float connectionPotential, float curvThres, float inexBalance, float particlePotential); // get random position inside mask void DrawRandomPosition(vnl_vector_fixed& R); // external energy calculation virtual float ComputeExternalEnergy(vnl_vector_fixed& R, vnl_vector_fixed& N, Particle* dp) =0; // internal energy calculation virtual float ComputeInternalEnergyConnection(Particle *p1,int ep1) = 0; virtual float ComputeInternalEnergyConnection(Particle *p1,int ep1, Particle *p2, int ep2) = 0; virtual float ComputeInternalEnergy(Particle *dp) = 0; int GetNumActiveVoxels(); protected: vnl_matrix_fixed m_RotationMatrix; SphereInterpolator* m_SphereInterpolator; ParticleGrid* m_ParticleGrid; ItkRandGenType* m_RandGen; -// ItkQBallImgType* m_Image; ItkFloatImageType* m_Mask; vnl_vector_fixed m_Size; vnl_vector_fixed m_Spacing; std::vector< float > m_CumulatedSpatialProbability; std::vector< int > m_ActiveIndices; // indices inside mask bool m_UseTrilinearInterpolation; // is deactivated if less than 3 image slices are available int m_NumActiveVoxels; // voxels inside mask float m_ConnectionPotential; // larger value results in larger energy value -> higher proposal acceptance probability float m_ParticleChemicalPotential; // larger value results in larger energy value -> higher proposal acceptance probability float gamma_s; float gamma_reg_s; float m_ParticleWeight; // defines how much one particle contributes to the artificial signal float m_ExtStrength; // weighting factor for external energy float m_IntStrength; // weighting factor for internal energy float m_ParticleLength; // particle length float m_SquaredParticleLength; // squared particle length float m_CurvatureThreshold; // maximum angle accepted between two connected particles float SpatProb(vnl_vector_fixed pos); float EvaluateOdf(vnl_vector_fixed &pos, vnl_vector_fixed dir); float mbesseli0(float x); float mexp(float x); }; #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp index 40b2058dfe..173bd79d41 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp @@ -1,478 +1,499 @@ /*=================================================================== 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 "mitkMetropolisHastingsSampler.h" using namespace mitk; MetropolisHastingsSampler::MetropolisHastingsSampler(ParticleGrid* grid, EnergyComputer* enComp, ItkRandGenType* randGen, float curvThres) : m_ExTemp(0.01) , m_BirthProb(0.25) , m_DeathProb(0.05) , m_ShiftProb(0.15) , m_OptShiftProb(0.1) , m_ConnectionProb(0.45) , m_TractProb(0.5) , m_DelProb(0.1) , m_ChempotParticle(0.0) , m_AcceptedProposals(0) { m_RandGen = randGen; m_ParticleGrid = grid; m_EnergyComputer = enComp; m_ParticleLength = m_ParticleGrid->m_ParticleLength; m_DistanceThreshold = m_ParticleLength*m_ParticleLength; m_Sigma = m_ParticleLength/8.0; m_Gamma = 1/(m_Sigma*m_Sigma*2); m_Z = pow(2*M_PI*m_Sigma,3.0/2.0)*(M_PI*m_Sigma/m_ParticleLength); m_CurvatureThreshold = curvThres; m_StopProb = exp(-1/m_TractProb); } void MetropolisHastingsSampler::SetProbabilities(float birth, float death, float shift, float optShift, float connect) { m_BirthProb = birth; m_DeathProb = death; m_ShiftProb = shift; m_OptShiftProb = optShift; m_ConnectionProb = connect; float sum = m_BirthProb+m_DeathProb+m_ShiftProb+m_OptShiftProb+m_ConnectionProb; if (sum!=1 && sum>mitk::eps) { m_BirthProb /= sum; m_DeathProb /= sum; m_ShiftProb /= sum; m_OptShiftProb /= sum; m_ConnectionProb /= sum; } - std::cout << "Update proposal probabilities:" << std::endl; + std::cout << "Update proposal probabilities" << std::endl; std::cout << "Birth: " << m_BirthProb << std::endl; std::cout << "Death: " << m_DeathProb << std::endl; std::cout << "Shift: " << m_ShiftProb << std::endl; std::cout << "Optimal shift: " << m_OptShiftProb << std::endl; std::cout << "Connection: " << m_ConnectionProb << std::endl; } +// print proposal times +void MetropolisHastingsSampler::PrintProposalTimes() +{ + double sum = m_BirthTime.GetTotal()+m_DeathTime.GetTotal()+m_ShiftTime.GetTotal()+m_OptShiftTime.GetTotal()+m_ConnectionTime.GetTotal(); + std::cout << "Proposal time probes (toal%/mean)" << std::endl; + std::cout << "Birth: " << 100*m_BirthTime.GetTotal()/sum << "/" << m_BirthTime.GetMean()*1000 << std::endl; + std::cout << "Death: " << 100*m_DeathTime.GetTotal()/sum << "/" << m_DeathTime.GetMean()*1000 << std::endl; + std::cout << "Shift: " << 100*m_ShiftTime.GetTotal()/sum << "/" << m_ShiftTime.GetMean()*1000 << std::endl; + std::cout << "Optimal shift: " << 100*m_OptShiftTime.GetTotal()/sum << " - " << m_OptShiftTime.GetMean()*1000 << std::endl; + std::cout << "Connection: " << 100*m_ConnectionTime.GetTotal()/sum << "/" << m_ConnectionTime.GetMean()*1000 << std::endl; +} + // update temperature of simulated annealing process void MetropolisHastingsSampler::SetTemperature(float val) { m_InTemp = val; m_Density = exp(-m_ChempotParticle/m_InTemp); } // add small random number drawn from gaussian to each vector element void MetropolisHastingsSampler::DistortVector(float sigma, vnl_vector_fixed& vec) { vec[0] += m_RandGen->GetNormalVariate(0.0, sigma); vec[1] += m_RandGen->GetNormalVariate(0.0, sigma); vec[2] += m_RandGen->GetNormalVariate(0.0, sigma); } // generate normalized random vector vnl_vector_fixed MetropolisHastingsSampler::GetRandomDirection() { vnl_vector_fixed vec; vec[0] = m_RandGen->GetNormalVariate(); vec[1] = m_RandGen->GetNormalVariate(); vec[2] = m_RandGen->GetNormalVariate(); vec.normalize(); return vec; } // generate actual proposal (birth, death, shift and connection of particle) void MetropolisHastingsSampler::MakeProposal() { float randnum = m_RandGen->GetVariate(); // Birth Proposal if (randnum < m_BirthProb) { + m_BirthTime.Start(); vnl_vector_fixed R; m_EnergyComputer->DrawRandomPosition(R); vnl_vector_fixed N = GetRandomDirection(); Particle prop; prop.GetPos() = R; prop.GetDir() = N; float prob = m_Density * m_DeathProb /((m_BirthProb)*(m_ParticleGrid->m_NumParticles+1)); float ex_energy = m_EnergyComputer->ComputeExternalEnergy(R,N,0); float in_energy = m_EnergyComputer->ComputeInternalEnergy(&prop); prob *= exp((in_energy/m_InTemp+ex_energy/m_ExTemp)) ; if (prob > 1 || m_RandGen->GetVariate() < prob) { Particle *p = m_ParticleGrid->NewParticle(R); if (p!=0) { p->GetPos() = R; p->GetDir() = N; m_AcceptedProposals++; } } + m_BirthTime.Stop(); } // Death Proposal else if (randnum < m_BirthProb+m_DeathProb) { + m_DeathTime.Start(); if (m_ParticleGrid->m_NumParticles > 0) { int pnum = m_RandGen->GetIntegerVariate()%m_ParticleGrid->m_NumParticles; Particle *dp = m_ParticleGrid->GetParticle(pnum); if (dp->pID == -1 && dp->mID == -1) { float ex_energy = m_EnergyComputer->ComputeExternalEnergy(dp->GetPos(),dp->GetDir(),dp); float in_energy = m_EnergyComputer->ComputeInternalEnergy(dp); float prob = m_ParticleGrid->m_NumParticles * (m_BirthProb) /(m_Density*m_DeathProb); //*SpatProb(dp->R); prob *= exp(-(in_energy/m_InTemp+ex_energy/m_ExTemp)) ; if (prob > 1 || m_RandGen->GetVariate() < prob) { m_ParticleGrid->RemoveParticle(pnum); m_AcceptedProposals++; } } } - + m_DeathTime.Stop(); } // Shift Proposal else if (randnum < m_BirthProb+m_DeathProb+m_ShiftProb) { if (m_ParticleGrid->m_NumParticles > 0) { + m_ShiftTime.Start(); int pnum = m_RandGen->GetIntegerVariate()%m_ParticleGrid->m_NumParticles; Particle *p = m_ParticleGrid->GetParticle(pnum); Particle prop_p = *p; DistortVector(m_Sigma, prop_p.GetPos()); DistortVector(m_Sigma/(2*m_ParticleLength), prop_p.GetDir()); prop_p.GetDir().normalize(); float ex_energy = m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),p) - m_EnergyComputer->ComputeExternalEnergy(p->GetPos(),p->GetDir(),p); float in_energy = m_EnergyComputer->ComputeInternalEnergy(&prop_p) - m_EnergyComputer->ComputeInternalEnergy(p); float prob = exp(ex_energy/m_ExTemp+in_energy/m_InTemp); if (m_RandGen->GetVariate() < prob) { vnl_vector_fixed Rtmp = p->GetPos(); vnl_vector_fixed Ntmp = p->GetDir(); p->GetPos() = prop_p.GetPos(); p->GetDir() = prop_p.GetDir(); if (!m_ParticleGrid->TryUpdateGrid(pnum)) { p->GetPos() = Rtmp; p->GetDir() = Ntmp; } m_AcceptedProposals++; } + m_ShiftTime.Stop(); } } // Optimal Shift Proposal else if (randnum < m_BirthProb+m_DeathProb+m_ShiftProb+m_OptShiftProb) { if (m_ParticleGrid->m_NumParticles > 0) { - + m_OptShiftTime.Start(); int pnum = m_RandGen->GetIntegerVariate()%m_ParticleGrid->m_NumParticles; Particle *p = m_ParticleGrid->GetParticle(pnum); bool no_proposal = false; Particle prop_p = *p; if (p->pID != -1 && p->mID != -1) { Particle *plus = m_ParticleGrid->GetParticle(p->pID); int ep_plus = (plus->pID == p->ID)? 1 : -1; Particle *minus = m_ParticleGrid->GetParticle(p->mID); int ep_minus = (minus->pID == p->ID)? 1 : -1; prop_p.GetPos() = (plus->GetPos() + plus->GetDir() * (m_ParticleLength * ep_plus) + minus->GetPos() + minus->GetDir() * (m_ParticleLength * ep_minus)); prop_p.GetPos() *= 0.5; prop_p.GetDir() = plus->GetPos() - minus->GetPos(); prop_p.GetDir().normalize(); } else if (p->pID != -1) { Particle *plus = m_ParticleGrid->GetParticle(p->pID); int ep_plus = (plus->pID == p->ID)? 1 : -1; prop_p.GetPos() = plus->GetPos() + plus->GetDir() * (m_ParticleLength * ep_plus * 2); prop_p.GetDir() = plus->GetDir(); } else if (p->mID != -1) { Particle *minus = m_ParticleGrid->GetParticle(p->mID); int ep_minus = (minus->pID == p->ID)? 1 : -1; prop_p.GetPos() = minus->GetPos() + minus->GetDir() * (m_ParticleLength * ep_minus * 2); prop_p.GetDir() = minus->GetDir(); } else no_proposal = true; if (!no_proposal) { float cos = dot_product(prop_p.GetDir(), p->GetDir()); float p_rev = exp(-((prop_p.GetPos()-p->GetPos()).squared_magnitude() + (1-cos*cos))*m_Gamma)/m_Z; float ex_energy = m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),p) - m_EnergyComputer->ComputeExternalEnergy(p->GetPos(),p->GetDir(),p); float in_energy = m_EnergyComputer->ComputeInternalEnergy(&prop_p) - m_EnergyComputer->ComputeInternalEnergy(p); float prob = exp(ex_energy/m_ExTemp+in_energy/m_InTemp)*m_ShiftProb*p_rev/(m_OptShiftProb+m_ShiftProb*p_rev); if (m_RandGen->GetVariate() < prob) { vnl_vector_fixed Rtmp = p->GetPos(); vnl_vector_fixed Ntmp = p->GetDir(); p->GetPos() = prop_p.GetPos(); p->GetDir() = prop_p.GetDir(); if (!m_ParticleGrid->TryUpdateGrid(pnum)) { p->GetPos() = Rtmp; p->GetDir() = Ntmp; } m_AcceptedProposals++; } } + m_OptShiftTime.Stop(); } } + // Connection Proposal else { if (m_ParticleGrid->m_NumParticles > 0) { + m_ConnectionTime.Start(); int pnum = m_RandGen->GetIntegerVariate()%m_ParticleGrid->m_NumParticles; Particle *p = m_ParticleGrid->GetParticle(pnum); EndPoint P; P.p = p; - P.ep = (m_RandGen->GetVariate() > 0.5)? 1 : -1; + P.ep = (m_RandGen->GetVariate() > 0.5)? 1 : -1; // direction of the new tract - RemoveAndSaveTrack(P); + RemoveAndSaveTrack(P); // remove old tract and save it for later if (m_BackupTrack.m_Probability != 0) { - MakeTrackProposal(P); + MakeTrackProposal(P); // propose new tract starting from P float prob = (m_ProposalTrack.m_Energy-m_BackupTrack.m_Energy)/m_InTemp ; prob = exp(prob)*(m_BackupTrack.m_Probability * pow(m_DelProb,m_ProposalTrack.m_Length)) /(m_ProposalTrack.m_Probability * pow(m_DelProb,m_BackupTrack.m_Length)); if (m_RandGen->GetVariate() < prob) { - ImplementTrack(m_ProposalTrack); + ImplementTrack(m_ProposalTrack); // accept proposed tract m_AcceptedProposals++; } else { - ImplementTrack(m_BackupTrack); + ImplementTrack(m_BackupTrack); // reject proposed tract and restore old one } } else ImplementTrack(m_BackupTrack); + m_ConnectionTime.Stop(); } } } // establish connections between particles stored in input Track void MetropolisHastingsSampler::ImplementTrack(Track &T) { for (int k = 1; k < T.m_Length;k++) m_ParticleGrid->CreateConnection(T.track[k-1].p,T.track[k-1].ep,T.track[k].p,-T.track[k].ep); } // remove pending track from random particle, save it in m_BackupTrack and calculate its probability void MetropolisHastingsSampler::RemoveAndSaveTrack(EndPoint P) { EndPoint Current = P; int cnt = 0; float energy = 0; float AccumProb = 1.0; m_BackupTrack.track[cnt] = Current; EndPoint Next; for (;;) { Next.p = 0; if (Current.ep == 1) { if (Current.p->pID != -1) { Next.p = m_ParticleGrid->GetParticle(Current.p->pID); Current.p->pID = -1; m_ParticleGrid->m_NumConnections--; } } else if (Current.ep == -1) { if (Current.p->mID != -1) { Next.p = m_ParticleGrid->GetParticle(Current.p->mID); Current.p->mID = -1; m_ParticleGrid->m_NumConnections--; } } else { fprintf(stderr,"MetropolisHastingsSampler_randshift: Connection inconsistent 3\n"); break; } if (Next.p == 0) // no successor { Next.ep = 0; // mark as empty successor break; } else { if (Next.p->pID == Current.p->ID) { Next.p->pID = -1; Next.ep = 1; } else if (Next.p->mID == Current.p->ID) { Next.p->mID = -1; Next.ep = -1; } else { fprintf(stderr,"MetropolisHastingsSampler_randshift: Connection inconsistent 4\n"); break; } } ComputeEndPointProposalDistribution(Current); AccumProb *= (m_SimpSamp.probFor(Next)); if (Next.p == 0) // no successor -> break break; energy += m_EnergyComputer->ComputeInternalEnergyConnection(Current.p,Current.ep,Next.p,Next.ep); Current = Next; Current.ep *= -1; cnt++; m_BackupTrack.track[cnt] = Current; if (m_RandGen->GetVariate() > m_DelProb) break; } m_BackupTrack.m_Energy = energy; m_BackupTrack.m_Probability = AccumProb; m_BackupTrack.m_Length = cnt+1; } // generate new track using kind of a local tracking starting from P in the given direction, store it in m_ProposalTrack and calculate its probability void MetropolisHastingsSampler::MakeTrackProposal(EndPoint P) { EndPoint Current = P; int cnt = 0; float energy = 0; float AccumProb = 1.0; m_ProposalTrack.track[cnt++] = Current; Current.p->label = 1; for (;;) { // next candidate is already connected if ((Current.ep == 1 && Current.p->pID != -1) || (Current.ep == -1 && Current.p->mID != -1)) break; // track too long // if (cnt > 250) // break; ComputeEndPointProposalDistribution(Current); int k = m_SimpSamp.draw(m_RandGen->GetVariate()); // stop tracking proposed if (k==0) break; EndPoint Next = m_SimpSamp.objs[k]; float probability = m_SimpSamp.probFor(k); // accumulate energy and proposal distribution energy += m_EnergyComputer->ComputeInternalEnergyConnection(Current.p,Current.ep,Next.p,Next.ep); AccumProb *= probability; // track to next endpoint Current = Next; Current.ep *= -1; Current.p->label = 1; // put label to avoid loops m_ProposalTrack.track[cnt++] = Current; } m_ProposalTrack.m_Energy = energy; m_ProposalTrack.m_Probability = AccumProb; m_ProposalTrack.m_Length = cnt; // clear labels for (int j = 0; j < m_ProposalTrack.m_Length;j++) m_ProposalTrack.track[j].p->label = 0; } // get neigbouring particles of P and calculate the according connection probabilities void MetropolisHastingsSampler::ComputeEndPointProposalDistribution(EndPoint P) { Particle *p = P.p; int ep = P.ep; float dist,dot; vnl_vector_fixed R = p->GetPos() + (p->GetDir() * (ep*m_ParticleLength) ); m_ParticleGrid->ComputeNeighbors(R); m_SimpSamp.clear(); m_SimpSamp.add(m_StopProb,EndPoint(0,0)); for (;;) { Particle *p2 = m_ParticleGrid->GetNextNeighbor(); if (p2 == 0) break; if (p!=p2 && p2->label == 0) { if (p2->mID == -1) { dist = (p2->GetPos() - p2->GetDir() * m_ParticleLength - R).squared_magnitude(); if (dist < m_DistanceThreshold) { dot = dot_product(p2->GetDir(),p->GetDir()) * ep; if (dot > m_CurvatureThreshold) { float en = m_EnergyComputer->ComputeInternalEnergyConnection(p,ep,p2,-1); m_SimpSamp.add(exp(en/m_TractProb),EndPoint(p2,-1)); } } } if (p2->pID == -1) { dist = (p2->GetPos() + p2->GetDir() * m_ParticleLength - R).squared_magnitude(); if (dist < m_DistanceThreshold) { dot = dot_product(p2->GetDir(),p->GetDir()) * (-ep); if (dot > m_CurvatureThreshold) { float en = m_EnergyComputer->ComputeInternalEnergyConnection(p,ep,p2,+1); m_SimpSamp.add(exp(en/m_TractProb),EndPoint(p2,+1)); } } } } } } // return number of accepted proposals int MetropolisHastingsSampler::GetNumAcceptedProposals() { return m_AcceptedProposals; } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h index 11e340cfcd..d4a80c524e 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h @@ -1,101 +1,110 @@ /*=================================================================== 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. ===================================================================*/ #ifndef _SAMPLER #define _SAMPLER // MITK #include #include #include #include // ITK #include +#include #include // MISC #include namespace mitk { /** * \brief Generates ne proposals of particle configurations. */ class FiberTracking_EXPORT MetropolisHastingsSampler { public: typedef itk::Image< float, 3 > ItkFloatImageType; typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType; MetropolisHastingsSampler(ParticleGrid* grid, EnergyComputer* enComp, ItkRandGenType* randGen, float curvThres); void SetTemperature(float val); - void MakeProposal(); + void MakeProposal(); ///< make proposal for birth/death/shift/connection of particles int GetNumAcceptedProposals(); - void SetProbabilities(float birth, float death, float shift, float optShift, float connect); + void SetProbabilities(float birth, float death, float shift, float optShift, float connect); ///< update the probabilities of the single proposals + void PrintProposalTimes(); ///< print the state of the proposal time probes protected: - // connection proposal related methods + /** connection proposal related methods */ void ImplementTrack(Track& T); void RemoveAndSaveTrack(EndPoint P); void MakeTrackProposal(EndPoint P); void ComputeEndPointProposalDistribution(EndPoint P); - // generate random vectors + /** generate random vectors */ void DistortVector(float sigma, vnl_vector_fixed& vec); vnl_vector_fixed GetRandomDirection(); - ItkRandGenType* m_RandGen; // random generator - Track m_ProposalTrack; // stores proposal track - Track m_BackupTrack; // stores track removed for new proposal traCK - SimpSamp m_SimpSamp; // neighbouring particles and their probabilities for the local tracking + ItkRandGenType* m_RandGen; ///< random generator + Track m_ProposalTrack; ///< stores proposal track + Track m_BackupTrack; ///< stores track removed for new proposal traCK + SimpSamp m_SimpSamp; ///< neighbouring particles and their probabilities for the local tracking - float m_InTemp; // simulated annealing temperature - float m_ExTemp; // simulated annealing temperature + float m_InTemp; ///< simulated annealing temperature + float m_ExTemp; ///< simulated annealing temperature float m_Density; - float m_BirthProb; // probability for particle birth - float m_DeathProb; // probability for particle death - float m_ShiftProb; // probability for particle shift - float m_OptShiftProb; // probability for optimal particle shift - float m_ConnectionProb; // probability for particle connection proposal + float m_BirthProb; ///< probability for particle birth + float m_DeathProb; ///< probability for particle death + float m_ShiftProb; ///< probability for particle shift + float m_OptShiftProb; ///< probability for optimal particle shift + float m_ConnectionProb; ///< probability for particle connection proposal float m_Sigma; float m_Gamma; float m_Z; - float m_DistanceThreshold; // threshold for maximum distance between connected particles - float m_CurvatureThreshold; // threshold for maximum angle between connected particles + float m_DistanceThreshold; ///< threshold for maximum distance between connected particles + float m_CurvatureThreshold; ///< threshold for maximum angle between connected particles float m_TractProb; float m_StopProb; float m_DelProb; float m_ParticleLength; float m_ChempotParticle; - ParticleGrid* m_ParticleGrid; - EnergyComputer* m_EnergyComputer; - int m_AcceptedProposals; + ParticleGrid* m_ParticleGrid; ///< storest all particles + EnergyComputer* m_EnergyComputer; ///< computes internal and external energy of particles + unsigned int m_AcceptedProposals; ///< counts accepted proposals + + /** Time probes for the single proposals */ + itk::TimeProbe m_BirthTime; + itk::TimeProbe m_DeathTime; + itk::TimeProbe m_ShiftTime; + itk::TimeProbe m_OptShiftTime; + itk::TimeProbe m_ConnectionTime; }; } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp index aae8412a66..68d8045b94 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp @@ -1,510 +1,512 @@ /*=================================================================== 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 "itkGibbsTrackingFilter.h" // MITK #include #include #include #include #include //#include #include #include // ITK #include #include #include // MISC #include // #include #include #include #include #include #include namespace itk{ template< class ItkQBallImageType > GibbsTrackingFilter< ItkQBallImageType >::GibbsTrackingFilter(): m_StartTemperature(0.1), m_EndTemperature(0.001), m_Iterations(500000), m_CurrentStep(0), m_ParticleWeight(0), m_ParticleWidth(0), m_ParticleLength(0), m_ConnectionPotential(10), m_InexBalance(0), m_ParticlePotential(0.2), m_MinFiberLength(10), m_AbortTracking(false), m_NumAcceptedFibers(0), m_BuildFibers(false), m_Steps(10), m_ProposalAcceptance(0), m_CurvatureThreshold(0.7), m_DuplicateImage(true), m_NumParticles(0), m_NumConnections(0), m_RandomSeed(-1), m_LoadParameterFile(""), m_LutPath(""), m_IsInValidState(true) { } template< class ItkQBallImageType > GibbsTrackingFilter< ItkQBallImageType >::~GibbsTrackingFilter() { } // fill output fiber bundle datastructure template< class ItkQBallImageType > typename GibbsTrackingFilter< ItkQBallImageType >::FiberPolyDataType GibbsTrackingFilter< ItkQBallImageType >::GetFiberBundle() { if (!m_AbortTracking) { m_BuildFibers = true; while (m_BuildFibers){} } return m_FiberPolyData; } template< class ItkQBallImageType > void GibbsTrackingFilter< ItkQBallImageType > ::EstimateParticleWeight() { MITK_INFO << "GibbsTrackingFilter: estimating particle weight"; float minSpacing; if(m_QBallImage->GetSpacing()[0]GetSpacing()[1] && m_QBallImage->GetSpacing()[0]GetSpacing()[2]) minSpacing = m_QBallImage->GetSpacing()[0]; else if (m_QBallImage->GetSpacing()[1] < m_QBallImage->GetSpacing()[2]) minSpacing = m_QBallImage->GetSpacing()[1]; else minSpacing = m_QBallImage->GetSpacing()[2]; float m_ParticleLength = 1.5*minSpacing; float m_ParticleWidth = 0.5*minSpacing; // seed random generators Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); if (m_RandomSeed>-1) randGen->SetSeed(m_RandomSeed); else randGen->SetSeed(); // instantiate all necessary components SphereInterpolator* interpolator = new SphereInterpolator(m_LutPath); // handle lookup table not found cases if( !interpolator->IsInValidState() ) { m_IsInValidState = false; m_AbortTracking = true; m_BuildFibers = false; mitkThrow() << "Unable to load lookup tables."; } ParticleGrid* particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity); GibbsEnergyComputer* encomp = new GibbsEnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen); // EnergyComputer* encomp = new EnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen); MetropolisHastingsSampler* sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold); float alpha = log(m_EndTemperature/m_StartTemperature); m_ParticleWeight = 0.01; int ppv = 0; // main loop int neededParts = 3000; while (ppvSetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotential*m_ParticleLength*m_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential); for( int step = 0; step < 10; step++ ) { // update temperatur for simulated annealing process float temperature = m_StartTemperature * exp(alpha*(((1.0)*step)/((1.0)*10))); sampler->SetTemperature(temperature); for (unsigned long i=0; i<10000; i++) sampler->MakeProposal(); } ppv = particleGrid->m_NumParticles; particleGrid->ResetGrid(); } delete sampler; delete encomp; delete particleGrid; delete interpolator; MITK_INFO << "GibbsTrackingFilter: finished estimating particle weight"; } // perform global tracking template< class ItkQBallImageType > void GibbsTrackingFilter< ItkQBallImageType >::GenerateData() { TimeProbe preClock; preClock.Start(); // check if input is qball or tensor image and generate qball if necessary if (m_QBallImage.IsNull() && m_TensorImage.IsNotNull()) { TensorImageToQBallImageFilter::Pointer filter = TensorImageToQBallImageFilter::New(); filter->SetInput( m_TensorImage ); filter->Update(); m_QBallImage = filter->GetOutput(); } else if (m_DuplicateImage) // generate local working copy of QBall image (if not disabled) { typedef itk::ImageDuplicator< ItkQBallImageType > DuplicateFilterType; typename DuplicateFilterType::Pointer duplicator = DuplicateFilterType::New(); duplicator->SetInputImage( m_QBallImage ); duplicator->Update(); m_QBallImage = duplicator->GetOutput(); } // perform mean subtraction on odfs typedef ImageRegionIterator< ItkQBallImageType > InputIteratorType; InputIteratorType it(m_QBallImage, m_QBallImage->GetLargestPossibleRegion() ); it.GoToBegin(); while (!it.IsAtEnd()) { itk::OrientationDistributionFunction odf(it.Get().GetDataPointer()); float mean = odf.GetMeanValue(); odf -= mean; it.Set(odf.GetDataPointer()); ++it; } // check if mask image is given if it needs resampling PrepareMaskImage(); // load parameter file LoadParameters(); // prepare parameters float minSpacing; if(m_QBallImage->GetSpacing()[0]GetSpacing()[1] && m_QBallImage->GetSpacing()[0]GetSpacing()[2]) minSpacing = m_QBallImage->GetSpacing()[0]; else if (m_QBallImage->GetSpacing()[1] < m_QBallImage->GetSpacing()[2]) minSpacing = m_QBallImage->GetSpacing()[1]; else minSpacing = m_QBallImage->GetSpacing()[2]; if(m_ParticleLength == 0) m_ParticleLength = 1.5*minSpacing; if(m_ParticleWidth == 0) m_ParticleWidth = 0.5*minSpacing; if(m_ParticleWeight == 0) EstimateParticleWeight(); float alpha = log(m_EndTemperature/m_StartTemperature); m_Steps = m_Iterations/10000; if (m_Steps<10) m_Steps = 10; if (m_Steps>m_Iterations) { MITK_INFO << "GibbsTrackingFilter: not enough iterations!"; m_AbortTracking = true; } if (m_CurvatureThreshold < mitk::eps) m_CurvatureThreshold = 0; unsigned long singleIts = (unsigned long)((1.0*m_Iterations) / (1.0*m_Steps)); // seed random generators Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); if (m_RandomSeed>-1) randGen->SetSeed(m_RandomSeed); else randGen->SetSeed(); // load sphere interpolator to evaluate the ODFs SphereInterpolator* interpolator = new SphereInterpolator(m_LutPath); // handle lookup table not found cases if( !interpolator->IsInValidState() ) { m_IsInValidState = false; m_AbortTracking = true; m_BuildFibers = false; mitkThrow() << "Unable to load lookup tables."; } // initialize the actual tracking components (ParticleGrid, Metropolis Hastings Sampler and Energy Computer) ParticleGrid* particleGrid; GibbsEnergyComputer* encomp; MetropolisHastingsSampler* sampler; try{ particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity); encomp = new GibbsEnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen); encomp->SetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotential*m_ParticleLength*m_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential); sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold); } catch(...) { MITK_ERROR << "Particle grid allocation failed. Not enough memory? Try to increase the particle length."; m_IsInValidState = false; m_AbortTracking = true; m_BuildFibers = false; return; } MITK_INFO << "----------------------------------------"; MITK_INFO << "Iterations: " << m_Iterations; MITK_INFO << "Steps: " << m_Steps; MITK_INFO << "Particle length: " << m_ParticleLength; MITK_INFO << "Particle width: " << m_ParticleWidth; MITK_INFO << "Particle weight: " << m_ParticleWeight; MITK_INFO << "Start temperature: " << m_StartTemperature; MITK_INFO << "End temperature: " << m_EndTemperature; MITK_INFO << "In/Ex balance: " << m_InexBalance; MITK_INFO << "Min. fiber length: " << m_MinFiberLength; MITK_INFO << "Curvature threshold: " << m_CurvatureThreshold; MITK_INFO << "Random seed: " << m_RandomSeed; MITK_INFO << "----------------------------------------"; // main loop preClock.Stop(); TimeProbe clock; clock.Start(); m_NumAcceptedFibers = 0; unsigned long counter = 1; boost::progress_display disp(m_Steps*singleIts); if (!m_AbortTracking) for( m_CurrentStep = 1; m_CurrentStep <= m_Steps; m_CurrentStep++ ) { // update temperatur for simulated annealing process float temperature = m_StartTemperature * exp(alpha*(((1.0)*m_CurrentStep)/((1.0)*m_Steps))); sampler->SetTemperature(temperature); for (unsigned long i=0; iMakeProposal(); if (m_BuildFibers || (i==singleIts-1 && m_CurrentStep==m_Steps)) { m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/counter; m_NumParticles = particleGrid->m_NumParticles; m_NumConnections = particleGrid->m_NumConnections; FiberBuilder fiberBuilder(particleGrid, m_MaskImage); m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength); m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines(); m_BuildFibers = false; } counter++; } m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/counter; m_NumParticles = particleGrid->m_NumParticles; m_NumConnections = particleGrid->m_NumConnections; if (m_AbortTracking) break; } if (m_AbortTracking) { FiberBuilder fiberBuilder(particleGrid, m_MaskImage); m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength); m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines(); } clock.Stop(); delete sampler; delete encomp; delete interpolator; delete particleGrid; m_AbortTracking = true; m_BuildFibers = false; int h = clock.GetTotal()/3600; int m = ((int)clock.GetTotal()%3600)/60; int s = (int)clock.GetTotal()%60; MITK_INFO << "GibbsTrackingFilter: finished gibbs tracking in " << h << "h, " << m << "m and " << s << "s"; m = (int)preClock.GetTotal()/60; s = (int)preClock.GetTotal()%60; MITK_INFO << "GibbsTrackingFilter: preparation of the data took " << m << "m and " << s << "s"; MITK_INFO << "GibbsTrackingFilter: " << m_NumAcceptedFibers << " fibers accepted"; +// sampler->PrintProposalTimes(); + SaveParameters(); } template< class ItkQBallImageType > void GibbsTrackingFilter< ItkQBallImageType >::PrepareMaskImage() { if(m_MaskImage.IsNull()) { MITK_INFO << "GibbsTrackingFilter: generating default mask image"; m_MaskImage = ItkFloatImageType::New(); m_MaskImage->SetSpacing( m_QBallImage->GetSpacing() ); m_MaskImage->SetOrigin( m_QBallImage->GetOrigin() ); m_MaskImage->SetDirection( m_QBallImage->GetDirection() ); m_MaskImage->SetRegions( m_QBallImage->GetLargestPossibleRegion() ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1.0); } else if ( m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=m_QBallImage->GetLargestPossibleRegion().GetSize()[0] || m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=m_QBallImage->GetLargestPossibleRegion().GetSize()[1] || m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=m_QBallImage->GetLargestPossibleRegion().GetSize()[2] || m_MaskImage->GetSpacing()[0]!=m_QBallImage->GetSpacing()[0] || m_MaskImage->GetSpacing()[1]!=m_QBallImage->GetSpacing()[1] || m_MaskImage->GetSpacing()[2]!=m_QBallImage->GetSpacing()[2] ) { MITK_INFO << "GibbsTrackingFilter: resampling mask image"; typedef itk::ResampleImageFilter< ItkFloatImageType, ItkFloatImageType, float > ResamplerType; ResamplerType::Pointer resampler = ResamplerType::New(); resampler->SetOutputSpacing( m_QBallImage->GetSpacing() ); resampler->SetOutputOrigin( m_QBallImage->GetOrigin() ); resampler->SetOutputDirection( m_QBallImage->GetDirection() ); resampler->SetSize( m_QBallImage->GetLargestPossibleRegion().GetSize() ); resampler->SetInput( m_MaskImage ); resampler->SetDefaultPixelValue(0.0); resampler->Update(); m_MaskImage = resampler->GetOutput(); MITK_INFO << "GibbsTrackingFilter: resampling finished"; } } // load tracking paramters from xml file (.gtp) template< class ItkQBallImageType > bool GibbsTrackingFilter< ItkQBallImageType >::LoadParameters() { m_AbortTracking = true; try { if( m_LoadParameterFile.length()==0 ) { m_AbortTracking = false; return true; } MITK_INFO << "GibbsTrackingFilter: loading parameter file " << m_LoadParameterFile; TiXmlDocument doc( m_LoadParameterFile ); doc.LoadFile(); TiXmlHandle hDoc(&doc); TiXmlElement* pElem; TiXmlHandle hRoot(0); pElem = hDoc.FirstChildElement().Element(); hRoot = TiXmlHandle(pElem); pElem = hRoot.FirstChildElement("parameter_set").Element(); string iterations(pElem->Attribute("iterations")); m_Iterations = boost::lexical_cast(iterations); string particleLength(pElem->Attribute("particle_length")); m_ParticleLength = boost::lexical_cast(particleLength); string particleWidth(pElem->Attribute("particle_width")); m_ParticleWidth = boost::lexical_cast(particleWidth); string partWeight(pElem->Attribute("particle_weight")); m_ParticleWeight = boost::lexical_cast(partWeight); string startTemp(pElem->Attribute("temp_start")); m_StartTemperature = boost::lexical_cast(startTemp); string endTemp(pElem->Attribute("temp_end")); m_EndTemperature = boost::lexical_cast(endTemp); string inExBalance(pElem->Attribute("inexbalance")); m_InexBalance = boost::lexical_cast(inExBalance); string fiberLength(pElem->Attribute("fiber_length")); m_MinFiberLength = boost::lexical_cast(fiberLength); string curvThres(pElem->Attribute("curvature_threshold")); m_CurvatureThreshold = cos(boost::lexical_cast(curvThres)*M_PI/180); m_AbortTracking = false; MITK_INFO << "GibbsTrackingFilter: parameter file loaded successfully"; return true; } catch(...) { MITK_INFO << "GibbsTrackingFilter: could not load parameter file"; return false; } } // save current tracking paramters to xml file (.gtp) template< class ItkQBallImageType > bool GibbsTrackingFilter< ItkQBallImageType >::SaveParameters() { try { if( m_SaveParameterFile.length()==0 ) { MITK_INFO << "GibbsTrackingFilter: no filename specified to save parameters"; return true; } MITK_INFO << "GibbsTrackingFilter: saving parameter file " << m_SaveParameterFile; TiXmlDocument documentXML; TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" ); documentXML.LinkEndChild( declXML ); TiXmlElement* mainXML = new TiXmlElement("global_tracking_parameter_file"); mainXML->SetAttribute("file_version", "0.1"); documentXML.LinkEndChild(mainXML); TiXmlElement* paramXML = new TiXmlElement("parameter_set"); paramXML->SetAttribute("iterations", boost::lexical_cast(m_Iterations)); paramXML->SetAttribute("particle_length", boost::lexical_cast(m_ParticleLength)); paramXML->SetAttribute("particle_width", boost::lexical_cast(m_ParticleWidth)); paramXML->SetAttribute("particle_weight", boost::lexical_cast(m_ParticleWeight)); paramXML->SetAttribute("temp_start", boost::lexical_cast(m_StartTemperature)); paramXML->SetAttribute("temp_end", boost::lexical_cast(m_EndTemperature)); paramXML->SetAttribute("inexbalance", boost::lexical_cast(m_InexBalance)); paramXML->SetAttribute("fiber_length", boost::lexical_cast(m_MinFiberLength)); paramXML->SetAttribute("curvature_threshold", boost::lexical_cast(m_CurvatureThreshold)); mainXML->LinkEndChild(paramXML); if(!boost::algorithm::ends_with(m_SaveParameterFile, ".gtp")) m_SaveParameterFile.append(".gtp"); documentXML.SaveFile( m_SaveParameterFile ); MITK_INFO << "GibbsTrackingFilter: parameter file saved successfully"; return true; } catch(...) { MITK_INFO << "GibbsTrackingFilter: could not save parameter file"; return false; } } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp index 3431e09f11..bb6620e40e 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,867 +1,870 @@ /*=================================================================== 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 "itkTractsToDWIImageFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace itk { template< class PixelType > TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter() : m_UseConstantRandSeed(false) { m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); m_RandGen->SetSeed(); } template< class PixelType > TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter() { } template< class PixelType > TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images ) { // create slice object ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); Vector< double, 2 > sliceSpacing; sliceSpacing[0] = m_UpsampledSpacing[0]; sliceSpacing[1] = m_UpsampledSpacing[1]; // frequency map slice SliceType::Pointer fMapSlice = NULL; if (m_Parameters.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); ImageRegion<2> region; region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); fMapSlice->SetLargestPossibleRegion( region ); fMapSlice->SetBufferedRegion( region ); fMapSlice->SetRequestedRegion( region ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } DoubleDwiType::Pointer newImage = DoubleDwiType::New(); newImage->SetSpacing( m_Parameters.m_ImageSpacing ); newImage->SetOrigin( m_Parameters.m_ImageOrigin ); newImage->SetDirection( m_Parameters.m_ImageDirection ); newImage->SetLargestPossibleRegion( m_Parameters.m_ImageRegion ); newImage->SetBufferedRegion( m_Parameters.m_ImageRegion ); newImage->SetRequestedRegion( m_Parameters.m_ImageRegion ); newImage->SetVectorLength( images.at(0)->GetVectorLength() ); newImage->Allocate(); std::vector< unsigned int > spikeVolume; for (unsigned int i=0; iGetIntegerVariate()%images.at(0)->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(2*images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%images.at(0)->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetLargestPossibleRegion().GetSize(2); z++) { std::vector< SliceType::Pointer > compartmentSlices; std::vector< double > t2Vector; for (unsigned int i=0; i* signalModel; if (iSetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->SetSpacing(sliceSpacing); slice->Allocate(); slice->FillBuffer(0.0); // extract slice from channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; slice->SetPixel(index2D, images.at(i)->GetPixel(index3D)[g]); if (fMapSlice.IsNotNull() && i==0) fMapSlice->SetPixel(index2D, m_Parameters.m_FrequencyMap->GetPixel(index3D)); } compartmentSlices.push_back(slice); t2Vector.push_back(signalModel->GetT2()); } if (this->GetAbortGenerateData()) return NULL; // create k-sapce (inverse fourier transform slices) itk::Size<2> outSize; outSize.SetElement(0, m_Parameters.m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_Parameters.m_ImageRegion.GetSize(1)); itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetT2(t2Vector); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(m_Parameters); idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0); idft->SetDiffusionGradientDirection(m_Parameters.GetGradientDirection(g)); idft->SetFrequencyMapSlice(fMapSlice); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); ComplexSliceType::Pointer fSlice; fSlice = idft->GetOutput(); ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; // fourier transform slice SliceType::Pointer newSlice; itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D); pix3D[g] = newSlice->GetPixel(index2D); newImage->SetPixel(index3D, pix3D); } ++disp; newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; return newImage; } template< class PixelType > void TractsToDWIImageFilter< PixelType >::GenerateData() { m_StartTime = clock(); m_StatusText = "Starting simulation\n"; // check input data if (m_FiberBundle.IsNull()) itkExceptionMacro("Input fiber bundle is NULL!"); if (m_Parameters.m_DoDisablePartialVolume) while (m_Parameters.m_FiberModelList.size()>1) m_Parameters.m_FiberModelList.pop_back(); if (m_Parameters.m_NonFiberModelList.empty()) itkExceptionMacro("No diffusion model for non-fiber compartments defined!"); int baselineIndex = m_Parameters.GetFirstBaselineIndex(); if (baselineIndex<0) itkExceptionMacro("No baseline index found!"); if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); // initialize output dwi image ImageRegion<3> croppedRegion = m_Parameters.m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Parameters.m_CroppingFactor); itk::Point shiftedOrigin = m_Parameters.m_ImageOrigin; shiftedOrigin[1] += (m_Parameters.m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Parameters.m_ImageSpacing[1]/2; typename OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( m_Parameters.m_ImageSpacing ); outImage->SetOrigin( shiftedOrigin ); outImage->SetDirection( m_Parameters.m_ImageDirection ); outImage->SetLargestPossibleRegion( croppedRegion ); outImage->SetBufferedRegion( croppedRegion ); outImage->SetRequestedRegion( croppedRegion ); outImage->SetVectorLength( m_Parameters.GetNumVolumes() ); outImage->Allocate(); typename OutputImageType::PixelType temp; temp.SetSize(m_Parameters.GetNumVolumes()); temp.Fill(0.0); outImage->FillBuffer(temp); // ADJUST GEOMETRY FOR FURTHER PROCESSING // is input slize size a power of two? unsigned int x=m_Parameters.m_ImageRegion.GetSize(0); unsigned int y=m_Parameters.m_ImageRegion.GetSize(1); ItkDoubleImgType::SizeType pad; pad[0]=x%2; pad[1]=y%2; pad[2]=0; m_Parameters.m_ImageRegion.SetSize(0, x+pad[0]); m_Parameters.m_ImageRegion.SetSize(1, y+pad[1]); if (m_Parameters.m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_FrequencyMap); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_FrequencyMap = zeroPadder->GetOutput(); } if (m_Parameters.m_MaskImage.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_MaskImage); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_MaskImage = zeroPadder->GetOutput(); } // Apply in-plane upsampling for Gibbs ringing artifact double upsampling = 1; if (m_Parameters.m_DoAddGibbsRinging) upsampling = 2; m_UpsampledSpacing = m_Parameters.m_ImageSpacing; m_UpsampledSpacing[0] /= upsampling; m_UpsampledSpacing[1] /= upsampling; m_UpsampledImageRegion = m_Parameters.m_ImageRegion; m_UpsampledImageRegion.SetSize(0, m_Parameters.m_ImageRegion.GetSize()[0]*upsampling); m_UpsampledImageRegion.SetSize(1, m_Parameters.m_ImageRegion.GetSize()[1]*upsampling); m_UpsampledOrigin = m_Parameters.m_ImageOrigin; m_UpsampledOrigin[0] -= m_Parameters.m_ImageSpacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2; m_UpsampledOrigin[1] -= m_Parameters.m_ImageSpacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2; m_UpsampledOrigin[2] -= m_Parameters.m_ImageSpacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2; // generate double images to store the individual compartment signals std::vector< DoubleDwiType::Pointer > compartments; for (unsigned int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_UpsampledOrigin ); doubleDwi->SetDirection( m_Parameters.m_ImageDirection ); doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleDwi->SetBufferedRegion( m_UpsampledImageRegion ); doubleDwi->SetRequestedRegion( m_UpsampledImageRegion ); doubleDwi->SetVectorLength( m_Parameters.GetNumVolumes() ); doubleDwi->Allocate(); DoubleDwiType::PixelType pix; pix.SetSize(m_Parameters.GetNumVolumes()); pix.Fill(0.0); doubleDwi->FillBuffer(pix); compartments.push_back(doubleDwi); } // initialize volume fraction images m_VolumeFractions.clear(); for (unsigned int i=0; iSetSpacing( m_UpsampledSpacing ); doubleImg->SetOrigin( m_UpsampledOrigin ); doubleImg->SetDirection( m_Parameters.m_ImageDirection ); doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleImg->SetBufferedRegion( m_UpsampledImageRegion ); doubleImg->SetRequestedRegion( m_UpsampledImageRegion ); doubleImg->Allocate(); doubleImg->FillBuffer(0); m_VolumeFractions.push_back(doubleImg); } // resample mask image and frequency map to fit upsampled geometry if (m_Parameters.m_DoAddGibbsRinging) { if (m_Parameters.m_MaskImage.IsNotNull()) { // rescale mask image (otherwise there are problems with the resampling) itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_Parameters.m_MaskImage); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); // resample mask image itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(rescaler->GetOutput()); resampler->SetOutputParametersFromImage(m_Parameters.m_MaskImage); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); resampler->Update(); m_Parameters.m_MaskImage = resampler->GetOutput(); } // resample frequency map if (m_Parameters.m_FrequencyMap.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(m_Parameters.m_FrequencyMap); resampler->SetOutputParametersFromImage(m_Parameters.m_FrequencyMap); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); resampler->Update(); m_Parameters.m_FrequencyMap = resampler->GetOutput(); } } // no input tissue mask is set -> create default bool maskImageSet = true; if (m_Parameters.m_MaskImage.IsNull()) { m_StatusText += "No tissue mask set\n"; MITK_INFO << "No tissue mask set"; m_Parameters.m_MaskImage = ItkUcharImgType::New(); m_Parameters.m_MaskImage->SetSpacing( m_UpsampledSpacing ); m_Parameters.m_MaskImage->SetOrigin( m_UpsampledOrigin ); m_Parameters.m_MaskImage->SetDirection( m_Parameters.m_ImageDirection ); m_Parameters.m_MaskImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->SetBufferedRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->SetRequestedRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->Allocate(); m_Parameters.m_MaskImage->FillBuffer(1); maskImageSet = false; } else { m_StatusText += "Using tissue mask\n"; MITK_INFO << "Using tissue mask"; } m_Parameters.m_ImageRegion = croppedRegion; x=m_Parameters.m_ImageRegion.GetSize(0); y=m_Parameters.m_ImageRegion.GetSize(1); if ( x%2 == 1 ) m_Parameters.m_ImageRegion.SetSize(0, x+1); if ( y%2 == 1 ) m_Parameters.m_ImageRegion.SetSize(1, y+1); // resample fiber bundle for sufficient voxel coverage m_StatusText += "\n"+this->GetTime()+" > Resampling fibers ...\n"; double segmentVolume = 0.0001; float minSpacing = 1; if(m_UpsampledSpacing[0]GetDeepCopy(); double volumeAccuracy = 10; fiberBundle->ResampleFibers(minSpacing/volumeAccuracy); double mmRadius = m_Parameters.m_AxonRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/volumeAccuracy; double maxVolume = 0; double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; if (m_Parameters.m_DoAddMotion) { if (m_Parameters.m_DoRandomizeMotion) { m_StatusText += "Adding random motion artifacts:\n"; m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast(m_Parameters.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_Parameters.m_Translation) + "mm\n"; } else { m_StatusText += "Adding linear motion artifacts:\n"; m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_Parameters.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: " + boost::lexical_cast(m_Parameters.m_Translation) + "mm\n"; } MITK_INFO << "Adding motion artifacts"; MITK_INFO << "Maximum rotation: " << m_Parameters.m_Rotation; MITK_INFO << "Maxmimum translation: " << m_Parameters.m_Translation; } maxVolume = 0; m_StatusText += "\n"+this->GetTime()+" > Generating signal of " + boost::lexical_cast(m_Parameters.m_FiberModelList.size()) + " fiber compartments\n"; MITK_INFO << "Generating signal of " << m_Parameters.m_FiberModelList.size() << " fiber compartments"; int numFibers = m_FiberBundle->GetNumFibers(); boost::progress_display disp(numFibers*m_Parameters.GetNumVolumes()); ofstream logFile; logFile.open("fiberfox_motion.log"); logFile << "0 rotation: 0,0,0; translation: 0,0,0\n"; // get transform for motion artifacts FiberBundleType fiberBundleTransformed = fiberBundle; VectorType rotation = m_Parameters.m_Rotation/m_Parameters.GetNumVolumes(); VectorType translation = m_Parameters.m_Translation/m_Parameters.GetNumVolumes(); // creat image to hold transformed mask (motion artifact) ItkUcharImgType::Pointer tempTissueMask = ItkUcharImgType::New(); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_Parameters.m_MaskImage); duplicator->Update(); tempTissueMask = duplicator->GetOutput(); // second upsampling needed for motion artifacts ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; itk::Vector upsampledSpacing = m_UpsampledSpacing; upsampledSpacing[0] /= 4; upsampledSpacing[1] /= 4; upsampledSpacing[2] /= 4; upsampledImageRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]*4); upsampledImageRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]*4); upsampledImageRegion.SetSize(2, m_UpsampledImageRegion.GetSize()[2]*4); itk::Point upsampledOrigin = m_UpsampledOrigin; upsampledOrigin[0] -= m_UpsampledSpacing[0]/2; upsampledOrigin[0] += upsampledSpacing[0]/2; upsampledOrigin[1] -= m_UpsampledSpacing[1]/2; upsampledOrigin[1] += upsampledSpacing[1]/2; upsampledOrigin[2] -= m_UpsampledSpacing[2]/2; upsampledOrigin[2] += upsampledSpacing[2]/2; ItkUcharImgType::Pointer upsampledTissueMask = ItkUcharImgType::New(); itk::ResampleImageFilter::Pointer upsampler = itk::ResampleImageFilter::New(); upsampler->SetInput(m_Parameters.m_MaskImage); upsampler->SetOutputParametersFromImage(m_Parameters.m_MaskImage); upsampler->SetSize(upsampledImageRegion.GetSize()); upsampler->SetOutputSpacing(upsampledSpacing); upsampler->SetOutputOrigin(upsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); upsampler->SetInterpolator(nn_interpolator); upsampler->Update(); upsampledTissueMask = upsampler->GetOutput(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; for (unsigned int g=0; gGetFiberPolyData(); - ItkDoubleImgType::Pointer intraAxonalVolume = ItkDoubleImgType::New(); - intraAxonalVolume->SetSpacing( m_UpsampledSpacing ); - intraAxonalVolume->SetOrigin( m_UpsampledOrigin ); - intraAxonalVolume->SetDirection( m_Parameters.m_ImageDirection ); - intraAxonalVolume->SetLargestPossibleRegion( m_UpsampledImageRegion ); - intraAxonalVolume->SetBufferedRegion( m_UpsampledImageRegion ); - intraAxonalVolume->SetRequestedRegion( m_UpsampledImageRegion ); - intraAxonalVolume->Allocate(); - intraAxonalVolume->FillBuffer(0); + ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); + intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); + intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); + intraAxonalVolumeImage->SetDirection( m_Parameters.m_ImageDirection ); + intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); + intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); + intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); + intraAxonalVolumeImage->Allocate(); + intraAxonalVolumeImage->FillBuffer(0); // generate fiber signal (if there are any fiber models present) if (!m_Parameters.m_FiberModelList.empty()) for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; for( int j=0; jGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } double* temp = points->GetPoint(j); itk::Point vertex = GetItkPoint(temp); itk::Vector v = GetItkVector(temp); itk::Vector dir(3); if (jGetPoint(j+1))-v; else dir = v-GetItkVector(points->GetPoint(j-1)); if (dir.GetSquaredNorm()<0.0001 || dir[0]!=dir[0] || dir[1]!=dir[1] || dir[2]!=dir[2]) continue; itk::Index<3> idx; itk::ContinuousIndex contIndex; tempTissueMask->TransformPhysicalPointToIndex(vertex, idx); tempTissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex); if (!tempTissueMask->GetLargestPossibleRegion().IsInside(idx) || tempTissueMask->GetPixel(idx)<=0) continue; // generate signal for each fiber compartment for (unsigned int k=0; kSetFiberDirection(dir); - DoubleDwiType::PixelType pix = doubleDwi->GetPixel(idx); + DoubleDwiType::PixelType pix = compartments.at(k)->GetPixel(idx); pix[g] += segmentVolume*m_Parameters.m_FiberModelList[k]->SimulateMeasurement(g); - doubleDwi->SetPixel(idx, pix ); - double vol = intraAxonalVolume->GetPixel(idx) + segmentVolume; - intraAxonalVolume->SetPixel(idx, vol ); - - if (g==0 && vol>maxVolume) - maxVolume = vol; + compartments.at(k)->SetPixel(idx, pix); } + + // update fiber volume image + double vol = intraAxonalVolumeImage->GetPixel(idx) + segmentVolume; + intraAxonalVolumeImage->SetPixel(idx, vol); + if (g==0 && vol>maxVolume) + maxVolume = vol; } + + // progress report ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } // generate non-fiber signal ImageRegionIterator it3(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); double fact = 1; - if (m_Parameters.m_AxonRadius<0.0001) + if (m_Parameters.m_AxonRadius<0.0001 || maxVolume>voxelVolume) fact = voxelVolume/maxVolume; while(!it3.IsAtEnd()) { if (it3.Get()>0) { DoubleDwiType::IndexType index = it3.GetIndex(); // get fiber volume fraction - DoubleDwiType::Pointer fiberDwi = compartments.at(0); - DoubleDwiType::PixelType fiberPix = fiberDwi->GetPixel(index); // intra axonal compartment - if (fact>1) // auto scale intra-axonal if no fiber radius is specified + double intraAxonalVolume = intraAxonalVolumeImage->GetPixel(index)*fact; + + for (unsigned int i=0; iSetPixel(index, fiberPix); + DoubleDwiType::PixelType pix = compartments.at(i)->GetPixel(index); + pix[g] *= fact; + compartments.at(i)->SetPixel(index, pix); } - double f = intraAxonalVolume->GetPixel(index)*fact; - if (f>voxelVolume || (f>0.0 && m_Parameters.m_DoDisablePartialVolume) ) // more fiber than space in voxel? + if (intraAxonalVolume>0.0001 && m_Parameters.m_DoDisablePartialVolume) // only fiber in voxel { - fiberPix[g] *= voxelVolume/f; - fiberDwi->SetPixel(index, fiberPix); + DoubleDwiType::PixelType pix = compartments.at(0)->GetPixel(index); + pix[g] *= voxelVolume/intraAxonalVolume; + compartments.at(0)->SetPixel(index, pix); m_VolumeFractions.at(0)->SetPixel(index, 1); + for (unsigned int i=1; iGetPixel(index); + pix[g] = 0; + compartments.at(i)->SetPixel(index, pix); + } } else { - m_VolumeFractions.at(0)->SetPixel(index, f/voxelVolume); + m_VolumeFractions.at(0)->SetPixel(index, intraAxonalVolume/voxelVolume); - double nonf = voxelVolume-f; // non-fiber volume - double inter = 0; + double extraAxonalVolume = voxelVolume-intraAxonalVolume; // non-fiber volume + double interAxonalVolume = 0; if (m_Parameters.m_FiberModelList.size()>1) - inter = nonf * f/voxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f - double other = nonf - inter; // rest of compartment - double singleinter = inter/(m_Parameters.m_FiberModelList.size()-1); + interAxonalVolume = extraAxonalVolume * intraAxonalVolume/voxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f + double other = extraAxonalVolume - interAxonalVolume; // rest of compartment + double singleinter = interAxonalVolume/(m_Parameters.m_FiberModelList.size()-1); // adjust non-fiber and intra-axonal signal for (unsigned int i=1; iGetPixel(index); - if (f>0) - pix[g] /= f; + DoubleDwiType::PixelType pix = compartments.at(i)->GetPixel(index); + if (intraAxonalVolume>0) // remove scaling by intra-axonal volume from inter-axonal compartment + pix[g] /= intraAxonalVolume; pix[g] *= singleinter; - doubleDwi->SetPixel(index, pix); + compartments.at(i)->SetPixel(index, pix); m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume); } for (unsigned int i=0; iGetPixel(index); - // if (dynamic_cast< mitk::AstroStickModel* >(m_Parameters.m_NonFiberModelList.at(i))) - // { - // mitk::AstroStickModel* model = dynamic_cast< mitk::AstroStickModel* >(m_Parameters.m_NonFiberModelList.at(i)); - // model->SetSeed(8111984); - // } pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g)*other*m_Parameters.m_NonFiberModelList[i]->GetWeight(); doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(i+m_Parameters.m_FiberModelList.size())->SetPixel(index, other/voxelVolume*m_Parameters.m_NonFiberModelList[i]->GetWeight()); } } } ++it3; } // move fibers if (m_Parameters.m_DoAddMotion) { if (m_Parameters.m_DoRandomizeMotion) { fiberBundleTransformed = fiberBundle->GetDeepCopy(); rotation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[0]*2)-m_Parameters.m_Rotation[0]; rotation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[1]*2)-m_Parameters.m_Rotation[1]; rotation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[2]*2)-m_Parameters.m_Rotation[2]; translation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[0]*2)-m_Parameters.m_Translation[0]; translation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[1]*2)-m_Parameters.m_Translation[1]; translation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[2]*2)-m_Parameters.m_Translation[2]; } // rotate mask image if (maskImageSet) { ImageRegionIterator maskIt(upsampledTissueMask, upsampledTissueMask->GetLargestPossibleRegion()); tempTissueMask->FillBuffer(0); while(!maskIt.IsAtEnd()) { if (maskIt.Get()<=0) { ++maskIt; continue; } DoubleDwiType::IndexType index = maskIt.GetIndex(); itk::Point point; upsampledTissueMask->TransformIndexToPhysicalPoint(index, point); if (m_Parameters.m_DoRandomizeMotion) point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]); else point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0]*(g+1),rotation[1]*(g+1),rotation[2]*(g+1),translation[0]*(g+1),translation[1]*(g+1),translation[2]*(g+1)); tempTissueMask->TransformPhysicalPointToIndex(point, index); if (tempTissueMask->GetLargestPossibleRegion().IsInside(index)) tempTissueMask->SetPixel(index,100); ++maskIt; } } // rotate fibers logFile << g+1 << " rotation:" << rotation[0] << "," << rotation[1] << "," << rotation[2] << ";"; logFile << " translation:" << translation[0] << "," << translation[1] << "," << translation[2] << "\n"; fiberBundleTransformed->TransformFibers(rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]); } } logFile.close(); m_StatusText += "\n\n"; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } // do k-space stuff DoubleDwiType::Pointer doubleOutImage; if (m_Parameters.m_Spikes>0 || m_Parameters.m_FrequencyMap.IsNotNull() || m_Parameters.m_KspaceLineOffset>0 || m_Parameters.m_DoSimulateRelaxation || m_Parameters.m_EddyStrength>0 || m_Parameters.m_DoAddGibbsRinging || m_Parameters.m_CroppingFactor<1.0) { m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; MITK_INFO << "Adjusting complex signal:"; if (m_Parameters.m_DoSimulateRelaxation) m_StatusText += "Simulating signal relaxation\n"; if (m_Parameters.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; if (m_Parameters.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; if (m_Parameters.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; if (m_Parameters.m_Spikes>0) m_StatusText += "Simulating spikes\n"; if (m_Parameters.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; if (m_Parameters.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; doubleOutImage = DoKspaceStuff(compartments); m_Parameters.m_SignalScale = 1; } else { m_StatusText += this->GetTime()+" > Summing compartments\n"; MITK_INFO << "Summing compartments"; doubleOutImage = compartments.at(0); for (unsigned int i=1; i::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New(); adder->SetInput1(doubleOutImage); adder->SetInput2(compartments.at(i)); adder->Update(); doubleOutImage = adder->GetOutput(); } } if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } m_StatusText += this->GetTime()+" > Finalizing image\n"; MITK_INFO << "Finalizing image"; if (m_Parameters.m_SignalScale>1) m_StatusText += " Scaling signal\n"; if (m_Parameters.m_NoiseModel!=NULL) m_StatusText += " Adding noise\n"; unsigned int window = 0; unsigned int min = itk::NumericTraits::max(); ImageRegionIterator it4 (outImage, outImage->GetLargestPossibleRegion()); DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.GetNumVolumes()); boost::progress_display disp2(outImage->GetLargestPossibleRegion().GetNumberOfPixels()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; lastTick = 0; while(!it4.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp2; unsigned long newTick = 50*disp2.count()/disp2.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename OutputImageType::IndexType index = it4.GetIndex(); signal = doubleOutImage->GetPixel(index)*m_Parameters.m_SignalScale; if (m_Parameters.m_NoiseModel!=NULL) { DoubleDwiType::PixelType accu = signal; accu.Fill(0.0); for (unsigned int i=0; iAddNoise(temp); accu += temp; } signal = accu/m_Parameters.m_Repetitions; } for (unsigned int i=0; i0) signal[i] = floor(signal[i]+0.5); else signal[i] = ceil(signal[i]-0.5); if (!m_Parameters.IsBaselineIndex(i) && signal[i]>window) window = signal[i]; if (!m_Parameters.IsBaselineIndex(i) && signal[i]SetNthOutput(0, outImage); m_StatusText += "\n\n"; m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); } template< class PixelType > itk::Point TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > itk::Vector TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector& vector) { vnl_vector_fixed vnlVector; vnlVector[0] = vector[0]; vnlVector[1] = vector[1]; vnlVector[2] = vector[2]; return vnlVector; } template< class PixelType > std::string TractsToDWIImageFilter< PixelType >::GetTime() { unsigned long total = (double)(clock() - m_StartTime)/CLOCKS_PER_SEC; unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); return out; } } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp index 9a348782d1..63f211e585 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,478 +1,478 @@ /*=================================================================== 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 #include #include #include #include #include #include #include template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::FiberfoxParameters() : m_Repetitions(1) , m_SignalScale(100) , m_tEcho(100) , m_tLine(1) , m_tInhom(50) , m_Bvalue(1000) , m_AxonRadius(0) , m_Spikes(0) , m_SpikeAmplitude(1) , m_KspaceLineOffset(0) , m_EddyStrength(0) , m_Tau(70) , m_CroppingFactor(1) , m_DoAddGibbsRinging(false) , m_DoSimulateRelaxation(true) , m_DoDisablePartialVolume(false) , m_DoAddMotion(false) , m_DoRandomizeMotion(true) , m_NoiseModel(NULL) , m_FrequencyMap(NULL) , m_MaskImage(NULL) , m_ResultNode(mitk::DataNode::New()) , m_ParentNode(NULL) , m_SignalModelString("") , m_ArtifactModelString("") , m_OutputPath("") , m_NumBaseline(1) , m_NumGradients(6) { m_ImageDirection.SetIdentity(); m_ImageOrigin.Fill(0.0); m_ImageRegion.SetSize(0, 11); m_ImageRegion.SetSize(1, 11); m_ImageRegion.SetSize(2, 3); m_ImageSpacing.Fill(2.0); m_Translation.Fill(0.0); m_Rotation.Fill(0.0); GenerateGradientHalfShell(); } template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::~FiberfoxParameters() { // if (m_NoiseModel!=NULL) // delete m_NoiseModel; } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::GenerateGradientHalfShell() { int NPoints = 2*m_NumGradients; m_GradientDirections.clear(); m_NumBaseline = NPoints/20; if (m_NumBaseline==0) m_NumBaseline=1; GradientType g; g.Fill(0.0); for (unsigned int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector< int > mitk::FiberfoxParameters< ScalarType >::GetBaselineIndices() { std::vector< int > result; for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) result.push_back(i); return result; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetFirstBaselineIndex() { for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) return i; return -1; } template< class ScalarType > bool mitk::FiberfoxParameters< ScalarType >::IsBaselineIndex(unsigned int idx) { if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001) return true; return false; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumWeightedVolumes() { return m_NumGradients; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumBaselineVolumes() { return m_NumBaseline; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumVolumes() { return m_GradientDirections.size(); } template< class ScalarType > typename mitk::FiberfoxParameters< ScalarType >::GradientListType mitk::FiberfoxParameters< ScalarType >::GetGradientDirections() { return m_GradientDirections; } template< class ScalarType > typename mitk::FiberfoxParameters< ScalarType >::GradientType mitk::FiberfoxParameters< ScalarType >::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SetNumWeightedGradients(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SetGradienDirections(GradientListType gradientList) { m_GradientDirections = gradientList; m_NumGradients = 0; m_NumBaseline = 0; for( unsigned int i=0; im_GradientDirections.size(); i++) { if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList) { m_NumGradients = 0; m_NumBaseline = 0; m_GradientDirections.clear(); for( unsigned int i=0; iSize(); i++) { GradientType g; g[0] = gradientList->at(i)[0]; g[1] = gradientList->at(i)[1]; g[2] = gradientList->at(i)[2]; m_GradientDirections.push_back(g); if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::LoadParameters(string filename) { boost::property_tree::ptree parameters; boost::property_tree::xml_parser::read_xml(filename, parameters); m_FiberModelList.clear(); m_NonFiberModelList.clear(); if (m_NoiseModel!=NULL) delete m_NoiseModel; BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") ) { if( v1.first == "image" ) { m_ImageRegion.SetSize(0, v1.second.get("basic.size.x")); m_ImageRegion.SetSize(1, v1.second.get("basic.size.y")); m_ImageRegion.SetSize(2, v1.second.get("basic.size.z")); m_ImageSpacing[0] = v1.second.get("basic.spacing.x"); m_ImageSpacing[1] = v1.second.get("basic.spacing.y"); m_ImageSpacing[2] = v1.second.get("basic.spacing.z"); m_NumGradients = v1.second.get("basic.numgradients"); GenerateGradientHalfShell(); m_Bvalue = v1.second.get("basic.bvalue"); m_Repetitions = v1.second.get("repetitions"); m_SignalScale = v1.second.get("signalScale"); m_tEcho = v1.second.get("tEcho"); m_tLine = v1.second.get("tLine"); m_tInhom = v1.second.get("tInhom"); m_AxonRadius = v1.second.get("axonRadius"); m_DoSimulateRelaxation = v1.second.get("doSimulateRelaxation"); m_DoDisablePartialVolume = v1.second.get("doDisablePartialVolume"); if (v1.second.get("artifacts.addnoise")) { switch (v1.second.get("artifacts.noisedistribution")) { case 0: { m_NoiseModel = new mitk::RicianNoiseModel< ScalarType >(); break; } case 1: { m_NoiseModel = new mitk::ChiSquareNoiseModel< ScalarType >(); break; } default: { m_NoiseModel = new mitk::RicianNoiseModel< ScalarType >(); } } m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); } - m_KspaceLineOffset = v1.second.get("artifacts.m_KspaceLineOffset"); + m_KspaceLineOffset = v1.second.get("artifacts.kspaceLineOffset"); m_CroppingFactor = (100-v1.second.get("artifacts.aliasingfactor"))/100; - m_Spikes = v1.second.get("artifacts.m_Spikesnum"); - m_SpikeAmplitude = v1.second.get("artifacts.m_Spikesscale"); - m_EddyStrength = v1.second.get("artifacts.m_EddyStrength"); + m_Spikes = v1.second.get("artifacts.spikesnum"); + m_SpikeAmplitude = v1.second.get("artifacts.spikesscale"); + m_EddyStrength = v1.second.get("artifacts.eddyStrength"); m_DoAddGibbsRinging = v1.second.get("artifacts.addringing"); - m_DoAddMotion = v1.second.get("artifacts.m_DoAddMotion"); - m_DoRandomizeMotion = v1.second.get("artifacts.m_RandomMotion"); - m_Translation[0] = v1.second.get("artifacts.m_Translation0"); - m_Translation[1] = v1.second.get("artifacts.m_Translation1"); - m_Translation[2] = v1.second.get("artifacts.m_Translation2"); - m_Rotation[0] = v1.second.get("artifacts.m_Rotation0"); - m_Rotation[1] = v1.second.get("artifacts.m_Rotation1"); - m_Rotation[2] = v1.second.get("artifacts.m_Rotation2"); + m_DoAddMotion = v1.second.get("artifacts.doAddMotion"); + m_DoRandomizeMotion = v1.second.get("artifacts.randomMotion"); + m_Translation[0] = v1.second.get("artifacts.translation0"); + m_Translation[1] = v1.second.get("artifacts.translation1"); + m_Translation[2] = v1.second.get("artifacts.translation2"); + m_Rotation[0] = v1.second.get("artifacts.rotation0"); + m_Rotation[1] = v1.second.get("artifacts.rotation1"); + m_Rotation[2] = v1.second.get("artifacts.rotation2"); // compartment 1 switch (v1.second.get("compartment1.index")) { case 0: { mitk::StickModel* stickModel = new mitk::StickModel(); stickModel->SetGradientList(m_GradientDirections); stickModel->SetBvalue(m_Bvalue); stickModel->SetDiffusivity(v1.second.get("compartment1.stick.d")); stickModel->SetT2(v1.second.get("compartment1.stick.t2")); m_FiberModelList.push_back(stickModel); break; } case 1: { mitk::TensorModel* zeppelinModel = new mitk::TensorModel(); zeppelinModel->SetGradientList(m_GradientDirections); zeppelinModel->SetBvalue(m_Bvalue); zeppelinModel->SetDiffusivity1(v1.second.get("compartment1.zeppelin.d1")); zeppelinModel->SetDiffusivity2(v1.second.get("compartment1.zeppelin.d2")); zeppelinModel->SetDiffusivity3(v1.second.get("compartment1.zeppelin.d2")); zeppelinModel->SetT2(v1.second.get("compartment1.zeppelin.t2")); m_FiberModelList.push_back(zeppelinModel); break; } case 2: { mitk::TensorModel* tensorModel = new mitk::TensorModel(); tensorModel->SetGradientList(m_GradientDirections); tensorModel->SetBvalue(m_Bvalue); tensorModel->SetDiffusivity1(v1.second.get("compartment1.tensor.d1")); tensorModel->SetDiffusivity2(v1.second.get("compartment1.tensor.d2")); tensorModel->SetDiffusivity3(v1.second.get("compartment1.tensor.d3")); tensorModel->SetT2(v1.second.get("compartment1.tensor.t2")); m_FiberModelList.push_back(tensorModel); break; } } // compartment 2 switch (v1.second.get("compartment2.index")) { case 0: { mitk::StickModel* stickModel = new mitk::StickModel(); stickModel->SetGradientList(m_GradientDirections); stickModel->SetBvalue(m_Bvalue); stickModel->SetDiffusivity(v1.second.get("compartment2.stick.d")); stickModel->SetT2(v1.second.get("compartment2.stick.t2")); m_FiberModelList.push_back(stickModel); break; } case 1: { mitk::TensorModel* zeppelinModel = new mitk::TensorModel(); zeppelinModel->SetGradientList(m_GradientDirections); zeppelinModel->SetBvalue(m_Bvalue); zeppelinModel->SetDiffusivity1(v1.second.get("compartment2.zeppelin.d1")); zeppelinModel->SetDiffusivity2(v1.second.get("compartment2.zeppelin.d2")); zeppelinModel->SetDiffusivity3(v1.second.get("compartment2.zeppelin.d2")); zeppelinModel->SetT2(v1.second.get("compartment2.zeppelin.t2")); m_FiberModelList.push_back(zeppelinModel); break; } case 2: { mitk::TensorModel* tensorModel = new mitk::TensorModel(); tensorModel->SetGradientList(m_GradientDirections); tensorModel->SetBvalue(m_Bvalue); tensorModel->SetDiffusivity1(v1.second.get("compartment2.tensor.d1")); tensorModel->SetDiffusivity2(v1.second.get("compartment2.tensor.d2")); tensorModel->SetDiffusivity3(v1.second.get("compartment2.tensor.d3")); tensorModel->SetT2(v1.second.get("compartment2.tensor.t2")); m_FiberModelList.push_back(tensorModel); break; } } // compartment 3 switch (v1.second.get("compartment3.index")) { case 0: { mitk::BallModel* ballModel = new mitk::BallModel(); ballModel->SetGradientList(m_GradientDirections); ballModel->SetBvalue(m_Bvalue); ballModel->SetDiffusivity(v1.second.get("compartment3.ball.d")); ballModel->SetT2(v1.second.get("compartment3.ball.t2")); ballModel->SetWeight(v1.second.get("compartment3.weight")); m_NonFiberModelList.push_back(ballModel); break; } case 1: { mitk::AstroStickModel* astrosticksModel = new mitk::AstroStickModel(); astrosticksModel->SetGradientList(m_GradientDirections); astrosticksModel->SetBvalue(m_Bvalue); astrosticksModel->SetDiffusivity(v1.second.get("compartment3.astrosticks.d")); astrosticksModel->SetT2(v1.second.get("compartment3.astrosticks.t2")); astrosticksModel->SetRandomizeSticks(v1.second.get("compartment3.astrosticks.randomize")); astrosticksModel->SetWeight(v1.second.get("compartment3.weight")); m_NonFiberModelList.push_back(astrosticksModel); break; } case 2: { mitk::DotModel* dotModel = new mitk::DotModel(); dotModel->SetGradientList(m_GradientDirections); dotModel->SetT2(v1.second.get("compartment3.dot.t2")); dotModel->SetWeight(v1.second.get("compartment3.weight")); m_NonFiberModelList.push_back(dotModel); break; } } // compartment 4 switch (v1.second.get("compartment4.index")) { case 0: { mitk::BallModel* ballModel = new mitk::BallModel(); ballModel->SetGradientList(m_GradientDirections); ballModel->SetBvalue(m_Bvalue); ballModel->SetDiffusivity(v1.second.get("compartment4.ball.d")); ballModel->SetT2(v1.second.get("compartment4.ball.t2")); ballModel->SetWeight(v1.second.get("compartment4.weight")); m_NonFiberModelList.push_back(ballModel); break; } case 1: { mitk::AstroStickModel* astrosticksModel = new mitk::AstroStickModel(); astrosticksModel->SetGradientList(m_GradientDirections); astrosticksModel->SetBvalue(m_Bvalue); astrosticksModel->SetDiffusivity(v1.second.get("compartment4.astrosticks.d")); astrosticksModel->SetT2(v1.second.get("compartment4.astrosticks.t2")); astrosticksModel->SetRandomizeSticks(v1.second.get("compartment4.astrosticks.randomize")); astrosticksModel->SetWeight(v1.second.get("compartment4.weight")); m_NonFiberModelList.push_back(astrosticksModel); break; } case 2: { mitk::DotModel* dotModel = new mitk::DotModel(); dotModel->SetGradientList(m_GradientDirections); dotModel->SetT2(v1.second.get("compartment4.dot.t2")); dotModel->SetWeight(v1.second.get("compartment4.weight")); m_NonFiberModelList.push_back(dotModel); break; } } } } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::PrintSelf() { MITK_INFO << "m_ImageRegion: " << m_ImageRegion; MITK_INFO << "m_ImageSpacing: " << m_ImageSpacing; MITK_INFO << "m_ImageOrigin: " << m_ImageOrigin; MITK_INFO << "m_ImageDirection: " << m_ImageDirection; MITK_INFO << "m_NumGradients: " << m_NumGradients; MITK_INFO << "m_Bvalue: " << m_Bvalue; MITK_INFO << "m_Repetitions: " << m_Repetitions; MITK_INFO << "m_SignalScale: " << m_SignalScale; MITK_INFO << "m_tEcho: " << m_tEcho; MITK_INFO << "m_tLine: " << m_tLine; MITK_INFO << "m_tInhom: " << m_tInhom; MITK_INFO << "m_AxonRadius: " << m_AxonRadius; MITK_INFO << "m_KspaceLineOffset: " << m_KspaceLineOffset; MITK_INFO << "m_AddGibbsRinging: " << m_DoAddGibbsRinging; MITK_INFO << "m_EddyStrength: " << m_EddyStrength; MITK_INFO << "m_Spikes: " << m_Spikes; MITK_INFO << "m_SpikeAmplitude: " << m_SpikeAmplitude; MITK_INFO << "m_CroppingFactor: " << m_CroppingFactor; MITK_INFO << "m_DoSimulateRelaxation: " << m_DoSimulateRelaxation; MITK_INFO << "m_DoDisablePartialVolume: " << m_DoDisablePartialVolume; MITK_INFO << "m_DoAddMotion: " << m_DoAddMotion; MITK_INFO << "m_RandomMotion: " << m_DoRandomizeMotion; MITK_INFO << "m_Translation: " << m_Translation; MITK_INFO << "m_Rotation: " << m_Rotation; MITK_INFO << "m_SignalModelString: " << m_SignalModelString; MITK_INFO << "m_ArtifactModelString: " << m_ArtifactModelString; MITK_INFO << "m_OutputPath: " << m_OutputPath; } diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp index 15175d0a6e..8f8cd06696 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp @@ -1,191 +1,191 @@ /*=================================================================== 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 #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /**Documentation * Test the Fiberfox simulation functions (diffusion weighted image -> diffusion weighted image) */ class mitkFiberfoxAddArtifactsToDwiTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkFiberfoxAddArtifactsToDwiTestSuite); MITK_TEST(Spikes); MITK_TEST(GibbsRinging); MITK_TEST(Ghost); MITK_TEST(Aliasing); MITK_TEST(Eddy); MITK_TEST(RicianNoise); MITK_TEST(ChiSquareNoise); MITK_TEST(Distortions); CPPUNIT_TEST_SUITE_END(); private: mitk::DiffusionImage::Pointer m_InputDwi; FiberfoxParameters m_Parameters; public: void setUp() { // reference files m_InputDwi = dynamic_cast*>(mitk::IOUtil::LoadDataNode(GetTestDataFilePath("DiffusionImaging/Fiberfox/StickBall_RELAX.dwi"))->GetData()); // parameter setup m_Parameters = FiberfoxParameters(); m_Parameters.m_ImageRegion = m_InputDwi->GetVectorImage()->GetLargestPossibleRegion(); m_Parameters.m_ImageSpacing = m_InputDwi->GetVectorImage()->GetSpacing(); m_Parameters.m_ImageOrigin = m_InputDwi->GetVectorImage()->GetOrigin(); m_Parameters.m_ImageDirection = m_InputDwi->GetVectorImage()->GetDirection(); m_Parameters.m_Bvalue = m_InputDwi->GetB_Value(); m_Parameters.SetGradienDirections(m_InputDwi->GetDirections()); } bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2) { typedef itk::VectorImage< short, 3 > DwiImageType; try{ itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion()); while(!it1.IsAtEnd()) { if (it1.Get()!=it2.Get()) return false; ++it1; ++it2; } } catch(...) { return false; } return true; } void StartSimulation(string testFileName) { mitk::DiffusionImage::Pointer refImage = NULL; if (!testFileName.empty()) CPPUNIT_ASSERT(refImage = dynamic_cast*>(mitk::IOUtil::LoadDataNode(testFileName)->GetData())); itk::AddArtifactsToDwiImageFilter< short >::Pointer artifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); artifactsToDwiFilter->SetUseConstantRandSeed(true); artifactsToDwiFilter->SetInput(m_InputDwi->GetVectorImage()); artifactsToDwiFilter->SetParameters(m_Parameters); CPPUNIT_ASSERT_NO_THROW(artifactsToDwiFilter->Update()); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( artifactsToDwiFilter->GetOutput() ); testImage->SetB_Value(m_Parameters.m_Bvalue); testImage->SetDirections(m_Parameters.GetGradientDirections()); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { bool ok = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()); if (!ok) { mitk::IOUtil::SaveBaseData(testImage, "/tmp/test2.dwi"); mitk::IOUtil::SaveBaseData(refImage, "/tmp/ref2.dwi"); } CPPUNIT_ASSERT_MESSAGE(testFileName, ok); } else { mitk::IOUtil::SaveBaseData(testImage, "/local/distortions2.dwi"); } } void Spikes() { m_Parameters.m_Spikes = 5; m_Parameters.m_SpikeAmplitude = 1; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/spikes2.dwi") ); } void GibbsRinging() { m_Parameters.m_DoAddGibbsRinging = true; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/gibbsringing2.dwi") ); } void Ghost() { m_Parameters.m_KspaceLineOffset = 0.25; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/ghost2.dwi") ); } void Aliasing() { m_Parameters.m_CroppingFactor = 0.4; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/aliasing2.dwi") ); } void Eddy() { m_Parameters.m_EddyStrength = 0.05; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/eddy2.dwi") ); } void RicianNoise() { mitk::RicianNoiseModel* ricianNoiseModel = new mitk::RicianNoiseModel(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); m_Parameters.m_NoiseModel = ricianNoiseModel; -// StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/riciannoise2.dwi") ); + StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/riciannoise2.dwi") ); delete m_Parameters.m_NoiseModel; } void ChiSquareNoise() { mitk::ChiSquareNoiseModel* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); chiSquareNoiseModel->SetNoiseVariance(1000000); chiSquareNoiseModel->SetSeed(0); m_Parameters.m_NoiseModel = chiSquareNoiseModel; -// StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/chisquarenoise2.dwi") ); + StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/chisquarenoise2.dwi") ); delete m_Parameters.m_NoiseModel; } void Distortions() { mitk::Image::Pointer mitkFMap = dynamic_cast(mitk::IOUtil::LoadDataNode( GetTestDataFilePath("DiffusionImaging/Fiberfox/Fieldmap.nrrd") )->GetData()); typedef itk::Image ItkDoubleImgType; ItkDoubleImgType::Pointer fMap = ItkDoubleImgType::New(); mitk::CastToItkImage(mitkFMap, fMap); m_Parameters.m_FrequencyMap = fMap; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/distortions2.dwi") ); } }; MITK_TEST_SUITE_REGISTRATION(mitkFiberfoxAddArtifactsToDwi) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox index 4bd210e205..4b783adc26 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox @@ -1,44 +1,44 @@ /** \page org_mitk_views_gibbstracking Gibbs Tracking View This view provides the user interface for the Gibbs Tracking algorithm, a global fiber tracking algorithm, originally proposed by Reisert et.al. [1]. Available sections: - \ref QmitkGibbsTrackingUserManualInputData - \ref QmitkGibbsTrackingUserManualParameters - \ref QmitkGibbsTrackingUserManualTrackingSurveillance - \ref QmitkGibbsTrackingUserManualReferences \image html gibbstrackingview.png The Gibbs Tracking View \section QmitkGibbsTrackingUserManualInputData Input Data Mandatory Input: \li One Q-Ball or tensor image selected in the datamanager Optional Input: -\li Mask Image: Float image used as probability mask for the generation of fiber segments. Usually used as binary brain mask to reduce the searchspace of the algorithm and to avoid fibers resulting from noise outside of the brain. +\li Mask Image: White matter probability mask. Corresponds to the probability to generate fiber segments in the respective voxel. \section QmitkGibbsTrackingUserManualParameters Q-Ball Reconstruction \li Number of iterations: More iterations causes the algorithm to be more stable but also to take longer to finish the tracking. Rcommended: 10⁷-10⁹ iterations. \li Particle length/width/weight controlling the contribution of each particle to the model M \li Start and end temperature controlling how fast the process reaches a stable state. (usually no change needed) \li Weighting between the internal (affinity of the model to long and straigt fibers) and external energy (affinity of the model towards the data). (usually no change needed). \li Minimum fiber length constraint (in mm). Shorter fibers are discarded after the tracking. The automatic selection of parameters for the particle length/width and weight are determined directly from the input image using information about the image spacing and GFA. \image html gibbstrackingviewadvanced.png Advanced Tracking Parameters \section QmitkGibbsTrackingUserManualTrackingSurveillance Surveilance of the tracking process Once started, the tracking can be monitored via the textual output that informs about the tracking progress and several stats of the current state of the algorithm. If enabled, the intermediate tracking results are displayed in the renderwindows each second. This live visualization should usually be disabled for performance reasons. It can be turned on and off during the tracking process via the according checkbox. The button next to this checkbox allows the visualization of only the next iteration step. \section QmitkGibbsTrackingUserManualReferences References [1] Reisert, M., Mader, I., Anastasopoulos, C., Weigel, M., Schnell, S., Kiselev, V.: Global fiber reconstruction becomes practical. Neuroimage 54 (2011) 955-962 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp index a12d1718da..958df7daeb 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2223 +1,2226 @@ /*=================================================================== 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. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "usModuleRegistry.h" #include #include #include +#include #define _USE_MATH_DEFINES #include QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ switch (m_FilterType) { case 0: m_View->m_TractsToDwiFilter->Update(); break; case 1: m_View->m_ArtifactsToDwiFilter->Update(); break; } } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) , m_OutputPath("") , m_Worker(this) , m_ThreadIsRunning(false) { m_Worker.moveToThread(&m_Thread); connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run())); connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread())); connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_SimulationTimer = new QTimer(this); } void QmitkFiberfoxView::KillThread() { MITK_INFO << "Aborting DWI simulation."; switch (m_Worker.m_FilterType) { case 0: m_TractsToDwiFilter->SetAbortGenerateData(true); break; case 1: m_ArtifactsToDwiFilter->SetAbortGenerateData(true); break; } } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_Controls->m_AbortSimulationButton->setVisible(true); m_Controls->m_GenerateImageButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(true); m_ThreadIsRunning = true; } void QmitkFiberfoxView::AfterThread() { UpdateSimulationStatus(); m_SimulationTimer->stop(); m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_GenerateImageButton->setVisible(true); //m_Controls->m_SimulationStatusText->setVisible(false); m_ThreadIsRunning = false; FiberfoxParameters parameters; mitk::DiffusionImage::Pointer mitkImage = mitk::DiffusionImage::New(); switch (m_Worker.m_FilterType) { case 0: { if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage->SetVectorImage( m_TractsToDwiFilter->GetOutput() ); mitkImage->SetB_Value(parameters.m_Bvalue); mitkImage->SetDirections(parameters.GetGradientDirections()); mitkImage->InitializeFromVectorImage(); parameters.m_ResultNode->SetData( mitkImage ); parameters.m_ResultNode->SetName(parameters.m_ParentNode->GetName() +"_D"+QString::number(parameters.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(parameters.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(parameters.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(parameters.m_ImageSpacing[0]).toStdString() +"-"+QString::number(parameters.m_ImageSpacing[1]).toStdString() +"-"+QString::number(parameters.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(parameters.m_Bvalue).toStdString() +"_"+parameters.m_SignalModelString +parameters.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); parameters.m_ResultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(parameters.m_ParentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, parameters.m_ParentNode); } } m_TractsToDwiFilter = NULL; break; } case 1: { if (m_ArtifactsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_ArtifactsToDwiFilter->GetParameters().CopyParameters(); mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(parameters.m_ParentNode->GetData()); mitkImage = mitk::DiffusionImage::New(); mitkImage->SetVectorImage( m_ArtifactsToDwiFilter->GetOutput() ); mitkImage->SetB_Value(diffImg->GetB_Value()); mitkImage->SetDirections(diffImg->GetDirections()); mitkImage->InitializeFromVectorImage(); parameters.m_ResultNode->SetData( mitkImage ); parameters.m_ResultNode->SetName(parameters.m_ParentNode->GetName()+parameters.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); m_ArtifactsToDwiFilter = NULL; break; } } mitk::BaseData::Pointer basedata = parameters.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!parameters.m_OutputPath.empty()) { try{ QString status("Saving output image to "); status += QString(parameters.m_OutputPath.c_str()); status += parameters.m_ResultNode->GetName().c_str(); status += ".dwi"; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::SaveBaseData(mitkImage, parameters.m_OutputPath+parameters.m_ResultNode->GetName()+".dwi"); m_Controls->m_SimulationStatusText->append("File saved successfully."); } catch (itk::ExceptionObject &e) { QString status("Exception during DWI writing: "); status += e.GetDescription(); m_Controls->m_SimulationStatusText->append(status); } catch (...) { m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!"); } } parameters.m_FrequencyMap = NULL; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText; switch (m_Worker.m_FilterType) { case 0: statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); break; case 1: statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); break; } if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); statusText = "
"+statusText+"
"; m_Controls->m_SimulationStatusText->setText(statusText); + QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar(); + vScrollBar->triggerAction(QScrollBar::SliderToMaximum); } } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { delete m_SimulationTimer; } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_SpikeFrame->setVisible(false); m_Controls->m_AliasingFrame->setVisible(false); m_Controls->m_MotionArtifactFrame->setVisible(false); m_ParameterFile = QDir::currentPath()+"/param.ffp"; m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate); connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) ); connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread())); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnFiberSamplingChanged(double))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int))); connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int))); connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int))); connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters())); connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters())); connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath())); } } template< class ScalarType > FiberfoxParameters< ScalarType > QmitkFiberfoxView::UpdateImageParameters() { FiberfoxParameters< ScalarType > parameters; parameters.m_OutputPath = m_OutputPath; parameters.m_MaskImage = m_ItkMaskImage; if (m_SelectedDWI.IsNotNull()) // use parameters of selected DWI { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); parameters.m_ImageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); parameters.m_ImageSpacing = dwi->GetVectorImage()->GetSpacing(); parameters.m_ImageOrigin = dwi->GetVectorImage()->GetOrigin(); parameters.m_ImageDirection = dwi->GetVectorImage()->GetDirection(); parameters.m_Bvalue = dwi->GetB_Value(); parameters.SetGradienDirections(dwi->GetDirections()); } else if (m_SelectedImage.IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_SelectedImage->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); parameters.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_ImageDirection = itkImg->GetDirection(); parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); parameters.m_Bvalue = m_Controls->m_BvalueBox->value(); } else // use GUI parameters { parameters.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); parameters.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); parameters.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); parameters.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); parameters.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); parameters.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); parameters.m_ImageOrigin[0] = parameters.m_ImageSpacing[0]/2; parameters.m_ImageOrigin[1] = parameters.m_ImageSpacing[1]/2; parameters.m_ImageOrigin[2] = parameters.m_ImageSpacing[2]/2; parameters.m_ImageDirection.SetIdentity(); parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); parameters.m_Bvalue = m_Controls->m_BvalueBox->value(); parameters.GenerateGradientHalfShell(); } // signal relaxation parameters.m_DoSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked(); if (parameters.m_DoSimulateRelaxation && m_SelectedBundles.size()>0 ) parameters.m_ArtifactModelString += "_RELAX"; // N/2 ghosts if (m_Controls->m_AddGhosts->isChecked()) { parameters.m_ArtifactModelString += "_GHOST"; parameters.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); parameters.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(parameters.m_KspaceLineOffset)); } else parameters.m_KspaceLineOffset = 0; // Aliasing if (m_Controls->m_AddAliasing->isChecked()) { parameters.m_ArtifactModelString += "_ALIASING"; parameters.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; parameters.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Motion parameters.m_DoAddMotion = m_Controls->m_AddMotion->isChecked(); parameters.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); parameters.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); parameters.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); parameters.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); parameters.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); parameters.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); parameters.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); if ( m_Controls->m_AddMotion->isChecked() && m_SelectedBundles.size()>0 ) { parameters.m_ArtifactModelString += "_MOTION"; parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(parameters.m_DoRandomizeMotion)); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(parameters.m_Translation[0])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(parameters.m_Translation[1])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(parameters.m_Translation[2])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(parameters.m_Rotation[0])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(parameters.m_Rotation[1])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(parameters.m_Rotation[2])); } // other imaging parameters parameters.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); parameters.m_tInhom = m_Controls->m_T2starBox->value(); parameters.m_tEcho = m_Controls->m_TEbox->value(); parameters.m_Repetitions = m_Controls->m_RepetitionsBox->value(); parameters.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); parameters.m_AxonRadius = m_Controls->m_FiberRadius->value(); parameters.m_SignalScale = m_Controls->m_SignalScaleBox->value(); if (m_Controls->m_AddSpikes->isChecked()) { parameters.m_Spikes = m_Controls->m_SpikeNumBox->value(); parameters.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); parameters.m_ArtifactModelString += "_SPIKES"; parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(parameters.m_Spikes)); parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(parameters.m_SpikeAmplitude)); } // adjust echo time if needed if ( parameters.m_tEcho < parameters.m_ImageRegion.GetSize(1)*parameters.m_tLine ) { this->m_Controls->m_TEbox->setValue( parameters.m_ImageRegion.GetSize(1)*parameters.m_tLine ); parameters.m_tEcho = m_Controls->m_TEbox->value(); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(parameters.m_tEcho)+" ms"); } // rician noise if (m_Controls->m_AddNoise->isChecked()) { double noiseVariance = m_Controls->m_NoiseLevel->value(); { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_ArtifactModelString += "_RICIAN-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); break; } case 1: { parameters.m_NoiseModel = new mitk::ChiSquareNoiseModel(); parameters.m_ArtifactModelString += "_CHISQUARED-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); break; } default: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_ArtifactModelString += "_RICIAN-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); } } } parameters.m_NoiseModel->SetNoiseVariance(noiseVariance); parameters.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } // gibbs ringing parameters.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); if (m_Controls->m_AddGibbsRinging->isChecked()) { parameters.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); parameters.m_ArtifactModelString += "_RINGING"; } // adjusting line readout time to the adapted image size needed for the DFT unsigned int y = parameters.m_ImageRegion.GetSize(1); y += y%2; if ( y>parameters.m_ImageRegion.GetSize(1) ) parameters.m_tLine *= (double)parameters.m_ImageRegion.GetSize(1)/y; // add distortions if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); CastToItkImage< ItkDoubleImgType >(img, itkImg); if (parameters.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && parameters.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && parameters.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { parameters.m_FrequencyMap = itkImg; parameters.m_ArtifactModelString += "_DISTORTED"; parameters.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } } parameters.m_EddyStrength = 0; if (m_Controls->m_AddEddy->isChecked()) { parameters.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); parameters.m_ArtifactModelString += "_EDDY"; parameters.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(parameters.m_EddyStrength)); } // signal models double m_Comp3Weight = 1; double m_Comp4Weight = 0; if (m_Controls->m_Compartment4Box->currentIndex()>0) { m_Comp4Weight = m_Controls->m_Comp4FractionBox->value(); m_Comp3Weight -= m_Comp4Weight; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.weight", DoubleProperty::New(m_Comp3Weight)); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.weight", DoubleProperty::New(m_Comp4Weight)); } // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: m_StickModel1.SetGradientList(parameters.GetGradientDirections()); m_StickModel1.SetBvalue(parameters.m_Bvalue); m_StickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); m_StickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_StickModel1); parameters.m_SignalModelString += "Stick"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_StickModel1.GetT2()) ); break; case 1: m_ZeppelinModel1.SetGradientList(parameters.GetGradientDirections()); m_ZeppelinModel1.SetBvalue(parameters.m_Bvalue); m_ZeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); m_ZeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); m_ZeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); m_ZeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_ZeppelinModel1); parameters.m_SignalModelString += "Zeppelin"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); break; case 2: m_TensorModel1.SetGradientList(parameters.GetGradientDirections()); m_TensorModel1.SetBvalue(parameters.m_Bvalue); m_TensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); m_TensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); m_TensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); m_TensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_TensorModel1); parameters.m_SignalModelString += "Tensor"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); break; } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: m_StickModel2.SetGradientList(parameters.GetGradientDirections()); m_StickModel2.SetBvalue(parameters.m_Bvalue); m_StickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); m_StickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_StickModel2); parameters.m_SignalModelString += "Stick"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_StickModel2.GetT2()) ); break; case 2: m_ZeppelinModel2.SetGradientList(parameters.GetGradientDirections()); m_ZeppelinModel2.SetBvalue(parameters.m_Bvalue); m_ZeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); m_ZeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); m_ZeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); m_ZeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_ZeppelinModel2); parameters.m_SignalModelString += "Zeppelin"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); break; case 3: m_TensorModel2.SetGradientList(parameters.GetGradientDirections()); m_TensorModel2.SetBvalue(parameters.m_Bvalue); m_TensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); m_TensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); m_TensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); m_TensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_TensorModel2); parameters.m_SignalModelString += "Tensor"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); break; } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: m_BallModel1.SetGradientList(parameters.GetGradientDirections()); m_BallModel1.SetBvalue(parameters.m_Bvalue); m_BallModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); m_BallModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); m_BallModel1.SetWeight(m_Comp3Weight); parameters.m_NonFiberModelList.push_back(&m_BallModel1); parameters.m_SignalModelString += "Ball"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_BallModel1.GetT2()) ); break; case 1: m_AstrosticksModel1.SetGradientList(parameters.GetGradientDirections()); m_AstrosticksModel1.SetBvalue(parameters.m_Bvalue); m_AstrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); m_AstrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); m_AstrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); m_AstrosticksModel1.SetWeight(m_Comp3Weight); parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel1); parameters.m_SignalModelString += "Astrosticks"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_AstrosticksModel1.GetT2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; case 2: m_DotModel1.SetGradientList(parameters.GetGradientDirections()); m_DotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); m_DotModel1.SetWeight(m_Comp3Weight); parameters.m_NonFiberModelList.push_back(&m_DotModel1); parameters.m_SignalModelString += "Dot"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_DotModel1.GetT2()) ); break; } // compartment 4 switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: m_BallModel2.SetGradientList(parameters.GetGradientDirections()); m_BallModel2.SetBvalue(parameters.m_Bvalue); m_BallModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); m_BallModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); m_BallModel2.SetWeight(m_Comp4Weight); parameters.m_NonFiberModelList.push_back(&m_BallModel2); parameters.m_SignalModelString += "Ball"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_BallModel2.GetT2()) ); break; case 2: m_AstrosticksModel2.SetGradientList(parameters.GetGradientDirections()); m_AstrosticksModel2.SetBvalue(parameters.m_Bvalue); m_AstrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); m_AstrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); m_AstrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); m_AstrosticksModel2.SetWeight(m_Comp4Weight); parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel2); parameters.m_SignalModelString += "Astrosticks"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_AstrosticksModel2.GetT2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; case 3: m_DotModel2.SetGradientList(parameters.GetGradientDirections()); m_DotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); m_DotModel2.SetWeight(m_Comp4Weight); parameters.m_NonFiberModelList.push_back(&m_DotModel2); parameters.m_SignalModelString += "Dot"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_DotModel2.GetT2()) ); break; } parameters.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(parameters.m_SignalScale)); parameters.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(parameters.m_AxonRadius)); parameters.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(parameters.m_tInhom)); parameters.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(parameters.m_tLine)); parameters.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(parameters.m_tEcho)); parameters.m_ResultNode->AddProperty("Fiberfox.Repetitions", IntProperty::New(parameters.m_Repetitions)); parameters.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(parameters.m_Bvalue)); parameters.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(parameters.m_DoDisablePartialVolume)); parameters.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(parameters.m_DoSimulateRelaxation)); parameters.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); return parameters; } void QmitkFiberfoxView::SaveParameters() { FiberfoxParameters ffParamaters = UpdateImageParameters(); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; if(!filename.endsWith(".ffp")) filename += ".ffp"; m_ParameterFile = filename; boost::property_tree::ptree parameters; // fiber generation parameters parameters.put("fiberfox.fibers.realtime", m_Controls->m_RealTimeFibers->isChecked()); parameters.put("fiberfox.fibers.showadvanced", m_Controls->m_AdvancedOptionsBox->isChecked()); parameters.put("fiberfox.fibers.distribution", m_Controls->m_DistributionBox->currentIndex()); parameters.put("fiberfox.fibers.variance", m_Controls->m_VarianceBox->value()); parameters.put("fiberfox.fibers.density", m_Controls->m_FiberDensityBox->value()); parameters.put("fiberfox.fibers.spline.sampling", m_Controls->m_FiberSamplingBox->value()); parameters.put("fiberfox.fibers.spline.tension", m_Controls->m_TensionBox->value()); parameters.put("fiberfox.fibers.spline.continuity", m_Controls->m_ContinuityBox->value()); parameters.put("fiberfox.fibers.spline.bias", m_Controls->m_BiasBox->value()); parameters.put("fiberfox.fibers.constantradius", m_Controls->m_ConstantRadiusBox->isChecked()); - parameters.put("fiberfox.fibers.m_Rotation.x", m_Controls->m_XrotBox->value()); - parameters.put("fiberfox.fibers.m_Rotation.y", m_Controls->m_YrotBox->value()); - parameters.put("fiberfox.fibers.m_Rotation.z", m_Controls->m_ZrotBox->value()); - parameters.put("fiberfox.fibers.m_Translation.x", m_Controls->m_XtransBox->value()); - parameters.put("fiberfox.fibers.m_Translation.y", m_Controls->m_YtransBox->value()); - parameters.put("fiberfox.fibers.m_Translation.z", m_Controls->m_ZtransBox->value()); + parameters.put("fiberfox.fibers.rotation.x", m_Controls->m_XrotBox->value()); + parameters.put("fiberfox.fibers.rotation.y", m_Controls->m_YrotBox->value()); + parameters.put("fiberfox.fibers.rotation.z", m_Controls->m_ZrotBox->value()); + parameters.put("fiberfox.fibers.translation.x", m_Controls->m_XtransBox->value()); + parameters.put("fiberfox.fibers.translation.y", m_Controls->m_YtransBox->value()); + parameters.put("fiberfox.fibers.translation.z", m_Controls->m_ZtransBox->value()); parameters.put("fiberfox.fibers.scale.x", m_Controls->m_XscaleBox->value()); parameters.put("fiberfox.fibers.scale.y", m_Controls->m_YscaleBox->value()); parameters.put("fiberfox.fibers.scale.z", m_Controls->m_ZscaleBox->value()); parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked()); parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked()); // image generation parameters parameters.put("fiberfox.image.basic.size.x", ffParamaters.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", ffParamaters.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", ffParamaters.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", ffParamaters.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", ffParamaters.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", ffParamaters.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.numgradients", ffParamaters.GetNumWeightedVolumes()); parameters.put("fiberfox.image.basic.bvalue", ffParamaters.m_Bvalue); parameters.put("fiberfox.image.showadvanced", m_Controls->m_AdvancedOptionsBox_2->isChecked()); parameters.put("fiberfox.image.repetitions", ffParamaters.m_Repetitions); parameters.put("fiberfox.image.signalScale", ffParamaters.m_SignalScale); parameters.put("fiberfox.image.tEcho", ffParamaters.m_tEcho); parameters.put("fiberfox.image.tLine", m_Controls->m_LineReadoutTimeBox->value()); parameters.put("fiberfox.image.tInhom", ffParamaters.m_tInhom); parameters.put("fiberfox.image.axonRadius", ffParamaters.m_AxonRadius); parameters.put("fiberfox.image.doSimulateRelaxation", ffParamaters.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", ffParamaters.m_DoDisablePartialVolume); parameters.put("fiberfox.image.outputvolumefractions", m_Controls->m_VolumeFractionsBox->isChecked()); parameters.put("fiberfox.image.artifacts.addnoise", m_Controls->m_AddNoise->isChecked()); parameters.put("fiberfox.image.artifacts.noisedistribution", m_Controls->m_NoiseDistributionBox->currentIndex()); parameters.put("fiberfox.image.artifacts.noisevariance", m_Controls->m_NoiseLevel->value()); parameters.put("fiberfox.image.artifacts.addghost", m_Controls->m_AddGhosts->isChecked()); - parameters.put("fiberfox.image.artifacts.m_KspaceLineOffset", m_Controls->m_kOffsetBox->value()); + parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_Controls->m_kOffsetBox->value()); parameters.put("fiberfox.image.artifacts.distortions", m_Controls->m_AddDistortions->isChecked()); parameters.put("fiberfox.image.artifacts.addeddy", m_Controls->m_AddEddy->isChecked()); - parameters.put("fiberfox.image.artifacts.m_EddyStrength", m_Controls->m_EddyGradientStrength->value()); + parameters.put("fiberfox.image.artifacts.eddyStrength", m_Controls->m_EddyGradientStrength->value()); parameters.put("fiberfox.image.artifacts.addringing", m_Controls->m_AddGibbsRinging->isChecked()); parameters.put("fiberfox.image.artifacts.addspikes", m_Controls->m_AddSpikes->isChecked()); - parameters.put("fiberfox.image.artifacts.m_Spikesnum", m_Controls->m_SpikeNumBox->value()); - parameters.put("fiberfox.image.artifacts.m_Spikesscale", m_Controls->m_SpikeScaleBox->value()); + parameters.put("fiberfox.image.artifacts.spikesnum", m_Controls->m_SpikeNumBox->value()); + parameters.put("fiberfox.image.artifacts.spikesscale", m_Controls->m_SpikeScaleBox->value()); parameters.put("fiberfox.image.artifacts.addaliasing", m_Controls->m_AddAliasing->isChecked()); parameters.put("fiberfox.image.artifacts.aliasingfactor", m_Controls->m_WrapBox->value()); - parameters.put("fiberfox.image.artifacts.m_DoAddMotion", m_Controls->m_AddMotion->isChecked()); - parameters.put("fiberfox.image.artifacts.m_RandomMotion", m_Controls->m_RandomMotion->isChecked()); - parameters.put("fiberfox.image.artifacts.m_Translation0", m_Controls->m_MaxTranslationBoxX->value()); - parameters.put("fiberfox.image.artifacts.m_Translation1", m_Controls->m_MaxTranslationBoxY->value()); - parameters.put("fiberfox.image.artifacts.m_Translation2", m_Controls->m_MaxTranslationBoxZ->value()); - parameters.put("fiberfox.image.artifacts.m_Rotation0", m_Controls->m_MaxRotationBoxX->value()); - parameters.put("fiberfox.image.artifacts.m_Rotation1", m_Controls->m_MaxRotationBoxY->value()); - parameters.put("fiberfox.image.artifacts.m_Rotation2", m_Controls->m_MaxRotationBoxZ->value()); + parameters.put("fiberfox.image.artifacts.doAddMotion", m_Controls->m_AddMotion->isChecked()); + parameters.put("fiberfox.image.artifacts.randomMotion", m_Controls->m_RandomMotion->isChecked()); + parameters.put("fiberfox.image.artifacts.translation0", m_Controls->m_MaxTranslationBoxX->value()); + parameters.put("fiberfox.image.artifacts.translation1", m_Controls->m_MaxTranslationBoxY->value()); + parameters.put("fiberfox.image.artifacts.translation2", m_Controls->m_MaxTranslationBoxZ->value()); + parameters.put("fiberfox.image.artifacts.rotation0", m_Controls->m_MaxRotationBoxX->value()); + parameters.put("fiberfox.image.artifacts.rotation1", m_Controls->m_MaxRotationBoxY->value()); + parameters.put("fiberfox.image.artifacts.rotation2", m_Controls->m_MaxRotationBoxZ->value()); parameters.put("fiberfox.image.compartment1.index", m_Controls->m_Compartment1Box->currentIndex()); parameters.put("fiberfox.image.compartment2.index", m_Controls->m_Compartment2Box->currentIndex()); parameters.put("fiberfox.image.compartment3.index", m_Controls->m_Compartment3Box->currentIndex()); parameters.put("fiberfox.image.compartment4.index", m_Controls->m_Compartment4Box->currentIndex()); parameters.put("fiberfox.image.compartment1.stick.d", m_Controls->m_StickWidget1->GetD()); parameters.put("fiberfox.image.compartment1.stick.t2", m_Controls->m_StickWidget1->GetT2()); parameters.put("fiberfox.image.compartment1.zeppelin.d1", m_Controls->m_ZeppelinWidget1->GetD1()); parameters.put("fiberfox.image.compartment1.zeppelin.d2", m_Controls->m_ZeppelinWidget1->GetD2()); parameters.put("fiberfox.image.compartment1.zeppelin.t2", m_Controls->m_ZeppelinWidget1->GetT2()); parameters.put("fiberfox.image.compartment1.tensor.d1", m_Controls->m_TensorWidget1->GetD1()); parameters.put("fiberfox.image.compartment1.tensor.d2", m_Controls->m_TensorWidget1->GetD2()); parameters.put("fiberfox.image.compartment1.tensor.d3", m_Controls->m_TensorWidget1->GetD3()); parameters.put("fiberfox.image.compartment1.tensor.t2", m_Controls->m_TensorWidget1->GetT2()); parameters.put("fiberfox.image.compartment2.stick.d", m_Controls->m_StickWidget2->GetD()); parameters.put("fiberfox.image.compartment2.stick.t2", m_Controls->m_StickWidget2->GetT2()); parameters.put("fiberfox.image.compartment2.zeppelin.d1", m_Controls->m_ZeppelinWidget2->GetD1()); parameters.put("fiberfox.image.compartment2.zeppelin.d2", m_Controls->m_ZeppelinWidget2->GetD2()); parameters.put("fiberfox.image.compartment2.zeppelin.t2", m_Controls->m_ZeppelinWidget2->GetT2()); parameters.put("fiberfox.image.compartment2.tensor.d1", m_Controls->m_TensorWidget2->GetD1()); parameters.put("fiberfox.image.compartment2.tensor.d2", m_Controls->m_TensorWidget2->GetD2()); parameters.put("fiberfox.image.compartment2.tensor.d3", m_Controls->m_TensorWidget2->GetD3()); parameters.put("fiberfox.image.compartment2.tensor.t2", m_Controls->m_TensorWidget2->GetT2()); parameters.put("fiberfox.image.compartment3.ball.d", m_Controls->m_BallWidget1->GetD()); parameters.put("fiberfox.image.compartment3.ball.t2", m_Controls->m_BallWidget1->GetT2()); parameters.put("fiberfox.image.compartment3.astrosticks.d", m_Controls->m_AstrosticksWidget1->GetD()); parameters.put("fiberfox.image.compartment3.astrosticks.t2", m_Controls->m_AstrosticksWidget1->GetT2()); parameters.put("fiberfox.image.compartment3.astrosticks.randomize", m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); parameters.put("fiberfox.image.compartment3.dot.t2", m_Controls->m_DotWidget1->GetT2()); parameters.put("fiberfox.image.compartment4.ball.d", m_Controls->m_BallWidget2->GetD()); parameters.put("fiberfox.image.compartment4.ball.t2", m_Controls->m_BallWidget2->GetT2()); parameters.put("fiberfox.image.compartment4.astrosticks.d", m_Controls->m_AstrosticksWidget2->GetD()); parameters.put("fiberfox.image.compartment4.astrosticks.t2", m_Controls->m_AstrosticksWidget2->GetT2()); parameters.put("fiberfox.image.compartment4.astrosticks.randomize", m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); parameters.put("fiberfox.image.compartment4.dot.t2", m_Controls->m_DotWidget2->GetT2()); parameters.put("fiberfox.image.compartment4.weight", m_Controls->m_Comp4FractionBox->value()); boost::property_tree::xml_parser::write_xml(filename.toStdString(), parameters); } void QmitkFiberfoxView::LoadParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; boost::property_tree::ptree parameters; boost::property_tree::xml_parser::read_xml(filename.toStdString(), parameters); BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") ) { if( v1.first == "fibers" ) { m_Controls->m_RealTimeFibers->setChecked(v1.second.get("realtime")); m_Controls->m_AdvancedOptionsBox->setChecked(v1.second.get("showadvanced")); m_Controls->m_DistributionBox->setCurrentIndex(v1.second.get("distribution")); m_Controls->m_VarianceBox->setValue(v1.second.get("variance")); m_Controls->m_FiberDensityBox->setValue(v1.second.get("density")); m_Controls->m_IncludeFiducials->setChecked(v1.second.get("includeFiducials")); m_Controls->m_ConstantRadiusBox->setChecked(v1.second.get("constantradius")); BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second ) { if( v2.first == "spline" ) { m_Controls->m_FiberSamplingBox->setValue(v2.second.get("sampling")); m_Controls->m_TensionBox->setValue(v2.second.get("tension")); m_Controls->m_ContinuityBox->setValue(v2.second.get("continuity")); m_Controls->m_BiasBox->setValue(v2.second.get("bias")); } if( v2.first == "rotation" ) { m_Controls->m_XrotBox->setValue(v2.second.get("x")); m_Controls->m_YrotBox->setValue(v2.second.get("y")); m_Controls->m_ZrotBox->setValue(v2.second.get("z")); } if( v2.first == "translation" ) { m_Controls->m_XtransBox->setValue(v2.second.get("x")); m_Controls->m_YtransBox->setValue(v2.second.get("y")); m_Controls->m_ZtransBox->setValue(v2.second.get("z")); } if( v2.first == "scale" ) { m_Controls->m_XscaleBox->setValue(v2.second.get("x")); m_Controls->m_YscaleBox->setValue(v2.second.get("y")); m_Controls->m_ZscaleBox->setValue(v2.second.get("z")); } } } if( v1.first == "image" ) { m_Controls->m_SizeX->setValue(v1.second.get("basic.size.x")); m_Controls->m_SizeY->setValue(v1.second.get("basic.size.y")); m_Controls->m_SizeZ->setValue(v1.second.get("basic.size.z")); m_Controls->m_SpacingX->setValue(v1.second.get("basic.spacing.x")); m_Controls->m_SpacingY->setValue(v1.second.get("basic.spacing.y")); m_Controls->m_SpacingZ->setValue(v1.second.get("basic.spacing.z")); m_Controls->m_NumGradientsBox->setValue(v1.second.get("basic.numgradients")); m_Controls->m_BvalueBox->setValue(v1.second.get("basic.bvalue")); m_Controls->m_AdvancedOptionsBox_2->setChecked(v1.second.get("showadvanced")); m_Controls->m_RepetitionsBox->setValue(v1.second.get("repetitions")); m_Controls->m_SignalScaleBox->setValue(v1.second.get("signalScale")); m_Controls->m_TEbox->setValue(v1.second.get("tEcho")); m_Controls->m_LineReadoutTimeBox->setValue(v1.second.get("tLine")); m_Controls->m_T2starBox->setValue(v1.second.get("tInhom")); m_Controls->m_FiberRadius->setValue(v1.second.get("axonRadius")); m_Controls->m_RelaxationBox->setChecked(v1.second.get("doSimulateRelaxation")); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(v1.second.get("doDisablePartialVolume")); m_Controls->m_VolumeFractionsBox->setChecked(v1.second.get("outputvolumefractions")); m_Controls->m_AddNoise->setChecked(v1.second.get("artifacts.addnoise")); m_Controls->m_NoiseDistributionBox->setCurrentIndex(v1.second.get("artifacts.noisedistribution")); m_Controls->m_NoiseLevel->setValue(v1.second.get("artifacts.noisevariance")); m_Controls->m_AddGhosts->setChecked(v1.second.get("artifacts.addghost")); - m_Controls->m_kOffsetBox->setValue(v1.second.get("artifacts.m_KspaceLineOffset")); + m_Controls->m_kOffsetBox->setValue(v1.second.get("artifacts.kspaceLineOffset")); m_Controls->m_AddAliasing->setChecked(v1.second.get("artifacts.addaliasing")); m_Controls->m_WrapBox->setValue(v1.second.get("artifacts.aliasingfactor")); m_Controls->m_AddDistortions->setChecked(v1.second.get("artifacts.distortions")); m_Controls->m_AddSpikes->setChecked(v1.second.get("artifacts.addspikes")); - m_Controls->m_SpikeNumBox->setValue(v1.second.get("artifacts.m_Spikesnum")); - m_Controls->m_SpikeScaleBox->setValue(v1.second.get("artifacts.m_Spikesscale")); + m_Controls->m_SpikeNumBox->setValue(v1.second.get("artifacts.spikesnum")); + m_Controls->m_SpikeScaleBox->setValue(v1.second.get("artifacts.spikesscale")); m_Controls->m_AddEddy->setChecked(v1.second.get("artifacts.addeddy")); - m_Controls->m_EddyGradientStrength->setValue(v1.second.get("artifacts.m_EddyStrength")); + m_Controls->m_EddyGradientStrength->setValue(v1.second.get("artifacts.eddyStrength")); m_Controls->m_AddGibbsRinging->setChecked(v1.second.get("artifacts.addringing")); - m_Controls->m_AddMotion->setChecked(v1.second.get("artifacts.m_DoAddMotion")); - m_Controls->m_RandomMotion->setChecked(v1.second.get("artifacts.m_RandomMotion")); - m_Controls->m_MaxTranslationBoxX->setValue(v1.second.get("artifacts.m_Translation0")); - m_Controls->m_MaxTranslationBoxY->setValue(v1.second.get("artifacts.m_Translation1")); - m_Controls->m_MaxTranslationBoxZ->setValue(v1.second.get("artifacts.m_Translation2")); - m_Controls->m_MaxRotationBoxX->setValue(v1.second.get("artifacts.m_Rotation0")); - m_Controls->m_MaxRotationBoxY->setValue(v1.second.get("artifacts.m_Rotation1")); - m_Controls->m_MaxRotationBoxZ->setValue(v1.second.get("artifacts.m_Rotation2")); + m_Controls->m_AddMotion->setChecked(v1.second.get("artifacts.doAddMotion")); + m_Controls->m_RandomMotion->setChecked(v1.second.get("artifacts.randomMotion")); + m_Controls->m_MaxTranslationBoxX->setValue(v1.second.get("artifacts.translation0")); + m_Controls->m_MaxTranslationBoxY->setValue(v1.second.get("artifacts.translation1")); + m_Controls->m_MaxTranslationBoxZ->setValue(v1.second.get("artifacts.translation2")); + m_Controls->m_MaxRotationBoxX->setValue(v1.second.get("artifacts.rotation0")); + m_Controls->m_MaxRotationBoxY->setValue(v1.second.get("artifacts.rotation1")); + m_Controls->m_MaxRotationBoxZ->setValue(v1.second.get("artifacts.rotation2")); m_Controls->m_Compartment1Box->setCurrentIndex(v1.second.get("compartment1.index")); m_Controls->m_Compartment2Box->setCurrentIndex(v1.second.get("compartment2.index")); m_Controls->m_Compartment3Box->setCurrentIndex(v1.second.get("compartment3.index")); m_Controls->m_Compartment4Box->setCurrentIndex(v1.second.get("compartment4.index")); m_Controls->m_StickWidget1->SetD(v1.second.get("compartment1.stick.d")); m_Controls->m_StickWidget1->SetT2(v1.second.get("compartment1.stick.t2")); m_Controls->m_ZeppelinWidget1->SetD1(v1.second.get("compartment1.zeppelin.d1")); m_Controls->m_ZeppelinWidget1->SetD2(v1.second.get("compartment1.zeppelin.d2")); m_Controls->m_ZeppelinWidget1->SetT2(v1.second.get("compartment1.zeppelin.t2")); m_Controls->m_TensorWidget1->SetD1(v1.second.get("compartment1.tensor.d1")); m_Controls->m_TensorWidget1->SetD2(v1.second.get("compartment1.tensor.d2")); m_Controls->m_TensorWidget1->SetD3(v1.second.get("compartment1.tensor.d3")); m_Controls->m_TensorWidget1->SetT2(v1.second.get("compartment1.tensor.t2")); m_Controls->m_StickWidget2->SetD(v1.second.get("compartment2.stick.d")); m_Controls->m_StickWidget2->SetT2(v1.second.get("compartment2.stick.t2")); m_Controls->m_ZeppelinWidget2->SetD1(v1.second.get("compartment2.zeppelin.d1")); m_Controls->m_ZeppelinWidget2->SetD2(v1.second.get("compartment2.zeppelin.d2")); m_Controls->m_ZeppelinWidget2->SetT2(v1.second.get("compartment2.zeppelin.t2")); m_Controls->m_TensorWidget2->SetD1(v1.second.get("compartment2.tensor.d1")); m_Controls->m_TensorWidget2->SetD2(v1.second.get("compartment2.tensor.d2")); m_Controls->m_TensorWidget2->SetD3(v1.second.get("compartment2.tensor.d3")); m_Controls->m_TensorWidget2->SetT2(v1.second.get("compartment2.tensor.t2")); m_Controls->m_BallWidget1->SetD(v1.second.get("compartment3.ball.d")); m_Controls->m_BallWidget1->SetT2(v1.second.get("compartment3.ball.t2")); m_Controls->m_AstrosticksWidget1->SetD(v1.second.get("compartment3.astrosticks.d")); m_Controls->m_AstrosticksWidget1->SetT2(v1.second.get("compartment3.astrosticks.t2")); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(v1.second.get("compartment3.astrosticks.randomize")); m_Controls->m_DotWidget1->SetT2(v1.second.get("compartment3.dot.t2")); m_Controls->m_BallWidget2->SetD(v1.second.get("compartment4.ball.d")); m_Controls->m_BallWidget2->SetT2(v1.second.get("compartment4.ball.t2")); m_Controls->m_AstrosticksWidget2->SetD(v1.second.get("compartment4.astrosticks.d")); m_Controls->m_AstrosticksWidget2->SetT2(v1.second.get("compartment4.astrosticks.t2")); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(v1.second.get("compartment4.astrosticks.randomize")); m_Controls->m_DotWidget2->SetT2(v1.second.get("compartment4.dot.t2")); m_Controls->m_Comp4FractionBox->setValue(v1.second.get("compartment4.weight")); } } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->setVisible(false); } void QmitkFiberfoxView::OnAddAliasing(int value) { if (value>0) m_Controls->m_AliasingFrame->setVisible(true); else m_Controls->m_AliasingFrame->setVisible(false); } void QmitkFiberfoxView::OnAddSpikes(int value) { if (value>0) m_Controls->m_SpikeFrame->setVisible(true); else m_Controls->m_SpikeFrame->setVisible(false); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for(unsigned int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for(unsigned int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( node ); } UpdateGui(); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; vector< vector< unsigned int > > fliplist; for (unsigned int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { fiducials.push_back(fib); fliplist.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetFiducials(fiducials); filter->SetFlipList(fliplist); switch(m_Controls->m_DistributionBox->currentIndex()){ case 0: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); break; case 1: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); filter->SetVariance(m_Controls->m_VarianceBox->value()); break; } filter->SetDensity(m_Controls->m_FiberDensityBox->value()); filter->SetTension(m_Controls->m_TensionBox->value()); filter->SetContinuity(m_Controls->m_ContinuityBox->value()); filter->SetBias(m_Controls->m_BiasBox->value()); filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (unsigned int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::GenerateImage() { if (m_SelectedBundles.empty() && m_SelectedDWI.IsNull()) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); } else if (!m_SelectedBundles.empty()) SimulateImageFromFibers(m_SelectedBundles.at(0)); else if (m_SelectedDWI.IsNotNull()) SimulateForExistingDwi(m_SelectedDWI); } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { if (!dynamic_cast*>(imageNode->GetData())) return; FiberfoxParameters parameters = UpdateImageParameters(); if (parameters.m_NoiseModel==NULL && parameters.m_Spikes==0 && parameters.m_FrequencyMap.IsNull() && parameters.m_KspaceLineOffset<=0.000001 && !parameters.m_DoAddGibbsRinging && !(parameters.m_EddyStrength>0) && parameters.m_CroppingFactor>0.999) { QMessageBox::information( NULL, "Simulation cancelled", "No valid artifact enabled! Motion artifacts and relaxation effects can NOT be added to an existing diffusion weighted image."); return; } mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(imageNode->GetData()); m_ArtifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); m_ArtifactsToDwiFilter->SetInput(diffImg->GetVectorImage()); parameters.m_ParentNode = imageNode; m_ArtifactsToDwiFilter->SetParameters(parameters); m_Worker.m_FilterType = 1; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) return; FiberfoxParameters parameters = UpdateImageParameters(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); parameters.m_ParentNode = fiberNode; m_TractsToDwiFilter->SetParameters(parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Worker.m_FilterType = 0; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for(unsigned int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { for (std::vector::const_iterator it = selectedBundles.begin(); it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); } } } } } else { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } for (std::vector::const_iterator it = m_SelectedBundles.begin(); it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_FiberBundleLabel->setText("mandatory"); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_ItkMaskImage.IsNotNull() || m_SelectedImage.IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedDWI.IsNotNull()) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (!m_SelectedBundles.empty()) { m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); m_Controls->m_FiberBundleLabel->setText(m_SelectedBundles.at(0)->GetName().c_str()); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; m_SelectedDWI = NULL; m_ItkMaskImage = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; mitk::Image::Pointer image = dynamic_cast(node->GetData()); bool isbinary = false; node->GetPropertyValue("binary", isbinary); if (isbinary) { mitk::CastToItkImage(image, m_ItkMaskImage); m_Controls->m_TissueMaskLabel->setText(node->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if (dynamic_cast(node->GetData())) { m_SelectedBundles.clear(); m_SelectedBundles2.clear(); } else if (dynamic_cast(node->GetData())) m_SelectedImages.clear(); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( nonConstNode ); } MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG m_OutputPath = QFileDialog::getExistingDirectory(NULL, "Save images to...", QString(m_OutputPath.c_str())).toStdString(); if (m_OutputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { m_OutputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(m_OutputPath.c_str())); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp index 403a36cfce..77d08e2882 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp @@ -1,760 +1,759 @@ /*=================================================================== 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. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkGibbsTrackingView.h" #include // Qt #include #include #include // MITK #include #include #include #include #include // ITK #include #include #include // MISC #include QmitkTrackingWorker::QmitkTrackingWorker(QmitkGibbsTrackingView* view) : m_View(view) { } void QmitkTrackingWorker::run() { m_View->m_GlobalTracker = QmitkGibbsTrackingView::GibbsTrackingFilterType::New(); m_View->m_GlobalTracker->SetQBallImage(m_View->m_ItkQBallImage); m_View->m_GlobalTracker->SetTensorImage(m_View->m_ItkTensorImage); m_View->m_GlobalTracker->SetMaskImage(m_View->m_MaskImage); m_View->m_GlobalTracker->SetStartTemperature((float)m_View->m_Controls->m_StartTempSlider->value()/100); m_View->m_GlobalTracker->SetEndTemperature((float)m_View->m_Controls->m_EndTempSlider->value()/10000); m_View->m_GlobalTracker->SetIterations(m_View->m_Iterations); m_View->m_GlobalTracker->SetParticleWeight((float)m_View->m_Controls->m_ParticleWeightSlider->value()/10000); m_View->m_GlobalTracker->SetParticleWidth((float)(m_View->m_Controls->m_ParticleWidthSlider->value())/10); m_View->m_GlobalTracker->SetParticleLength((float)(m_View->m_Controls->m_ParticleLengthSlider->value())/10); m_View->m_GlobalTracker->SetInexBalance((float)m_View->m_Controls->m_InExBalanceSlider->value()/10); m_View->m_GlobalTracker->SetMinFiberLength(m_View->m_Controls->m_FiberLengthSlider->value()); m_View->m_GlobalTracker->SetCurvatureThreshold(cos((float)m_View->m_Controls->m_CurvatureThresholdSlider->value()*M_PI/180)); m_View->m_GlobalTracker->SetRandomSeed(m_View->m_Controls->m_RandomSeedSlider->value()); try{ m_View->m_GlobalTracker->Update(); } catch( mitk::Exception e ) { MITK_ERROR << "Internal error occured: " << e.what() << "\nAborting"; } m_View->m_TrackingThread.quit(); } const std::string QmitkGibbsTrackingView::VIEW_ID = "org.mitk.views.gibbstracking"; QmitkGibbsTrackingView::QmitkGibbsTrackingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget(NULL) , m_FiberBundle(NULL) , m_MaskImage(NULL) , m_TensorImage(NULL) , m_QBallImage(NULL) , m_ItkQBallImage(NULL) , m_ItkTensorImage(NULL) , m_ImageNode(NULL) , m_MaskImageNode(NULL) , m_FiberBundleNode(NULL) , m_ThreadIsRunning(false) , m_ElapsedTime(0) , m_Iterations(10000000) , m_LastStep(0) , m_GlobalTracker(NULL) , m_TrackingWorker(this) { m_TrackingWorker.moveToThread(&m_TrackingThread); connect(&m_TrackingThread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_TrackingThread, SIGNAL(started()), &m_TrackingWorker, SLOT(run())); connect(&m_TrackingThread, SIGNAL(finished()), this, SLOT(AfterThread())); connect(&m_TrackingThread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_TrackingTimer = new QTimer(this); } QmitkGibbsTrackingView::~QmitkGibbsTrackingView() { delete m_TrackingTimer; } // update tracking status and generate fiber bundle void QmitkGibbsTrackingView::TimerUpdate() { int currentStep = m_GlobalTracker->GetCurrentStep(); mitk::ProgressBar::GetInstance()->Progress(currentStep-m_LastStep); UpdateTrackingStatus(); GenerateFiberBundle(); m_LastStep = currentStep; } // tell global tractography filter to stop after current step void QmitkGibbsTrackingView::StopGibbsTracking() { if (m_GlobalTracker.IsNull()) return; //mitk::ProgressBar::GetInstance()->Progress(m_GlobalTracker->GetSteps()-m_LastStep+1); m_GlobalTracker->SetAbortTracking(true); m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStop->setText("Stopping Tractography ..."); } // update gui elements and generate fiber bundle after tracking is finished void QmitkGibbsTrackingView::AfterThread() { m_ThreadIsRunning = false; m_TrackingTimer->stop(); mitk::ProgressBar::GetInstance()->Progress(m_GlobalTracker->GetSteps()-m_LastStep+1); UpdateGUI(); if( !m_GlobalTracker->GetIsInValidState() ) { QMessageBox::critical( NULL, "Gibbs Tracking", "An internal error occured. Tracking aborted.\n Please check the log for details." ); m_FiberBundleNode = NULL; return; } UpdateTrackingStatus(); if(m_Controls->m_ParticleWeightSlider->value()==0) { m_Controls->m_ParticleWeightLabel->setText(QString::number(m_GlobalTracker->GetParticleWeight())); m_Controls->m_ParticleWeightSlider->setValue(m_GlobalTracker->GetParticleWeight()*10000); } if(m_Controls->m_ParticleWidthSlider->value()==0) { m_Controls->m_ParticleWidthLabel->setText(QString::number(m_GlobalTracker->GetParticleWidth())); m_Controls->m_ParticleWidthSlider->setValue(m_GlobalTracker->GetParticleWidth()*10); } if(m_Controls->m_ParticleLengthSlider->value()==0) { m_Controls->m_ParticleLengthLabel->setText(QString::number(m_GlobalTracker->GetParticleLength())); m_Controls->m_ParticleLengthSlider->setValue(m_GlobalTracker->GetParticleLength()*10); } GenerateFiberBundle(); m_FiberBundleNode = 0; m_GlobalTracker = 0; // images not needed anymore ( relevant only for computation ) // we need to release them to remove the memory access block created through CastToItk<> calls this->m_ItkQBallImage = 0; this->m_ItkTensorImage = 0; } // start tracking timer and update gui elements before tracking is started void QmitkGibbsTrackingView::BeforeThread() { m_ThreadIsRunning = true; m_TrackingTime = QTime::currentTime(); m_ElapsedTime = 0; m_TrackingTimer->start(1000); m_LastStep = 0; UpdateGUI(); } // setup gui elements and signal/slot connections void QmitkGibbsTrackingView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkGibbsTrackingViewControls; m_Controls->setupUi( parent ); AdvancedSettings(); connect( m_TrackingTimer, SIGNAL(timeout()), this, SLOT(TimerUpdate()) ); connect( m_Controls->m_TrackingStop, SIGNAL(clicked()), this, SLOT(StopGibbsTracking()) ); connect( m_Controls->m_TrackingStart, SIGNAL(clicked()), this, SLOT(StartGibbsTracking()) ); connect( m_Controls->m_AdvancedSettingsCheckbox, SIGNAL(clicked()), this, SLOT(AdvancedSettings()) ); connect( m_Controls->m_SaveTrackingParameters, SIGNAL(clicked()), this, SLOT(SaveTrackingParameters()) ); connect( m_Controls->m_LoadTrackingParameters, SIGNAL(clicked()), this, SLOT(LoadTrackingParameters()) ); connect( m_Controls->m_IterationsSlider, SIGNAL(valueChanged(int)), this, SLOT(SetIterations(int)) ); connect( m_Controls->m_ParticleWidthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleWidth(int)) ); connect( m_Controls->m_ParticleLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleLength(int)) ); connect( m_Controls->m_InExBalanceSlider, SIGNAL(valueChanged(int)), this, SLOT(SetInExBalance(int)) ); connect( m_Controls->m_FiberLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetFiberLength(int)) ); connect( m_Controls->m_ParticleWeightSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleWeight(int)) ); connect( m_Controls->m_StartTempSlider, SIGNAL(valueChanged(int)), this, SLOT(SetStartTemp(int)) ); connect( m_Controls->m_EndTempSlider, SIGNAL(valueChanged(int)), this, SLOT(SetEndTemp(int)) ); connect( m_Controls->m_CurvatureThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(SetCurvatureThreshold(int)) ); connect( m_Controls->m_RandomSeedSlider, SIGNAL(valueChanged(int)), this, SLOT(SetRandomSeed(int)) ); connect( m_Controls->m_OutputFileButton, SIGNAL(clicked()), this, SLOT(SetOutputFile()) ); } } void QmitkGibbsTrackingView::SetInExBalance(int value) { m_Controls->m_InExBalanceLabel->setText(QString::number((float)value/10)); } void QmitkGibbsTrackingView::SetFiberLength(int value) { m_Controls->m_FiberLengthLabel->setText(QString::number(value)+"mm"); } void QmitkGibbsTrackingView::SetRandomSeed(int value) { if (value>=0) m_Controls->m_RandomSeedLabel->setText(QString::number(value)); else m_Controls->m_RandomSeedLabel->setText("auto"); } void QmitkGibbsTrackingView::SetParticleWeight(int value) { if (value>0) m_Controls->m_ParticleWeightLabel->setText(QString::number((float)value/10000)); else m_Controls->m_ParticleWeightLabel->setText("auto"); } void QmitkGibbsTrackingView::SetStartTemp(int value) { m_Controls->m_StartTempLabel->setText(QString::number((float)value/100)); } void QmitkGibbsTrackingView::SetEndTemp(int value) { m_Controls->m_EndTempLabel->setText(QString::number((float)value/10000)); } void QmitkGibbsTrackingView::SetParticleWidth(int value) { if (value>0) m_Controls->m_ParticleWidthLabel->setText(QString::number((float)value/10)+" mm"); else m_Controls->m_ParticleWidthLabel->setText("auto"); } void QmitkGibbsTrackingView::SetParticleLength(int value) { if (value>0) m_Controls->m_ParticleLengthLabel->setText(QString::number((float)value/10)+" mm"); else m_Controls->m_ParticleLengthLabel->setText("auto"); } void QmitkGibbsTrackingView::SetCurvatureThreshold(int value) { m_Controls->m_CurvatureThresholdLabel->setText(QString::number(value)+"°"); } void QmitkGibbsTrackingView::SetIterations(int value) { switch(value) { case 0: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^4"); m_Iterations = 10000; break; case 1: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^4"); m_Iterations = 50000; break; case 2: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^5"); m_Iterations = 100000; break; case 3: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^5"); m_Iterations = 500000; break; case 4: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^6"); m_Iterations = 1000000; break; case 5: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^6"); m_Iterations = 5000000; break; case 6: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^7"); m_Iterations = 10000000; break; case 7: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^7"); m_Iterations = 50000000; break; case 8: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^8"); m_Iterations = 100000000; break; case 9: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^8"); m_Iterations = 500000000; break; } } void QmitkGibbsTrackingView::StdMultiWidgetAvailable(QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkGibbsTrackingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } // called if datamanager selection changes void QmitkGibbsTrackingView::OnSelectionChanged( std::vector nodes ) { if (m_ThreadIsRunning) return; m_ImageNode = NULL; m_MaskImageNode = NULL; // iterate all selected objects for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) m_ImageNode = node; else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) m_ImageNode = node; else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { - bool isBinary = false; - node->GetPropertyValue("binary", isBinary); - if (isBinary) + mitk::Image::Pointer img = dynamic_cast(node->GetData()); + if (img->GetPixelType().GetPixelType()==itk::ImageIOBase::SCALAR) m_MaskImageNode = node; } } UpdateGUI(); } // update gui elements displaying trackings status void QmitkGibbsTrackingView::UpdateTrackingStatus() { if (m_GlobalTracker.IsNull()) return; m_ElapsedTime += m_TrackingTime.elapsed()/1000; m_TrackingTime.restart(); unsigned long hours = m_ElapsedTime/3600; unsigned long minutes = (m_ElapsedTime%3600)/60; unsigned long seconds = m_ElapsedTime%60; m_Controls->m_ProposalAcceptance->setText(QString::number(m_GlobalTracker->GetProposalAcceptance()*100)+"%"); m_Controls->m_TrackingTimeLabel->setText( QString::number(hours)+QString("h ")+QString::number(minutes)+QString("m ")+QString::number(seconds)+QString("s") ); m_Controls->m_NumConnectionsLabel->setText( QString::number(m_GlobalTracker->GetNumConnections()) ); m_Controls->m_NumParticlesLabel->setText( QString::number(m_GlobalTracker->GetNumParticles()) ); m_Controls->m_CurrentStepLabel->setText( QString::number(100*(float)(m_GlobalTracker->GetCurrentStep()-1)/m_GlobalTracker->GetSteps())+"%" ); m_Controls->m_AcceptedFibersLabel->setText( QString::number(m_GlobalTracker->GetNumAcceptedFibers()) ); } // update gui elements (enable/disable elements and set tooltips) void QmitkGibbsTrackingView::UpdateGUI() { if (m_ImageNode.IsNotNull()) { m_Controls->m_QballImageLabel->setText(m_ImageNode->GetName().c_str()); m_Controls->m_DataFrame->setTitle("Input Data"); } else { m_Controls->m_QballImageLabel->setText("mandatory"); m_Controls->m_DataFrame->setTitle("Please Select Input Data"); } if (m_MaskImageNode.IsNotNull()) m_Controls->m_MaskImageLabel->setText(m_MaskImageNode->GetName().c_str()); else m_Controls->m_MaskImageLabel->setText("optional"); if (!m_ThreadIsRunning && m_ImageNode.IsNotNull()) { m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStart->setEnabled(true); m_Controls->m_LoadTrackingParameters->setEnabled(true); m_Controls->m_IterationsSlider->setEnabled(true); m_Controls->m_AdvancedFrame->setEnabled(true); m_Controls->m_TrackingStop->setText("Stop Tractography"); m_Controls->m_TrackingStart->setToolTip("Start tractography. No further change of parameters possible."); m_Controls->m_TrackingStop->setToolTip(""); } else if (!m_ThreadIsRunning) { m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStart->setEnabled(false); m_Controls->m_LoadTrackingParameters->setEnabled(true); m_Controls->m_IterationsSlider->setEnabled(true); m_Controls->m_AdvancedFrame->setEnabled(true); m_Controls->m_TrackingStop->setText("Stop Tractography"); m_Controls->m_TrackingStart->setToolTip("No Q-Ball image selected."); m_Controls->m_TrackingStop->setToolTip(""); } else { m_Controls->m_TrackingStop->setEnabled(true); m_Controls->m_TrackingStart->setEnabled(false); m_Controls->m_LoadTrackingParameters->setEnabled(false); m_Controls->m_IterationsSlider->setEnabled(false); m_Controls->m_AdvancedFrame->setEnabled(false); m_Controls->m_AdvancedFrame->setVisible(false); m_Controls->m_AdvancedSettingsCheckbox->setChecked(false); m_Controls->m_TrackingStart->setToolTip("Tracking in progress."); m_Controls->m_TrackingStop->setToolTip("Stop tracking and display results."); } } // show/hide advanced settings frame void QmitkGibbsTrackingView::AdvancedSettings() { m_Controls->m_AdvancedFrame->setVisible(m_Controls->m_AdvancedSettingsCheckbox->isChecked()); } // set mask image data node void QmitkGibbsTrackingView::SetMask() { std::vector nodes = GetDataManagerSelection(); if (nodes.empty()) { m_MaskImageNode = NULL; m_Controls->m_MaskImageLabel->setText("-"); return; } for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_MaskImageNode = node; m_Controls->m_MaskImageLabel->setText(node->GetName().c_str()); return; } } } // check for mask and qbi and start tracking thread void QmitkGibbsTrackingView::StartGibbsTracking() { if(m_ThreadIsRunning) { MITK_WARN("QmitkGibbsTrackingView")<<"Thread already running!"; return; } m_GlobalTracker = NULL; if (m_ImageNode.IsNull()) { QMessageBox::information( NULL, "Warning", "Please load and select a qball image before starting image processing."); return; } if (dynamic_cast(m_ImageNode->GetData())) m_QBallImage = dynamic_cast(m_ImageNode->GetData()); else if (dynamic_cast(m_ImageNode->GetData())) m_TensorImage = dynamic_cast(m_ImageNode->GetData()); if (m_QBallImage.IsNull() && m_TensorImage.IsNull()) return; // cast qbi to itk m_ItkTensorImage = NULL; m_ItkQBallImage = NULL; m_MaskImage = NULL; if (m_QBallImage.IsNotNull()) { m_ItkQBallImage = ItkQBallImgType::New(); mitk::CastToItkImage(m_QBallImage, m_ItkQBallImage); } else { m_ItkTensorImage = ItkTensorImage::New(); mitk::CastToItkImage(m_TensorImage, m_ItkTensorImage); } // mask image found? // catch exceptions thrown by the itkAccess macros try{ if(m_MaskImageNode.IsNotNull()) { if (dynamic_cast(m_MaskImageNode->GetData())) mitk::CastToItkImage(dynamic_cast(m_MaskImageNode->GetData()), m_MaskImage); } } catch(...){}; unsigned int steps = m_Iterations/10000; if (steps<10) steps = 10; m_LastStep = 1; mitk::ProgressBar::GetInstance()->AddStepsToDo(steps); // start worker thread m_TrackingThread.start(QThread::LowestPriority); } // generate mitkFiberBundle from tracking filter output void QmitkGibbsTrackingView::GenerateFiberBundle() { if (m_GlobalTracker.IsNull() || (!(m_Controls->m_VisualizationCheckbox->isChecked() || m_Controls->m_VisualizeOnceButton->isChecked()) && m_ThreadIsRunning)) return; if (m_Controls->m_VisualizeOnceButton->isChecked()) m_Controls->m_VisualizeOnceButton->setChecked(false); vtkSmartPointer fiberBundle = m_GlobalTracker->GetFiberBundle(); if ( m_GlobalTracker->GetNumAcceptedFibers()==0 ) return; m_FiberBundle = mitk::FiberBundleX::New(fiberBundle); if (m_FiberBundleNode.IsNotNull()){ GetDefaultDataStorage()->Remove(m_FiberBundleNode); m_FiberBundleNode = 0; } m_FiberBundleNode = mitk::DataNode::New(); m_FiberBundleNode->SetData(m_FiberBundle); QString name("FiberBundle_"); name += m_ImageNode->GetName().c_str(); name += "_Gibbs"; m_FiberBundleNode->SetName(name.toStdString()); m_FiberBundleNode->SetVisibility(true); if (!m_OutputFileName.isEmpty()) { QString filename = m_OutputFileName; mitk::FiberBundleXWriter::Pointer writer = mitk::FiberBundleXWriter::New(); writer->SetFileName(filename.toStdString()); writer->SetInputFiberBundleX(m_FiberBundle.GetPointer()); try { writer->Update(); QMessageBox::information(NULL, "Fiber bundle saved to", filename); } catch (itk::ExceptionObject &ex) { QMessageBox::information(NULL, "Fiber bundle could not be saved", QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription())); if(m_ImageNode.IsNull()) GetDataStorage()->Add(m_FiberBundleNode); else GetDataStorage()->Add(m_FiberBundleNode, m_ImageNode); } } else { if(m_ImageNode.IsNull()) GetDataStorage()->Add(m_FiberBundleNode); else GetDataStorage()->Add(m_FiberBundleNode, m_ImageNode); } } void QmitkGibbsTrackingView::SetOutputFile() { // SELECT FOLDER DIALOG m_OutputFileName = QFileDialog::getSaveFileName(0, tr("Set file name"), QDir::currentPath()+"/FiberBundle.fib", tr("Fiber Bundle (*.fib)") ); if (m_OutputFileName.isEmpty()) m_Controls->m_OutputFileLabel->setText("N/A"); else m_Controls->m_OutputFileLabel->setText(m_OutputFileName); } // save current tracking paramters as xml file (.gtp) void QmitkGibbsTrackingView::SaveTrackingParameters() { TiXmlDocument documentXML; TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" ); documentXML.LinkEndChild( declXML ); TiXmlElement* mainXML = new TiXmlElement("global_tracking_parameter_file"); mainXML->SetAttribute("file_version", "0.1"); documentXML.LinkEndChild(mainXML); TiXmlElement* paramXML = new TiXmlElement("parameter_set"); paramXML->SetAttribute("iterations", QString::number(m_Iterations).toStdString()); paramXML->SetAttribute("particle_length", QString::number((float)m_Controls->m_ParticleLengthSlider->value()/10).toStdString()); paramXML->SetAttribute("particle_width", QString::number((float)m_Controls->m_ParticleWidthSlider->value()/10).toStdString()); paramXML->SetAttribute("particle_weight", QString::number((float)m_Controls->m_ParticleWeightSlider->value()/10000).toStdString()); paramXML->SetAttribute("temp_start", QString::number((float)m_Controls->m_StartTempSlider->value()/100).toStdString()); paramXML->SetAttribute("temp_end", QString::number((float)m_Controls->m_EndTempSlider->value()/10000).toStdString()); paramXML->SetAttribute("inexbalance", QString::number((float)m_Controls->m_InExBalanceSlider->value()/10).toStdString()); paramXML->SetAttribute("fiber_length", QString::number(m_Controls->m_FiberLengthSlider->value()).toStdString()); paramXML->SetAttribute("curvature_threshold", QString::number(m_Controls->m_CurvatureThresholdSlider->value()).toStdString()); mainXML->LinkEndChild(paramXML); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), QDir::currentPath()+"/param.gtp", tr("Global Tracking Parameters (*.gtp)") ); if(filename.isEmpty() || filename.isNull()) return; if(!filename.endsWith(".gtp")) filename += ".gtp"; documentXML.SaveFile( filename.toStdString() ); } void QmitkGibbsTrackingView::UpdateIteraionsGUI(unsigned long iterations) { switch(iterations) { case 10000: m_Controls->m_IterationsSlider->setValue(0); m_Controls->m_IterationsLabel->setText("Iterations: 10^4"); break; case 50000: m_Controls->m_IterationsSlider->setValue(1); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^4"); break; case 100000: m_Controls->m_IterationsSlider->setValue(2); m_Controls->m_IterationsLabel->setText("Iterations: 10^5"); break; case 500000: m_Controls->m_IterationsSlider->setValue(3); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^5"); break; case 1000000: m_Controls->m_IterationsSlider->setValue(4); m_Controls->m_IterationsLabel->setText("Iterations: 10^6"); break; case 5000000: m_Controls->m_IterationsSlider->setValue(5); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^6"); break; case 10000000: m_Controls->m_IterationsSlider->setValue(6); m_Controls->m_IterationsLabel->setText("Iterations: 10^7"); break; case 50000000: m_Controls->m_IterationsSlider->setValue(7); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^7"); break; case 100000000: m_Controls->m_IterationsSlider->setValue(8); m_Controls->m_IterationsLabel->setText("Iterations: 10^8"); break; case 500000000: m_Controls->m_IterationsSlider->setValue(9); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^8"); break; case 1000000000: m_Controls->m_IterationsSlider->setValue(10); m_Controls->m_IterationsLabel->setText("Iterations: 10^9"); break; case 5000000000: m_Controls->m_IterationsSlider->setValue(11); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^9"); break; } } // load current tracking paramters from xml file (.gtp) void QmitkGibbsTrackingView::LoadTrackingParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QDir::currentPath(), tr("Global Tracking Parameters (*.gtp)") ); if(filename.isEmpty() || filename.isNull()) return; TiXmlDocument doc( filename.toStdString() ); doc.LoadFile(); TiXmlHandle hDoc(&doc); TiXmlElement* pElem; TiXmlHandle hRoot(0); pElem = hDoc.FirstChildElement().Element(); hRoot = TiXmlHandle(pElem); pElem = hRoot.FirstChildElement("parameter_set").Element(); QString iterations(pElem->Attribute("iterations")); m_Iterations = iterations.toULong(); UpdateIteraionsGUI(m_Iterations); QString particleLength(pElem->Attribute("particle_length")); float pLength = particleLength.toFloat(); QString particleWidth(pElem->Attribute("particle_width")); float pWidth = particleWidth.toFloat(); if (pLength==0) m_Controls->m_ParticleLengthLabel->setText("auto"); else m_Controls->m_ParticleLengthLabel->setText(particleLength+" mm"); if (pWidth==0) m_Controls->m_ParticleWidthLabel->setText("auto"); else m_Controls->m_ParticleWidthLabel->setText(particleWidth+" mm"); m_Controls->m_ParticleWidthSlider->setValue(pWidth*10); m_Controls->m_ParticleLengthSlider->setValue(pLength*10); QString partWeight(pElem->Attribute("particle_weight")); m_Controls->m_ParticleWeightSlider->setValue(partWeight.toFloat()*10000); m_Controls->m_ParticleWeightLabel->setText(partWeight); QString startTemp(pElem->Attribute("temp_start")); m_Controls->m_StartTempSlider->setValue(startTemp.toFloat()*100); m_Controls->m_StartTempLabel->setText(startTemp); QString endTemp(pElem->Attribute("temp_end")); m_Controls->m_EndTempSlider->setValue(endTemp.toFloat()*10000); m_Controls->m_EndTempLabel->setText(endTemp); QString inExBalance(pElem->Attribute("inexbalance")); m_Controls->m_InExBalanceSlider->setValue(inExBalance.toFloat()*10); m_Controls->m_InExBalanceLabel->setText(inExBalance); QString fiberLength(pElem->Attribute("fiber_length")); m_Controls->m_FiberLengthSlider->setValue(fiberLength.toInt()); m_Controls->m_FiberLengthLabel->setText(fiberLength+"mm"); QString curvThres(pElem->Attribute("curvature_threshold")); m_Controls->m_CurvatureThresholdSlider->setValue(curvThres.toInt()); m_Controls->m_CurvatureThresholdLabel->setText(curvThres+"°"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingViewControls.ui index 539502c5c4..802b79836c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingViewControls.ui @@ -1,1088 +1,1115 @@ QmitkGibbsTrackingViewControls 0 0 463 1011 0 0 0 0 QmitkTemplate QFormLayout::AllNonFixedFieldsGrow Please Select Input Data Q-Ball/Tensor Image: Mandatory input <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Mask Image: - Optional input to limit the algorithms search space. + <html><head/><body><p>White matter probability mask image.</p></body></html> <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true QFrame::NoFrame QFrame::Plain 0 - + + 0 + + + 0 + + + 0 + + 0 0 false No Q-Ball image selected. Qt::LeftToRight Start Tractography :/qmitk/play.xpm:/qmitk/play.xpm false Qt::LeftToRight Stop Tractography :/qmitk/stop.xpm:/qmitk/stop.xpm Parameters 0 Iterations: 10^7 Specify number of iterations for the tracking algorithm. 9 6 Qt::Horizontal QSlider::TicksBelow true Activate continuous visualization of intermediate results. Visualize Tractography true Visualize intermediate result. :/QmitkDiffusionImaging/Refresh_48.png:/QmitkDiffusionImaging/Refresh_48.png true Advanced Settings Output File: QFrame::NoFrame QFrame::Plain 0 - + + 0 + + + 0 + + + 0 + + 0 0 Select output file name and folder. ... N/A true true QFrame::StyledPanel QFrame::Raised 9 0 9 0 4 Particle Width: 0 Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter 0.1 Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter Particle Weight: 1 99 1 10 Qt::Horizontal QSlider::NoTicks Start Temperature: automatic estimation from gfa map and q-ball data. 0 1000 1 0 Qt::Horizontal true QSlider::NoTicks IE Bias < 0 < EE Bias -50 50 1 Qt::Horizontal QSlider::NoTicks 0.001 Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter Curvature Threshold: Balance In/Ex Energy: 45° Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter auto = 0.5 * min. spacing; sigma 100 1 Qt::Horizontal QSlider::NoTicks Particle Length: auto Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter Min. Fiber Length: Only fibers longer than specified are accepted. 500 1 40 Qt::Horizontal QSlider::NoTicks Allow only fiber curvature values smaller than the selected threshold. 180 1 45 Qt::Horizontal QSlider::NoTicks End Temperature: 40mm Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter auto Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter 1 100 1 10 Qt::Horizontal false false QSlider::NoTicks auto Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter auto = 1.5 * min. spacing; l 100 1 Qt::Horizontal QSlider::NoTicks Random Seed auto Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter auto = 1.5 * min. spacing; l -1 100 1 -1 Qt::Horizontal QSlider::NoTicks QFrame::NoFrame QFrame::Plain 0 - + + 0 + + + 0 + + + 0 + + 0 0 true Save current parameters as xml (.gtp) Qt::LeftToRight Save Parameters :/qmitk/btnMoveDown.png:/qmitk/btnMoveDown.png true Load parameters from xml file (.gtp) Qt::LeftToRight Load Parameters :/qmitk/btnMoveUp.png:/qmitk/btnMoveUp.png Monitor Progress: - Will only be updated if tracking is visualized Will only be updated if tracking is visualized Accepted Fibers: Connections: Particles: Proposal Acceptance Rate: Tracking Time: Will only be updated if tracking is visualized - - - - - Qt::Vertical QSizePolicy::Expanding 0 0 - +