diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/FitFibersToImage.cpp b/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/FitFibersToImage.cpp
index 24917a8991..6c9dfe8ba8 100755
--- a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/FitFibersToImage.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/FitFibersToImage.cpp
@@ -1,554 +1,752 @@
/*===================================================================
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 <mitkBaseData.h>
#include <mitkImageCast.h>
#include <mitkImageToItk.h>
#include <metaCommand.h>
#include <mitkCommandLineParser.h>
#include <usAny.h>
#include <mitkIOUtil.h>
#include <boost/lexical_cast.hpp>
#include <itksys/SystemTools.hxx>
#include <itkDirectory.h>
#include <mitkFiberBundle.h>
#include <mitkPreferenceListReaderOptionsFunctor.h>
#include <mitkDiffusionPropertyHelper.h>
#include <vnl/vnl_linear_system.h>
#include <Eigen/Dense>
#include <mitkStickModel.h>
#include <mitkBallModel.h>
#include <vigra/regression.hxx>
#include <itkImageFileWriter.h>
#include <itkImageDuplicator.h>
#include <itkMersenneTwisterRandomVariateGenerator.h>
+#include <mitkPeakImage.h>
+#include <vnl/algo/vnl_lbfgsb.h>
+#include <vnl/vnl_sparse_matrix.h>
+#include <vnl/vnl_sparse_matrix_linear_system.h>
+#include <vnl/algo/vnl_lsqr.h>
+#include <itkImageDuplicator.h>
+#include <itkTimeProbe.h>
+#include <random>
+#include <itkParticleSwarmOptimizer.h>
+#include <itkOnePlusOneEvolutionaryOptimizer.h>
+#include <itkGradientDescentOptimizer.h>
+#include <itkSPSAOptimizer.h>
using namespace std;
typedef itksys::SystemTools ist;
-typedef itk::Image<unsigned char, 3> ItkUcharImgType;
-typedef std::tuple< ItkUcharImgType::Pointer, std::string > MaskType;
-typedef mitk::DiffusionPropertyHelper DPH;
-typedef itk::Point<float, 3> PointType;
typedef itk::Point<float, 4> PointType4;
-typedef mitk::StickModel<> ModelType;
-typedef mitk::BallModel<> BallModelType;
typedef itk::Image< float, 4 > PeakImgType;
+const float UPSCALE = 1000.0;
-vnl_vector_fixed<float,3> GetCLosestPeak(itk::Index<4> idx, PeakImgType::Pointer peak_image , vnl_vector_fixed<float,3> fiber_dir, bool flip_x, bool flip_y, bool flip_z )
+vnl_vector_fixed<float,3> GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer peak_image , vnl_vector_fixed<float,3> fiber_dir, int& id )
{
int m_NumDirs = peak_image->GetLargestPossibleRegion().GetSize()[3]/3;
vnl_vector_fixed<float,3> out_dir; out_dir.fill(0);
float angle = 0.8;
for (int i=0; i<m_NumDirs; i++)
{
vnl_vector_fixed<float,3> dir;
idx[3] = i*3;
dir[0] = peak_image->GetPixel(idx);
idx[3] += 1;
dir[1] = peak_image->GetPixel(idx);
idx[3] += 1;
dir[2] = peak_image->GetPixel(idx);
float mag = dir.magnitude();
if (mag<mitk::eps)
continue;
- if (flip_x)
- dir[0] *= -1;
- if (flip_y)
- dir[1] *= -1;
- if (flip_z)
- dir[2] *= -1;
-
dir.normalize();
float a = dot_product(dir, fiber_dir);
if (fabs(a)>angle)
{
angle = fabs(a);
if (a<0)
out_dir = -dir;
else
out_dir = dir;
out_dir *= mag;
- out_dir *= 1000;
+ out_dir *= UPSCALE; // for the fit it's better if the magnitude is larger since many fibers pass each voxel and otherwise the individual contributions would be very small
+ id = i;
}
}
return out_dir;
}
-std::vector<float> SolveLinear( std::string , std::vector< mitk::FiberBundle::Pointer > inputTractogram, mitk::Image::Pointer inputImage, bool flip_x=false, bool flip_y=false, bool flip_z=false )
+class VnlCostFunction : public vnl_cost_function
+{
+public:
+
+ vnl_sparse_matrix_linear_system< double >* S;
+ vnl_sparse_matrix< double > m_A;
+ vnl_vector< double > m_b;
+ itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen;
+
+ void SetProblem(vnl_sparse_matrix< double >& A, vnl_vector<double>& b)
+ {
+ S = new vnl_sparse_matrix_linear_system<double>(A, b);
+ m_A = A;
+ m_b = b;
+ randGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
+ }
+
+ VnlCostFunction(const int NumVars) : vnl_cost_function(NumVars)
+ {
+ }
+
+ double f_itk(vnl_vector<double> const &x) const
+ {
+ double min = x.min_value();
+ if( min<0 )
+ return 10000 * -min;
+
+ double cost = S->get_rms_error(x);
+ double regu = x.squared_magnitude()/x.size();
+ cost += regu;
+ return cost;
+ }
+
+ double f(vnl_vector<double> const &x)
+ {
+ double cost = S->get_rms_error(x);
+
+ double regu = x.squared_magnitude()/x.size();
+
+// unsigned int norm = 0;
+// for (unsigned int i=0; i<m_b.size(); ++i)
+// {
+// if (m_A.get_row(i).empty())
+// continue;
+
+// float mean = 0;
+// for (auto el : m_A.get_row(i))
+// mean += x[el.first];
+
+// mean /= m_A.get_row(i).size();
+
+// for (auto el : m_A.get_row(i))
+// {
+// float d = x[el.first] - mean;
+// {
+// regu += d*d;
+// norm++;
+// }
+// }
+// }
+// regu /= norm;
+
+ cost += regu;
+ return cost;
+ }
+
+ // Finite differences gradient (SLOW)
+// void gradf(vnl_vector<double> const &x, vnl_vector<double> &dx)
+// {
+// fdgradf(x, dx);
+// }
+
+ void gradf(vnl_vector<double> const &x, vnl_vector<double> &dx)
+ {
+ dx.fill(0.0);
+ double mag = x.magnitude();
+ unsigned int N = m_b.size();
+
+ vnl_vector<double> d; d.set_size(N);
+ S->multiply(x,d);
+ d -= m_b;
+
+ vnl_vector<double> numerator; numerator.set_size(x.size());
+ S->transpose_multiply(d, dx);
+ dx *= 2.0/N;
+
+ if (mag>0)
+ dx += x/mag;
+ }
+
+};
+
+class ItkCostFunction : public itk::SingleValuedCostFunction
+{
+public:
+ /** Standard class typedefs. */
+ typedef ItkCostFunction Self;
+ typedef SingleValuedCostFunction Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self)
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(ItkCostFunction, SingleValuedCostfunction)
+
+ void SetVnlCostFunction(VnlCostFunction& cf) { m_VnlCostFunction = cf; }
+ unsigned int GetNumberOfParameters(void) const { return m_VnlCostFunction.get_number_of_unknowns(); } // itk::CostFunction
+
+ MeasureType GetValue(const ParametersType & parameters) const
+ {
+ return m_VnlCostFunction.f_itk(parameters);
+ }
+
+ void GetDerivative(const ParametersType &, DerivativeType & ) const {
+ throw itk::ExceptionObject( __FILE__, __LINE__, "No derivative is available for this cost function.");
+ }
+
+protected:
+ ItkCostFunction(){}
+ ~ItkCostFunction(){}
+
+ VnlCostFunction m_VnlCostFunction = VnlCostFunction(1);
+
+private:
+ ItkCostFunction(const Self &); //purposely not implemented
+ void operator = (const Self &); //purposely not implemented
+};
+
+void OptimizeItk(VnlCostFunction& cf, vnl_vector<double>& x, int iter, double lb, double ub)
+{
+ ItkCostFunction::ParametersType p; p.SetData(x.data_block(), x.size());
+
+ ItkCostFunction::Pointer itk_cf = ItkCostFunction::New();
+ itk_cf->SetVnlCostFunction(cf);
+
+ std::pair< double, double > bounds; bounds.first = lb; bounds.second = ub;
+ MITK_INFO << bounds;
+
+// itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
+// itk::OnePlusOneEvolutionaryOptimizer::Pointer opt = itk::OnePlusOneEvolutionaryOptimizer::New();
+// opt->SetCostFunction(itk_cf);
+// opt->MinimizeOn();
+// opt->SetInitialPosition(p);
+// opt->SetNormalVariateGenerator(randGen);
+// opt->SetMaximumIteration(iter);
+// opt->StartOptimization();
+
+// itk::ParticleSwarmOptimizer::Pointer opt = itk::ParticleSwarmOptimizer::New();
+// opt->SetCostFunction(itk_cf);
+// opt->SetInitialPosition(p);
+// opt->SetParameterBounds(bounds, x.size());
+// opt->SetMaximalNumberOfIterations(iter);
+// opt->SetNumberOfParticles(100);
+// opt->SetParametersConvergenceTolerance(0.01, x.size());
+// opt->SetNumberOfGenerationsWithMinimalImprovement(3);
+// opt->StartOptimization();
+
+// itk::GradientDescentOptimizer::Pointer opt = itk::GradientDescentOptimizer::New();
+// opt->SetCostFunction(itk_cf);
+// opt->SetInitialPosition(p);
+// opt->SetMinimize(true);
+// opt->SetNumberOfIterations(iter);
+// opt->StartOptimization();
+
+ itk::SPSAOptimizer::Pointer opt = itk::SPSAOptimizer::New();
+ opt->SetCostFunction(itk_cf);
+ opt->SetInitialPosition(p);
+ opt->SetMinimize(true);
+ opt->SetNumberOfPerturbations(iter);
+ opt->StartOptimization();
+
+ x.copy_in(opt->GetCurrentPosition().data_block());
+ for (unsigned int i=0; i<x.size(); i++)
+ MITK_INFO << opt->GetCurrentPosition()[i];
+// MITK_INFO << "Cost: " << opt->GetCurrentCost();
+
+}
+
+std::vector<float> FitFibers( std::string , std::vector< mitk::FiberBundle::Pointer > input_tracts, mitk::Image::Pointer inputImage, bool single_fiber_fit, int max_iter, float g_tol, bool lb )
{
typedef mitk::ImageToItk< PeakImgType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(inputImage);
caster->Update();
PeakImgType::Pointer itkImage = caster->GetOutput();
unsigned int* image_size = inputImage->GetDimensions();
int sz_x = image_size[0];
int sz_y = image_size[1];
int sz_z = image_size[2];
+ int sz_peaks = image_size[3];
int num_voxels = sz_x*sz_y*sz_z;
- unsigned int num_unknowns = inputTractogram.size(); //inputTractogram->GetNumFibers();
- unsigned int number_of_residuals = num_voxels * 3;
+ unsigned int num_unknowns = input_tracts.size(); //inputTractogram->GetNumFibers();
+ if (single_fiber_fit)
+ {
+ num_unknowns = 0;
+ for (unsigned int bundle=0; bundle<input_tracts.size(); bundle++)
+ num_unknowns += input_tracts.at(bundle)->GetNumFibers();
+ }
+
+ unsigned int number_of_residuals = num_voxels * sz_peaks;
// create linear system
MITK_INFO << "Num. unknowns: " << num_unknowns;
MITK_INFO << "Num. residuals: " << number_of_residuals;
- vigra::MultiArray<2, double> test_m(vigra::Shape2(number_of_residuals, 1000000), 0.0);
- MITK_INFO << test_m.height();
+ MITK_INFO << "Creating system ...";
+ vnl_sparse_matrix< double > A; A.set_size(number_of_residuals, num_unknowns);
+ vnl_vector<double> b; b.set_size(number_of_residuals); b.fill(0.0);
- MITK_INFO << "Creating matrices ...";
- vigra::MultiArray<2, double> A(vigra::Shape2(number_of_residuals, num_unknowns), 0.0);
- vigra::MultiArray<2, double> b(vigra::Shape2(number_of_residuals, 1), 0.0);
- vigra::MultiArray<2, double> x(vigra::Shape2(num_unknowns, 1), 1.0);
+ float max_peak_mag = 0;
+ int max_peak_idx = -1;
- MITK_INFO << "Filling matrices ...";
- for (unsigned int bundle=0; bundle<inputTractogram.size(); bundle++)
+ float min_peak_mag = 999999999;
+ int min_peak_idx = -1;
+
+ unsigned int fiber_count = 0;
+ for (unsigned int bundle=0; bundle<input_tracts.size(); bundle++)
{
- vtkSmartPointer<vtkPolyData> polydata = inputTractogram.at(bundle)->GetFiberPolyData();
+ vtkSmartPointer<vtkPolyData> polydata = input_tracts.at(bundle)->GetFiberPolyData();
- for (int i=0; i<inputTractogram.at(bundle)->GetNumFibers(); ++i)
+ for (int i=0; i<input_tracts.at(bundle)->GetNumFibers(); ++i)
{
vtkCell* cell = polydata->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (numPoints<2)
MITK_INFO << "FIBER WITH ONLY ONE POINT ENCOUNTERED!";
for (int j=0; j<numPoints-1; ++j)
{
double* p1 = points->GetPoint(j);
PointType4 p;
p[0]=p1[0];
p[1]=p1[1];
p[2]=p1[2];
p[3]=0;
itk::Index<4> idx4;
itkImage->TransformPhysicalPointToIndex(p, idx4);
if (!itkImage->GetLargestPossibleRegion().IsInside(idx4))
continue;
double* p2 = points->GetPoint(j+1);
vnl_vector_fixed<float,3> fiber_dir;
fiber_dir[0] = p[0]-p2[0];
fiber_dir[1] = p[1]-p2[1];
fiber_dir[2] = p[2]-p2[2];
fiber_dir.normalize();
- vnl_vector_fixed<float,3> odf_peak = GetCLosestPeak(idx4, itkImage, fiber_dir, flip_x, flip_y, flip_z);
- if (odf_peak.magnitude()<0.001)
+ int peak_id = -1;
+ vnl_vector_fixed<float,3> odf_peak = GetClosestPeak(idx4, itkImage, fiber_dir, peak_id);
+ float peak_mag = odf_peak.magnitude();
+ if (peak_id<0)
continue;
int x = idx4[0];
int y = idx4[1];
int z = idx4[2];
- unsigned int linear_index = x + sz_x*y + sz_x*sz_y*z;
+ unsigned int linear_index = sz_peaks*(x + sz_x*y + sz_x*sz_y*z);
- for (unsigned int k=0; k<3; ++k)
+ if (peak_mag>max_peak_mag)
{
- b(3*linear_index + k, 0) = (double)odf_peak[k];
- A(3*linear_index + k, bundle) = A(3*linear_index + k, bundle) + (double)fiber_dir[k];
+ max_peak_mag = peak_mag;
+ max_peak_idx = linear_index + 3*peak_id;
}
- }
- }
- }
-
- MITK_INFO << "Solving linear system";
- vigra::linalg::nonnegativeLeastSquares(A, b, x);
-
- std::vector<float> weights;
- for (unsigned int i=0; i<num_unknowns; ++i)
- weights.push_back(x[i]);
-
- return weights;
-}
-
-std::vector<float> SolveEvo(mitk::FiberBundle* inputTractogram, mitk::Image::Pointer inputImage, ModelType signalModel, BallModelType ballModel, float start_weight, int num_iterations=1000)
-{
- std::vector<float> out_weights;
- DPH::ImageType::Pointer itkImage = DPH::GetItkVectorImage(inputImage);
- itk::VectorImage< double, 3>::Pointer simulatedImage = itk::VectorImage< double, 3>::New();
- simulatedImage->SetSpacing(itkImage->GetSpacing());
- simulatedImage->SetOrigin(itkImage->GetOrigin());
- simulatedImage->SetDirection(itkImage->GetDirection());
- simulatedImage->SetRegions(itkImage->GetLargestPossibleRegion());
- simulatedImage->SetVectorLength(itkImage->GetVectorLength());
- simulatedImage->Allocate();
- DPH::ImageType::PixelType zero_signal;
- zero_signal.SetSize(itkImage->GetVectorLength());
- zero_signal.Fill(0);
- simulatedImage->FillBuffer(zero_signal);
-
- MITK_INFO << "start_weight: " << start_weight;
- double step = start_weight/10;
-
- vtkSmartPointer<vtkPolyData> polydata = inputTractogram->GetFiberPolyData();
-
- unsigned int* image_size = inputImage->GetDimensions();
- int sz_x = image_size[0];
- int sz_y = image_size[1];
-
- MITK_INFO << "INITIALIZING";
- std::vector< std::vector< ModelType::PixelType > > fiber_model_signals;
- std::vector< std::vector< DPH::ImageType::IndexType > > fiber_image_indices;
- std::map< unsigned int, std::vector<int> > image_index_to_fiber_indices;
-
- std::vector< int > fiber_indices;
- int f = 0;
- for (int i=0; i<inputTractogram->GetNumFibers(); ++i)
- {
- vtkCell* cell = polydata->GetCell(i);
- int numPoints = cell->GetNumberOfPoints();
- vtkPoints* points = cell->GetPoints();
-
-// if (numPoints<2)
-// continue;
-
- std::vector< ModelType::PixelType > model_signals;
- std::vector< DPH::ImageType::IndexType > image_indices;
-
- for (int j=0; j<numPoints-1; ++j)
- {
- double* p1 = points->GetPoint(j);
- PointType p;
- p[0]=p1[0];
- p[1]=p1[1];
- p[2]=p1[2];
-
- DPH::ImageType::IndexType idx;
- itkImage->TransformPhysicalPointToIndex(p, idx);
- if (!itkImage->GetLargestPossibleRegion().IsInside(idx))
- continue;
-
- double* p2 = points->GetPoint(j+1);
- ModelType::GradientType d;
- d[0] = p[0]-p2[0];
- d[1] = p[1]-p2[1];
- d[2] = p[2]-p2[2];
- signalModel.SetFiberDirection(d);
-
- ModelType::PixelType sig = signalModel.SimulateMeasurement();
- simulatedImage->SetPixel(idx, simulatedImage->GetPixel(idx) + start_weight * sig);
-
- model_signals.push_back(step*sig);
- image_indices.push_back(idx);
- unsigned int linear_index = idx[0] + sz_x*idx[1] + sz_x*sz_y*idx[2];
-
- if (image_index_to_fiber_indices.count(linear_index)==0)
- {
- image_index_to_fiber_indices[linear_index] = {i};
- }
- else
- {
- std::vector< int > index_fiber_indices = image_index_to_fiber_indices[linear_index];
- if(std::find(index_fiber_indices.begin(), index_fiber_indices.end(), i) == index_fiber_indices.end())
+ if (peak_mag<min_peak_mag)
{
- image_index_to_fiber_indices[linear_index].push_back(i);
+ min_peak_mag = peak_mag;
+ min_peak_idx = linear_index + 3*peak_id;
}
- }
- }
-
- fiber_model_signals.push_back(model_signals);
- fiber_image_indices.push_back(image_indices);
- fiber_indices.push_back(f);
- out_weights.push_back(start_weight);
- ++f;
- }
- BallModelType::PixelType ballSignal = step*ballModel.SimulateMeasurement();
-
- // SINGLE WEIGHT ONLY ANISO FIT
-
-
- // FILL WITH ISO
-
- // ACTUAL WEIGHT ADAPTATION
-
- double T_start = 0.01;
- double T_end = 0.001;
- double alpha = log(T_end/T_start);
-
- unsigned int num_gradients = signalModel.GetGradientList().size();
- for (int i=0; i<num_iterations; ++i)
- {
- double T = T_start * exp(alpha*(double)i/num_iterations);
-// MITK_INFO << "Iteration " << i;
-// MITK_INFO << "Temp " << T;
- std::random_shuffle(fiber_indices.begin(), fiber_indices.end());
-
-
- int accepted = 0;
- for (auto f : fiber_indices)
- {
- std::vector< ModelType::PixelType > model_signals = fiber_model_signals.at(f);
- std::vector< DPH::ImageType::IndexType > image_indices = fiber_image_indices.at(f);
-
- double E_ext_old = 0;
- double E_ext_new = 0;
- double E_int_old = 0;
- double E_int_new = 0;
-
- int add = std::rand()%2;
-// add = 1;
- int use_ball = std::rand()%2;
- use_ball = 0;
-
- if (add==0 && use_ball==0 && out_weights[f]<step)
- add = 1;
-
- // possible weight change
- float old_weight = out_weights[f];
- float new_weight = old_weight;
- if (add==1 && use_ball==0)
- new_weight = old_weight+step;
- else if (use_ball==0)
- new_weight = old_weight-step;
-
- int c = 0;
- for (auto idx : image_indices)
- {
- DPH::ImageType::PixelType measured_val = itkImage->GetPixel(idx);
- ModelType::PixelType simulated_val = simulatedImage->GetPixel(idx);
- ModelType::PixelType model_val = model_signals.at(c); // value of fiber model at currnet fiber position
- if (use_ball==1)
- model_val = ballSignal;
-
- // EXTERNAL ENERGY
- for (unsigned int g=0; g<num_gradients; ++g)
+ for (unsigned int k=0; k<3; ++k)
{
- double delta = (double)measured_val[g] - simulated_val[g];
- MITK_INFO << fabs(delta) << " g " << g;
-
- E_ext_old += fabs(delta)/num_gradients; // external energy is simply the difference between sim and meas
-
- double delta2 = 0;
- if (add==1)
+ if (single_fiber_fit)
{
- delta2 = (double)measured_val[g] - (simulated_val[g] + model_val[g]);
- E_ext_new += fabs(delta2)/num_gradients;
+ b[linear_index + 3*peak_id + k] = (double)odf_peak[k];
+ A.put(linear_index + 3*peak_id + k, fiber_count, A.get(linear_index + 3*peak_id + k, fiber_count) + (double)fiber_dir[k]);
}
else
{
- delta2 = (double)measured_val[g] - (simulated_val[g] - model_val[g]);
- E_ext_new += fabs(delta2)/num_gradients;
+ b[linear_index + 3*peak_id + k] = (double)odf_peak[k];
+ A.put(linear_index + 3*peak_id + k, bundle, A.get(linear_index + 3*peak_id + k, bundle) + (double)fiber_dir[k]);
}
- MITK_INFO << fabs(delta2) << " g " << g;
}
- ++c;
-
- // INTERNAL ENERGY
- unsigned int linear_index = idx[0] + sz_x*idx[1] + sz_x*sz_y*idx[2];
- std::vector< int > index_fiber_indices = image_index_to_fiber_indices[linear_index];
-
- if (index_fiber_indices.size()>1)
- {
- float mean_weight = 0;
- for (auto neighbor_index : index_fiber_indices)
- {
- if (neighbor_index!=f)
- mean_weight += out_weights[neighbor_index];
- }
- mean_weight /= (index_fiber_indices.size()-1);
- E_int_old += fabs(mean_weight-old_weight);
- E_int_new += fabs(mean_weight-new_weight);
- }
}
- E_ext_old /= image_indices.size();
- E_ext_new /= image_indices.size();
- E_int_old /= image_indices.size();
- E_int_new /= image_indices.size();
-
-// MITK_INFO << "EXT: " << E_ext_old << " --> " << E_ext_new;
-// MITK_INFO << "INT: " << E_int_old-E_int_new;
-
- double R = exp( (E_ext_old-E_ext_new)/T + 0*(E_int_old-E_int_new)/T );
-// MITK_INFO << R;
-
- float p = static_cast <float> (rand()) / static_cast <float> (RAND_MAX);
-
- p = E_ext_new;
- R = E_ext_old;
-
- MITK_INFO << add << " - " << i;
- if (p<R)
- {
-// MITK_INFO << "EXT: " << E_ext_old - E_ext_new;
- MITK_INFO << "W: " << new_weight - old_weight;
- accepted++;
- c = 0;
- for (auto idx : image_indices)
- {
- ModelType::PixelType sVal = simulatedImage->GetPixel(idx);
- ModelType::PixelType dVal = model_signals.at(c);
- if (use_ball==1)
- dVal = ballSignal;
+ ++fiber_count;
+ }
+ }
- if (add==1)
- {
- sVal += dVal;
- }
- else
- {
- sVal -= dVal;
- }
+ vnl_vector_fixed<float,3> max_corr_fiber_dir; max_corr_fiber_dir.fill(0.0);
+ vnl_vector_fixed<float,3> min_corr_fiber_dir; min_corr_fiber_dir.fill(0.0);
+ for (unsigned int i=0; i<fiber_count; ++i)
+ {
+ max_corr_fiber_dir[0] += A.get(max_peak_idx, i);
+ max_corr_fiber_dir[1] += A.get(max_peak_idx+1, i);
+ max_corr_fiber_dir[2] += A.get(max_peak_idx+2, i);
- simulatedImage->SetPixel(idx, sVal);
- ++c;
- }
+ min_corr_fiber_dir[0] += A.get(min_peak_idx, i);
+ min_corr_fiber_dir[1] += A.get(min_peak_idx+1, i);
+ min_corr_fiber_dir[2] += A.get(min_peak_idx+2, i);
+ }
- out_weights[f] = new_weight;
- }
+ float upper_bound = max_peak_mag/max_corr_fiber_dir.magnitude();
+ float lower_bound = min_peak_mag/min_corr_fiber_dir.magnitude();
+
+ if (!lb || lower_bound>=upper_bound)
+ lower_bound = 0;
+
+ MITK_INFO << "Lower bound: " << lower_bound;
+ MITK_INFO << "Upper bound: " << upper_bound;
+
+ itk::TimeProbe clock;
+ clock.Start();
+
+ MITK_INFO << "Fitting fibers";
+ VnlCostFunction cost(num_unknowns);
+ cost.SetProblem(A, b);
+
+ MITK_INFO << g_tol << " " << max_iter;
+ vnl_vector<double> x; x.set_size(num_unknowns); x.fill( (upper_bound-lower_bound)/2 );
+// OptimizeItk(cost, x, max_iter, lower_bound, upper_bound);
+
+ vnl_lbfgsb minimizer(cost);
+ vnl_vector<double> l; l.set_size(num_unknowns); l.fill(lower_bound);
+ vnl_vector<double> u; u.set_size(num_unknowns); u.fill(upper_bound);
+ vnl_vector<long> bound_selection; bound_selection.set_size(num_unknowns); bound_selection.fill(2);
+ minimizer.set_bound_selection(bound_selection);
+ minimizer.set_lower_bound(l);
+ minimizer.set_upper_bound(u);
+ minimizer.set_trace(true);
+ minimizer.set_projected_gradient_tolerance(g_tol);
+ if (max_iter>0)
+ minimizer.set_max_function_evals(max_iter);
+ minimizer.minimize(x);
+ MITK_INFO << "Residual error: " << minimizer.get_end_error();
+ MITK_INFO << "NumEvals: " << minimizer.get_num_evaluations();
+ MITK_INFO << "NumIterations: " << minimizer.get_num_iterations();
+
+// vnl_sparse_matrix_linear_system<double> S(A, b);
+// vnl_lsqr linear_solver( S );
+// linear_solver.set_max_iterations(max_iter);
+// linear_solver.minimize(x);
+
+ clock.Stop();
+ int h = clock.GetTotal()/3600;
+ int m = ((int)clock.GetTotal()%3600)/60;
+ int s = (int)clock.GetTotal()%60;
+ MITK_INFO << "Optimization took " << h << "h, " << m << "m and " << s << "s";
- }
-// MITK_INFO << "Accepted: " << (float)accepted/fiber_indices.size();
+ std::vector<float> weights;
+ float max_w = 0;
+ for (unsigned int i=0; i<num_unknowns; ++i)
+ {
+// MITK_INFO << x[i];
+ if (x[i]>max_w)
+ max_w = x[i];
+ weights.push_back(x[i]);
}
+ MITK_INFO << "Max w: " << max_w;
- typedef itk::ImageFileWriter< itk::VectorImage< double, 3> > WriterType;
- WriterType::Pointer writer = WriterType::New();
- writer->SetFileName("/home/neher/Projects/TractPlausibility/model_signal.nrrd");
- writer->SetInput(simulatedImage);
- writer->Update();
-
- return out_weights;
+ return weights;
}
-
std::vector< string > get_file_list(const std::string& path)
{
std::vector< string > file_list;
-
itk::Directory::Pointer dir = itk::Directory::New();
if (dir->Load(path.c_str()))
{
int n = dir->GetNumberOfFiles();
for (int r = 0; r < n; r++)
{
const char *filename = dir->GetFile(r);
std::string ext = ist::GetFilenameExtension(filename);
if (ext==".fib" || ext==".trk")
file_list.push_back(path + '/' + filename);
}
}
-
return file_list;
}
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Fit Fibers To Image");
parser.setCategory("Fiber Tracking Evaluation");
parser.setDescription("");
parser.setContributor("MIC");
parser.setArgumentPrefix("--", "-");
- parser.addArgument("input_tractograms", "i1", mitkCommandLineParser::StringList, "Input tractograms:", "input tractograms (.fib, vtk ascii file format)", us::Any(), false);
- parser.addArgument("input_peaks", "i2", mitkCommandLineParser::InputFile, "Input peaks:", "input peak image", us::Any(), false);
- parser.addArgument("out", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false);
+ parser.addArgument("", "i1", mitkCommandLineParser::StringList, "Input tractograms:", "input tractograms (.fib, vtk ascii file format)", us::Any(), false);
+ parser.addArgument("", "i2", mitkCommandLineParser::InputFile, "Input peaks:", "input peak image", us::Any(), false);
+ parser.addArgument("", "it", mitkCommandLineParser::Int, "", "");
+ parser.addArgument("", "s", mitkCommandLineParser::Bool, "", "");
+ parser.addArgument("", "lb", mitkCommandLineParser::Bool, "", "");
+ parser.addArgument("", "g", mitkCommandLineParser::Float, "", "");
+ parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false);
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
- mitkCommandLineParser::StringContainerType fib_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["input_tractograms"]);
- string dwiFile = us::any_cast<string>(parsedArgs["input_peaks"]);
- string outRoot = us::any_cast<string>(parsedArgs["out"]);
+ mitkCommandLineParser::StringContainerType fib_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i1"]);
+ string dwiFile = us::any_cast<string>(parsedArgs["i2"]);
+ string outRoot = us::any_cast<string>(parsedArgs["o"]);
+
+ bool single_fib = false;
+ if (parsedArgs.count("s"))
+ single_fib = us::any_cast<bool>(parsedArgs["s"]);
+
+ int max_iter = 0;
+ if (parsedArgs.count("it"))
+ max_iter = us::any_cast<int>(parsedArgs["it"]);
+
+ float g_tol = 1e-5;
+ if (parsedArgs.count("g"))
+ g_tol = us::any_cast<float>(parsedArgs["g"]);
+
+ bool lb = false;
+ if (parsedArgs.count("lb"))
+ lb = us::any_cast<bool>(parsedArgs["lb"]);
try
{
- std::vector< mitk::FiberBundle::Pointer > bundles;
+ std::vector< mitk::FiberBundle::Pointer > input_tracts;
- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images", "Fiberbundles"}, {});
- mitk::Image::Pointer inputImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(dwiFile, &functor)[0].GetPointer());
+ mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image", "Fiberbundles"}, {});
+ mitk::Image::Pointer inputImage = dynamic_cast<mitk::PeakImage*>(mitk::IOUtil::Load(dwiFile, &functor)[0].GetPointer());
float minSpacing = 1;
if(inputImage->GetGeometry()->GetSpacing()[0]<inputImage->GetGeometry()->GetSpacing()[1] && inputImage->GetGeometry()->GetSpacing()[0]<inputImage->GetGeometry()->GetSpacing()[2])
minSpacing = inputImage->GetGeometry()->GetSpacing()[0];
else if (inputImage->GetGeometry()->GetSpacing()[1] < inputImage->GetGeometry()->GetSpacing()[2])
minSpacing = inputImage->GetGeometry()->GetSpacing()[1];
else
minSpacing = inputImage->GetGeometry()->GetSpacing()[2];
std::vector< std::string > fib_names;
for (auto item : fib_files)
{
if ( ist::FileIsDirectory(item) )
{
for ( auto fibFile : get_file_list(item) )
{
mitk::FiberBundle::Pointer inputTractogram = dynamic_cast<mitk::FiberBundle*>(mitk::IOUtil::Load(fibFile)[0].GetPointer());
if (inputTractogram.IsNull())
continue;
- inputTractogram->ResampleLinear(minSpacing/4);
- bundles.push_back(inputTractogram);
+ inputTractogram->ResampleLinear(minSpacing/10);
+ input_tracts.push_back(inputTractogram);
fib_names.push_back(fibFile);
}
}
else
{
mitk::FiberBundle::Pointer inputTractogram = dynamic_cast<mitk::FiberBundle*>(mitk::IOUtil::Load(item)[0].GetPointer());
if (inputTractogram.IsNull())
continue;
- inputTractogram->ResampleLinear(minSpacing/4);
- bundles.push_back(inputTractogram);
+ inputTractogram->ResampleLinear(minSpacing/10);
+ input_tracts.push_back(inputTractogram);
fib_names.push_back(item);
}
}
- std::vector<float> weights = SolveLinear(outRoot, bundles, inputImage);
+ std::vector<float> weights = FitFibers(outRoot, input_tracts, inputImage, single_fib, max_iter, g_tol, lb);
- for (unsigned int i=0; i<fib_names.size(); ++i)
+ if (single_fib)
{
- std::string name = fib_names.at(i);
- name = ist::GetFilenameWithoutExtension(name);
- MITK_INFO << name << ": " << weights.at(i);
- mitk::FiberBundle::Pointer bundle = bundles.at(i);
-// inputTractogram->SetFiberWeight(i, weights.at(i));
- bundle->SetFiberWeights(weights.at(i));
- mitk::IOUtil::Save(bundle, outRoot + name + "_fitted.fib");
+ unsigned int fiber_count = 0;
+
+ for (unsigned int bundle=0; bundle<input_tracts.size(); bundle++)
+ {
+ mitk::FiberBundle::Pointer fib = input_tracts.at(bundle);
+ for (int i=0; i<fib->GetNumFibers(); i++)
+ {
+ fib->SetFiberWeight(i, weights.at(fiber_count));
+ ++fiber_count;
+ }
+
+ std::string name = fib_names.at(bundle);
+ name = ist::GetFilenameWithoutExtension(name);
+ mitk::IOUtil::Save(fib, outRoot + name + "_fitted.fib");
+ }
+ }
+ else
+ {
+ for (unsigned int i=0; i<fib_names.size(); ++i)
+ {
+ std::string name = fib_names.at(i);
+ name = ist::GetFilenameWithoutExtension(name);
+ MITK_INFO << name << ": " << weights.at(i);
+ mitk::FiberBundle::Pointer bundle = input_tracts.at(i);
+ bundle->SetFiberWeights(weights.at(i));
+ mitk::IOUtil::Save(bundle, outRoot + name + "_fitted.fib");
+ }
+ }
+
+
+ // OUTPUT IMAGES
+ MITK_INFO << "Generating output images ...";
+ typedef mitk::ImageToItk< PeakImgType > CasterType;
+ CasterType::Pointer caster = CasterType::New();
+ caster->SetInput(inputImage);
+ caster->Update();
+ PeakImgType::Pointer itkImage = caster->GetOutput();
+
+ itk::ImageDuplicator< PeakImgType >::Pointer duplicator = itk::ImageDuplicator< PeakImgType >::New();
+ duplicator->SetInputImage(itkImage);
+ duplicator->Update();
+ PeakImgType::Pointer unexplained_image = duplicator->GetOutput();
+
+ duplicator->SetInputImage(unexplained_image);
+ duplicator->Update();
+ PeakImgType::Pointer residual_image = duplicator->GetOutput();
+
+ duplicator->SetInputImage(residual_image);
+ duplicator->Update();
+ PeakImgType::Pointer explained_image = duplicator->GetOutput();
+ explained_image->FillBuffer(0.0);
+
+ for (unsigned int bundle=0; bundle<input_tracts.size(); bundle++)
+ {
+ vtkSmartPointer<vtkPolyData> polydata = input_tracts.at(bundle)->GetFiberPolyData();
+
+ for (int i=0; i<input_tracts.at(bundle)->GetNumFibers(); ++i)
+ {
+ vtkCell* cell = polydata->GetCell(i);
+ int numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ if (numPoints<2)
+ MITK_INFO << "FIBER WITH ONLY ONE POINT ENCOUNTERED!";
+
+ float w = input_tracts.at(bundle)->GetFiberWeight(i)/UPSCALE;
+
+ for (int j=0; j<numPoints-1; ++j)
+ {
+ double* p1 = points->GetPoint(j);
+ PointType4 p;
+ p[0]=p1[0];
+ p[1]=p1[1];
+ p[2]=p1[2];
+ p[3]=0;
+
+ itk::Index<4> idx4;
+ itkImage->TransformPhysicalPointToIndex(p, idx4);
+ if (!itkImage->GetLargestPossibleRegion().IsInside(idx4))
+ continue;
+
+ double* p2 = points->GetPoint(j+1);
+ vnl_vector_fixed<float,3> fiber_dir;
+ fiber_dir[0] = p[0]-p2[0];
+ fiber_dir[1] = p[1]-p2[1];
+ fiber_dir[2] = p[2]-p2[2];
+ fiber_dir.normalize();
+
+ int peak_id = -1;
+ GetClosestPeak(idx4, itkImage, fiber_dir, peak_id);
+ if (peak_id<0)
+ continue;
+
+ vnl_vector_fixed<float,3> unexplained_dir;
+ vnl_vector_fixed<float,3> explained_dir;
+ vnl_vector_fixed<float,3> res_dir;
+ vnl_vector_fixed<float,3> peak_dir;
+
+ idx4[3] = peak_id*3;
+ unexplained_dir[0] = unexplained_image->GetPixel(idx4);
+ explained_dir[0] = explained_image->GetPixel(idx4);
+ peak_dir[0] = itkImage->GetPixel(idx4);
+ res_dir[0] = residual_image->GetPixel(idx4);
+
+ idx4[3] += 1;
+ unexplained_dir[1] = unexplained_image->GetPixel(idx4);
+ explained_dir[1] = explained_image->GetPixel(idx4);
+ peak_dir[1] = itkImage->GetPixel(idx4);
+ res_dir[1] = residual_image->GetPixel(idx4);
+
+ idx4[3] += 1;
+ unexplained_dir[2] = unexplained_image->GetPixel(idx4);
+ explained_dir[2] = explained_image->GetPixel(idx4);
+ peak_dir[2] = itkImage->GetPixel(idx4);
+ res_dir[2] = residual_image->GetPixel(idx4);
+
+ if (dot_product(peak_dir, fiber_dir)<0)
+ fiber_dir *= -1;
+ fiber_dir *= w;
+
+ idx4[3] = peak_id*3;
+ residual_image->SetPixel(idx4, res_dir[0] - fiber_dir[0]);
+
+ idx4[3] += 1;
+ residual_image->SetPixel(idx4, res_dir[1] - fiber_dir[1]);
+
+ idx4[3] += 1;
+ residual_image->SetPixel(idx4, res_dir[2] - fiber_dir[2]);
+
+
+ if ( fabs(unexplained_dir[0]) - fabs(fiber_dir[0]) < 0 ) // did we "overexplain" stuff?
+ fiber_dir = unexplained_dir;
+
+ idx4[3] = peak_id*3;
+ unexplained_image->SetPixel(idx4, unexplained_dir[0] - fiber_dir[0]);
+ explained_image->SetPixel(idx4, explained_dir[0] + fiber_dir[0]);
+
+ idx4[3] += 1;
+ unexplained_image->SetPixel(idx4, unexplained_dir[1] - fiber_dir[1]);
+ explained_image->SetPixel(idx4, explained_dir[1] + fiber_dir[1]);
+
+ idx4[3] += 1;
+ unexplained_image->SetPixel(idx4, unexplained_dir[2] - fiber_dir[2]);
+ explained_image->SetPixel(idx4, explained_dir[2] + fiber_dir[2]);
+ }
+
+ }
}
+
+ itk::ImageFileWriter< PeakImgType >::Pointer writer = itk::ImageFileWriter< PeakImgType >::New();
+ writer->SetInput(unexplained_image);
+ writer->SetFileName(outRoot + "unexplained_image.nrrd");
+ writer->Update();
+
+ writer->SetInput(explained_image);
+ writer->SetFileName(outRoot + "explained_image.nrrd");
+ writer->Update();
+
+ writer->SetInput(residual_image);
+ writer->SetFileName(outRoot + "residual_image.nrrd");
+ writer->Update();
}
catch (itk::ExceptionObject e)
{
std::cout << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}