diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..fde9427
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+Modules/FiberDissection/Interactor/mitkStreamlineInteractor (copy).cpp
diff --git a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
index 828d2a6..db6cc0a 100644
--- a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
+++ b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
@@ -1,2847 +1,2908 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center.
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 "mitkFiberBundle.h"
#include <mitkPlanarCircle.h>
#include <mitkPlanarPolygon.h>
#include <mitkPlanarFigureComposite.h>
#include <mitkDiffusionFunctionCollection.h>
#include <mitkPixelTypeMultiplex.h>
#include <vtkPointData.h>
#include <vtkDataArray.h>
#include <vtkUnsignedCharArray.h>
#include <vtkPolyLine.h>
#include <vtkCellArray.h>
#include <vtkCellData.h>
#include <vtkIdFilter.h>
#include <vtkClipPolyData.h>
#include <vtkPlane.h>
#include <vtkDoubleArray.h>
#include <vtkKochanekSpline.h>
#include <vtkParametricFunctionSource.h>
#include <vtkParametricSpline.h>
#include <vtkPolygon.h>
#include <vtkCleanPolyData.h>
#include <boost/timer/progress_display.hpp>
#include <vtkTransformPolyDataFilter.h>
#include <mitkTransferFunction.h>
#include <vtkLookupTable.h>
#include <mitkLookupTable.h>
#include <vtkCardinalSpline.h>
#include <vtkAppendPolyData.h>
#include <random>
#include <algorithm>
const char* mitk::FiberBundle::FIBER_ID_ARRAY = "Fiber_IDs";
mitk::FiberBundle::FiberBundle( vtkPolyData* fiberPolyData )
: m_NumFibers(0)
{
m_TrackVisHeader.hdr_size = 0;
m_FiberWeights = vtkSmartPointer<vtkFloatArray>::New();
m_FiberWeights->SetName("FIBER_WEIGHTS");
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
if (fiberPolyData != nullptr)
m_FiberPolyData = fiberPolyData;
else
{
this->m_FiberPolyData->SetPoints(vtkSmartPointer<vtkPoints>::New());
this->m_FiberPolyData->SetLines(vtkSmartPointer<vtkCellArray>::New());
}
this->UpdateFiberGeometry();
this->GenerateFiberIds();
this->ColorFibersByOrientation();
}
mitk::FiberBundle::~FiberBundle()
{
}
mitk::FiberBundle::Pointer mitk::FiberBundle::GetDeepCopy()
{
mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(m_FiberPolyData);
newFib->SetFiberColors(this->m_FiberColors);
newFib->SetFiberWeights(this->m_FiberWeights);
newFib->SetTrackVisHeader(this->GetTrackVisHeader());
return newFib;
}
vtkSmartPointer<vtkPolyData> mitk::FiberBundle::GeneratePolyDataByIds(std::vector<unsigned int> fiberIds, vtkSmartPointer<vtkFloatArray> weights)
{
vtkSmartPointer<vtkPolyData> newFiberPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> newLineSet = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> newPointSet = vtkSmartPointer<vtkPoints>::New();
weights->SetNumberOfValues(fiberIds.size());
int counter = 0;
auto finIt = fiberIds.begin();
while ( finIt != fiberIds.end() )
{
if (*finIt>GetNumFibers()){
MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt;
break;
}
vtkSmartPointer<vtkCell> fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber);
vtkSmartPointer<vtkPoints> fibPoints = fiber->GetPoints();
vtkSmartPointer<vtkPolyLine> newFiber = vtkSmartPointer<vtkPolyLine>::New();
newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() );
for(int i=0; i<fibPoints->GetNumberOfPoints(); i++)
{
newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints());
newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]);
}
weights->InsertValue(counter, this->GetFiberWeight(*finIt));
newLineSet->InsertNextCell(newFiber);
++finIt;
++counter;
}
newFiberPolyData->SetPoints(newPointSet);
newFiberPolyData->SetLines(newLineSet);
return newFiberPolyData;
}
// merge two fiber bundles
mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundles(std::vector< mitk::FiberBundle::Pointer > fibs)
{
vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
// add current fiber bundle
vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
auto num_weights = this->GetNumFibers();
for (auto fib : fibs)
num_weights += fib->GetNumFibers();
weights->SetNumberOfValues(num_weights);
unsigned int counter = 0;
for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); ++i)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (unsigned int j=0; j<numPoints; ++j)
{
double p[3];
points->GetPoint(j, p);
vtkIdType id = vNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
weights->InsertValue(counter, this->GetFiberWeight(i));
vNewLines->InsertNextCell(container);
counter++;
}
for (auto fib : fibs)
{
// add new fiber bundle
for (unsigned int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
{
vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (unsigned int j=0; j<numPoints; j++)
{
double p[3];
points->GetPoint(j, p);
vtkIdType id = vNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
weights->InsertValue(counter, fib->GetFiberWeight(i));
vNewLines->InsertNextCell(container);
counter++;
}
}
// initialize PolyData
vNewPolyData->SetPoints(vNewPoints);
vNewPolyData->SetLines(vNewLines);
// initialize fiber bundle
mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
newFib->SetFiberWeights(weights);
return newFib;
}
// merge two fiber bundles
mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundle(mitk::FiberBundle* fib)
{
if (fib==nullptr)
return this->GetDeepCopy();
MITK_INFO << "Adding fibers";
vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
// add current fiber bundle
vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers());
unsigned int counter = 0;
for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (unsigned int j=0; j<numPoints; j++)
{
double p[3];
points->GetPoint(j, p);
vtkIdType id = vNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
weights->InsertValue(counter, this->GetFiberWeight(i));
vNewLines->InsertNextCell(container);
counter++;
}
// add new fiber bundle
for (unsigned int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
{
vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (unsigned int j=0; j<numPoints; j++)
{
double p[3];
points->GetPoint(j, p);
vtkIdType id = vNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
weights->InsertValue(counter, fib->GetFiberWeight(i));
vNewLines->InsertNextCell(container);
counter++;
}
// initialize PolyData
vNewPolyData->SetPoints(vNewPoints);
vNewPolyData->SetLines(vNewLines);
// initialize fiber bundle
mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
newFib->SetFiberWeights(weights);
return newFib;
}
// Only retain fibers with a weight larger than the specified threshold
mitk::FiberBundle::Pointer mitk::FiberBundle::FilterByWeights(float weight_thr, bool invert)
{
vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
std::vector<float> weights;
for (unsigned int i=0; i<this->GetNumFibers(); i++)
{
if ( (invert && this->GetFiberWeight(i)>weight_thr) || (!invert && this->GetFiberWeight(i)<=weight_thr))
continue;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double p[3];
points->GetPoint(j, p);
vtkIdType id = vNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vNewLines->InsertNextCell(container);
weights.push_back(this->GetFiberWeight(i));
}
// initialize PolyData
vNewPolyData->SetPoints(vNewPoints);
vNewPolyData->SetLines(vNewLines);
// initialize fiber bundle
mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
for (unsigned int i=0; i<weights.size(); ++i)
newFib->SetFiberWeight(i, weights.at(i));
newFib->SetTrackVisHeader(this->GetTrackVisHeader());
return newFib;
}
// Only retain a subsample of the fibers
mitk::FiberBundle::Pointer mitk::FiberBundle::SubsampleFibers(float factor, bool random_seed)
{
vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
unsigned int new_num_fibs = static_cast<unsigned int>(std::round(this->GetNumFibers()*factor));
MITK_INFO << "Subsampling fibers with factor " << factor << "(" << new_num_fibs << "/" << this->GetNumFibers() << ")";
// add current fiber bundle
vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
weights->SetNumberOfValues(new_num_fibs);
std::vector< unsigned int > ids;
for (unsigned int i=0; i<this->GetNumFibers(); i++)
ids.push_back(i);
if (random_seed)
std::srand(static_cast<unsigned int>(std::time(nullptr)));
else
std::srand(0);
std::random_device rd;
std::mt19937 g(rd());
std::shuffle(ids.begin(), ids.end(), g);
unsigned int counter = 0;
for (unsigned int i=0; i<new_num_fibs; i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(ids.at(i));
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double p[3];
points->GetPoint(j, p);
vtkIdType id = vNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
weights->InsertValue(counter, this->GetFiberWeight(ids.at(i)));
vNewLines->InsertNextCell(container);
counter++;
}
// initialize PolyData
vNewPolyData->SetPoints(vNewPoints);
vNewPolyData->SetLines(vNewLines);
// initialize fiber bundle
mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
newFib->SetFiberWeights(weights);
newFib->SetTrackVisHeader(this->GetTrackVisHeader());
return newFib;
}
// subtract two fiber bundles
mitk::FiberBundle::Pointer mitk::FiberBundle::SubtractBundle(mitk::FiberBundle* fib)
{
if (fib==nullptr)
return this->GetDeepCopy();
MITK_INFO << "Subtracting fibers";
vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
std::vector< std::vector< itk::Point<float, 3> > > points1;
for(unsigned int i=0; i<m_NumFibers; i++ )
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (points==nullptr || numPoints<=0)
continue;
itk::Point<float, 3> start = mitk::imv::GetItkPoint(points->GetPoint(0));
itk::Point<float, 3> end = mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
points1.push_back( {start, end} );
}
std::vector< std::vector< itk::Point<float, 3> > > points2;
for(unsigned int i=0; i<fib->GetNumFibers(); i++ )
{
vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (points==nullptr || numPoints<=0)
continue;
itk::Point<float, 3> start =mitk::imv::GetItkPoint(points->GetPoint(0));
itk::Point<float, 3> end =mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
points2.push_back( {start, end} );
}
// int progress = 0;
std::vector< int > ids;
#pragma omp parallel for
for (int i=0; i<static_cast<int>(points1.size()); i++)
{
bool match = false;
for (unsigned int j=0; j<points2.size(); j++)
{
auto v1 = points1.at(static_cast<unsigned int>(i));
auto v2 = points2.at(j);
float dist=0;
for (unsigned int c=0; c<v1.size(); c++)
{
float d = v1[c][0]-v2[c][0];
dist += d*d;
d = v1[c][1]-v2[c][1];
dist += d*d;
d = v1[c][2]-v2[c][2];
dist += d*d;
}
dist /= v1.size();
if (dist<0.000001f)
{
match = true;
break;
}
dist=0;
for (unsigned int c=0; c<v1.size(); c++)
{
float d = v1[v1.size()-1-c][0]-v2[c][0];
dist += d*d;
d = v1[v1.size()-1-c][1]-v2[c][1];
dist += d*d;
d = v1[v1.size()-1-c][2]-v2[c][2];
dist += d*d;
}
dist /= v1.size();
if (dist<0.000001f)
{
match = true;
break;
}
}
#pragma omp critical
if (!match)
ids.push_back(i);
}
for( int i : ids )
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (points==nullptr || numPoints<=0)
continue;
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for( int j=0; j<numPoints; j++)
{
vtkIdType id = vNewPoints->InsertNextPoint(points->GetPoint(j));
container->GetPointIds()->InsertNextId(id);
}
vNewLines->InsertNextCell(container);
}
if(vNewLines->GetNumberOfCells()==0)
return mitk::FiberBundle::New();
// initialize PolyData
vNewPolyData->SetPoints(vNewPoints);
vNewPolyData->SetLines(vNewLines);
// initialize fiber bundle
return mitk::FiberBundle::New(vNewPolyData);
}
/*
* set PolyData (additional flag to recompute fiber geometry, default = true)
*/
void mitk::FiberBundle::SetFiberPolyData(vtkSmartPointer<vtkPolyData> fiberPD, bool updateGeometry)
{
if (fiberPD == nullptr)
this->m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
else
{
m_FiberPolyData->CopyStructure(fiberPD);
// m_FiberPolyData->DeepCopy(fiberPD);
}
m_NumFibers = static_cast<unsigned int>(m_FiberPolyData->GetNumberOfLines());
if (updateGeometry)
UpdateFiberGeometry();
GenerateFiberIds();
ColorFibersByOrientation();
}
/*
* return vtkPolyData
*/
vtkSmartPointer<vtkPolyData> mitk::FiberBundle::GetFiberPolyData() const
{
return m_FiberPolyData;
}
void mitk::FiberBundle::ColorFibersByLength(bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type)
{
if (m_MaxFiberLength<=0)
return;
auto numOfPoints = this->GetNumberOfPoints();
//colors and alpha value for each single point, RGBA = 4 components
unsigned char rgba[4] = {0,0,0,0};
m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
m_FiberColors->Allocate(numOfPoints * 4);
m_FiberColors->SetNumberOfComponents(4);
m_FiberColors->SetName("FIBER_COLORS");
auto numOfFibers = m_FiberPolyData->GetNumberOfLines();
if (numOfFibers < 1)
return;
mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
mitkLookup->SetType(type);
if (type!=mitk::LookupTable::MULTILABEL)
mitkLookup->GetVtkLookupTable()->SetTableRange(m_MinFiberLength, m_MaxFiberLength);
unsigned int count = 0;
for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
float l = m_FiberLengths.at(i)/m_MaxFiberLength;
double color[3];
mitkLookup->GetColor(m_FiberLengths.at(i), color);
for (int j=0; j<numPoints; j++)
{
rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
if (opacity)
rgba[3] = static_cast<unsigned char>(255.0f * l);
else
rgba[3] = static_cast<unsigned char>(255.0);
m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba);
count++;
}
if (weight_fibers)
this->SetFiberWeight(i, m_FiberLengths.at(i));
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
void mitk::FiberBundle::ColorSinglePoint(int f_idx, int p_idx, double rgb[3])
{
// vtkPoints* extrPoints = m_FiberPolyData->GetPoints();
// vtkIdType numOfPoints = 0;
// if (extrPoints!=nullptr)
// numOfPoints = extrPoints->GetNumberOfPoints();
// //colors and alpha value for each single point, RGBA = 4 components
unsigned char rgba[4] = {0,0,0,0};
// m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
// m_FiberColors->Allocate(numOfPoints * 4);
// m_FiberColors->SetNumberOfComponents(4);
// m_FiberColors->SetName("FIBER_COLORS");
// auto numOfFibers = m_FiberPolyData->GetNumberOfLines();
// if (numOfFibers < 1)
// return;
// /* extract single fibers of fiberBundle */
// vtkCellArray* fiberList = m_FiberPolyData->GetLines();
// fiberList->InitTraversal();
// for (int fi=0; fi<numOfFibers; ++fi)
// {
// vtkIdType* idList; // contains the point id's of the line
// vtkIdType num_points; // number of points for current line
//// fiberList->GetNextCell(num_points, idList);
// fiberList->GetCell(f_idx, num_points, idList);
vtkCell* cell = m_FiberPolyData->GetCell(f_idx);
// /* single fiber checkpoints: is number of points valid */
// if (p_idx < num_points)
// {
rgba[0] = static_cast<unsigned char>(255.0 * rgb[0]);
rgba[1] = static_cast<unsigned char>(255.0 * rgb[1]);
rgba[2] = static_cast<unsigned char>(255.0 * rgb[2]);
rgba[3] = 255;
m_FiberColors->InsertTypedTuple(cell->GetPointId(p_idx), rgba);
// }
// }
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
void mitk::FiberBundle::ColorFibersByOrientation()
{
//===== FOR WRITING A TEST ========================
// colorT size == tupelComponents * tupelElements
// compare color results
// to cover this code 100% also PolyData needed, where colorarray already exists
// + one fiber with exactly 1 point
// + one fiber with 0 points
//=================================================
vtkPoints* extrPoints = m_FiberPolyData->GetPoints();
vtkIdType numOfPoints = 0;
if (extrPoints!=nullptr)
numOfPoints = extrPoints->GetNumberOfPoints();
//colors and alpha value for each single point, RGBA = 4 components
unsigned char rgba[4] = {0,0,0,0};
m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
m_FiberColors->Allocate(numOfPoints * 4);
m_FiberColors->SetNumberOfComponents(4);
m_FiberColors->SetName("FIBER_COLORS");
auto numOfFibers = m_FiberPolyData->GetNumberOfLines();
if (numOfFibers < 1)
return;
/* extract single fibers of fiberBundle */
vtkCellArray* fiberList = m_FiberPolyData->GetLines();
fiberList->InitTraversal();
for (int fi=0; fi<numOfFibers; ++fi) {
vtkIdType const* idList; // contains the point id's of the line
vtkIdType pointsPerFiber; // number of points for current line
fiberList->GetNextCell(pointsPerFiber, idList);
/* single fiber checkpoints: is number of points valid */
if (pointsPerFiber > 1)
{
/* operate on points of single fiber */
for (int i=0; i <pointsPerFiber; ++i)
{
/* process all points elastV[0]ept starting and endpoint for calculating color value take current point, previous point and next point */
if (i<pointsPerFiber-1 && i > 0)
{
/* The color value of the current point is influenced by the previous point and next point. */
vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]);
vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]);
vnl_vector_fixed< double, 3 > diff1;
diff1 = currentPntvtk - nextPntvtk;
vnl_vector_fixed< double, 3 > diff2;
diff2 = currentPntvtk - prevPntvtk;
vnl_vector_fixed< double, 3 > diff;
diff = (diff1 - diff2) / 2.0;
diff.normalize();
rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff[0]));
rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff[1]));
rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff[2]));
rgba[3] = static_cast<unsigned char>(255.0);
}
else if (i==0)
{
/* First point has no previous point, therefore only diff1 is taken */
vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]);
vnl_vector_fixed< double, 3 > diff1;
diff1 = currentPntvtk - nextPntvtk;
diff1.normalize();
rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff1[0]));
rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff1[1]));
rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff1[2]));
rgba[3] = static_cast<unsigned char>(255.0);
}
else if (i==pointsPerFiber-1)
{
/* Last point has no next point, therefore only diff2 is taken */
vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]);
vnl_vector_fixed< double, 3 > diff2;
diff2 = currentPntvtk - prevPntvtk;
diff2.normalize();
rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff2[0]));
rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff2[1]));
rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff2[2]));
rgba[3] = static_cast<unsigned char>(255.0);
}
m_FiberColors->InsertTypedTuple(idList[i], rgba);
}
}
else if (pointsPerFiber == 1)
{
/* a single point does not define a fiber (use vertex mechanisms instead */
continue;
}
else
{
MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ;
continue;
}
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
void mitk::FiberBundle::ColorFibersByCurvature(bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type)
{
double window = 5;
//colors and alpha value for each single point, RGBA = 4 components
unsigned char rgba[4] = {0,0,0,0};
m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
m_FiberColors->SetNumberOfComponents(4);
m_FiberColors->SetName("FIBER_COLORS");
std::vector< double > values;
double min = 1;
double max = 0;
MITK_INFO << "Coloring fibers by curvature";
boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
double mean_curv = 0;
// calculate curvatures
for (int j=0; j<numPoints; j++)
{
double dist = 0;
int c = j;
std::vector< vnl_vector_fixed< double, 3 > > vectors;
vnl_vector_fixed< double, 3 > meanV; meanV.fill(0.0);
while(dist<window/2 && c>1)
{
double p1[3];
points->GetPoint(c-1, p1);
double p2[3];
points->GetPoint(c, p2);
vnl_vector_fixed< double, 3 > v;
v[0] = p2[0]-p1[0];
v[1] = p2[1]-p1[1];
v[2] = p2[2]-p1[2];
dist += v.magnitude();
v.normalize();
vectors.push_back(v);
meanV += v;
c--;
}
c = j;
dist = 0;
while(dist<window/2 && c<numPoints-1)
{
double p1[3];
points->GetPoint(c, p1);
double p2[3];
points->GetPoint(c+1, p2);
vnl_vector_fixed< double, 3 > v;
v[0] = p2[0]-p1[0];
v[1] = p2[1]-p1[1];
v[2] = p2[2]-p1[2];
dist += v.magnitude();
v.normalize();
vectors.push_back(v);
meanV += v;
c++;
}
meanV.normalize();
double dev = 0;
for (unsigned int c=0; c<vectors.size(); c++)
{
double angle = dot_product(meanV, vectors.at(c));
if (angle>1.0)
angle = 1.0;
if (angle<-1.0)
angle = -1.0;
dev += acos(angle)*180/itk::Math::pi;
}
if (vectors.size()>0)
dev /= vectors.size();
if (weight_fibers)
mean_curv += dev;
dev = 1.0-dev/180.0;
values.push_back(dev);
if (dev<min)
min = dev;
if (dev>max)
max = dev;
}
if (weight_fibers)
this->SetFiberWeight(i, mean_curv/numPoints);
}
mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
mitkLookup->SetType(type);
if (type!=mitk::LookupTable::MULTILABEL)
mitkLookup->GetVtkLookupTable()->SetTableRange(min, max);
unsigned int count = 0;
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
for (int j=0; j<numPoints; j++)
{
double color[3];
double dev = values.at(count);
mitkLookup->GetColor(dev, color);
rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
if (opacity)
rgba[3] = static_cast<unsigned char>(255.0f * dev/max);
else
rgba[3] = static_cast<unsigned char>(255.0);
m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba);
count++;
}
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
void mitk::FiberBundle::SetFiberOpacity(vtkDoubleArray* FAValArray)
{
for(long i=0; i<m_FiberColors->GetNumberOfTuples(); i++)
{
double faValue = FAValArray->GetValue(i);
faValue = faValue * 255.0;
m_FiberColors->SetComponent(i,3, static_cast<unsigned char>(faValue) );
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
void mitk::FiberBundle::ResetFiberOpacity()
{
for(long i=0; i<m_FiberColors->GetNumberOfTuples(); i++)
m_FiberColors->SetComponent(i,3, 255.0 );
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
void mitk::FiberBundle::ColorFibersByScalarMap(mitk::Image::Pointer FAimage, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap, bool interpolate)
{
if (FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned char" ||
FAimage->GetPixelType().GetComponentTypeAsString()=="char" ||
FAimage->GetPixelType().GetComponentTypeAsString()=="long" ||
FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned long" ||
FAimage->GetPixelType().GetComponentTypeAsString()=="short" ||
FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned short" ||
FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned int" ||
FAimage->GetPixelType().GetComponentTypeAsString()=="int")
{
typedef itk::Image<int, 3> ImageType;
ImageType::Pointer itkImage = ImageType::New();
CastToItkImage(FAimage, itkImage);
ColorFibersByScalarMap<int>(itkImage, opacity, weight_fibers, type, max_cap, interpolate );
}
else
{
typedef itk::Image<float, 3> ImageType;
ImageType::Pointer itkImage = ImageType::New();
CastToItkImage(FAimage, itkImage);
ColorFibersByScalarMap<float>(itkImage, opacity, weight_fibers, type, max_cap, interpolate );
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
template <typename TPixel>
void mitk::FiberBundle::ColorFibersByScalarMap(typename itk::Image<TPixel, 3>::Pointer image, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap, bool interpolate)
{
m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
m_FiberColors->SetNumberOfComponents(4);
m_FiberColors->SetName("FIBER_COLORS");
unsigned char rgba[4] = {0,0,0,0};
vtkPoints* pointSet = m_FiberPolyData->GetPoints();
if (type==mitk::LookupTable::MULTILABEL)
interpolate = false;
auto interpolator = itk::LinearInterpolateImageFunction< itk::Image<TPixel, 3>, float >::New();
interpolator->SetInputImage(image);
double min = 999999;
double max = -999999;
for (unsigned int i=0; i<m_NumFibers; i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
double mean_val = 0;
for (int j=0; j<numPoints; j++)
{
double p[3];
points->GetPoint(j, p);
auto pixelValue = mitk::imv::GetImageValue<TPixel>(mitk::imv::GetItkPoint(p), interpolate, interpolator);
if (pixelValue>max)
max = pixelValue;
if (pixelValue<min)
min = pixelValue;
if (weight_fibers)
mean_val += pixelValue;
}
if (weight_fibers)
this->SetFiberWeight(i, mean_val/numPoints);
}
mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
mitkLookup->SetType(type);
if (type!=mitk::LookupTable::MULTILABEL)
mitkLookup->GetVtkLookupTable()->SetTableRange(min, max*max_cap);
for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
{
itk::Point<float, 3> px;
px[0] = pointSet->GetPoint(i)[0];
px[1] = pointSet->GetPoint(i)[1];
px[2] = pointSet->GetPoint(i)[2];
auto pixelValue = mitk::imv::GetImageValue<TPixel>(px, interpolate, interpolator);
double color[3];
mitkLookup->GetColor(pixelValue, color);
rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
if (opacity)
rgba[3] = static_cast<unsigned char>(255.0 * pixelValue);
else
rgba[3] = static_cast<unsigned char>(255.0);
m_FiberColors->InsertTypedTuple(i, rgba);
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
void mitk::FiberBundle::ColorFibersByFiberWeights(bool opacity, mitk::LookupTable::LookupTableType type)
{
m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
m_FiberColors->SetNumberOfComponents(4);
m_FiberColors->SetName("FIBER_COLORS");
unsigned char rgba[4] = {0,0,0,0};
unsigned int counter = 0;
float max = -999999;
float min = 999999;
for (unsigned int i=0; i<m_NumFibers; i++)
{
float weight = this->GetFiberWeight(i);
if (weight>max)
max = weight;
if (weight<min)
min = weight;
}
if (fabs(max-min)<0.00001f)
{
max = 1;
min = 0;
}
mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
mitkLookup->SetType(type);
if (type!=mitk::LookupTable::MULTILABEL)
mitkLookup->GetVtkLookupTable()->SetTableRange(min, max);
for (unsigned int i=0; i<m_NumFibers; i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
auto weight = this->GetFiberWeight(i);
double color[3];
mitkLookup->GetColor(weight, color);
for (int j=0; j<numPoints; j++)
{
rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
if (opacity)
rgba[3] = static_cast<unsigned char>(255.0f * weight/max);
else
rgba[3] = static_cast<unsigned char>(255.0);
m_FiberColors->InsertTypedTuple(counter, rgba);
counter++;
}
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
+void mitk::FiberBundle::SetSingleFiberColor(float r, float g, float b, unsigned int cellId, float alpha)
+{
+// if (m_FiberColors==nullptr)
+ m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
+ m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
+ m_FiberColors->SetNumberOfComponents(4);
+ m_FiberColors->SetName("FIBER_COLORS");
+
+// MITK_INFO << color->GetNumberOfTuples();
+// MITK_INFO << m_FiberColors->GetNumberOfTuples();
+
+ unsigned char rgba[4] = {0,0,0,0};
+ unsigned int counter = 0;
+
+
+ for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = m_FiberPolyData->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+
+ if (i==cellId)
+ {
+ for (int j=0; j<numPoints; j++)
+ {
+ rgba[0] = static_cast<unsigned char>(r);
+ rgba[1] = static_cast<unsigned char>(b);
+ rgba[2] = static_cast<unsigned char>(g);
+ rgba[3] = static_cast<unsigned char>(alpha);
+// m_FiberColors->InsertTypedTuple(j, rgba);
+
+ m_FiberColors->InsertTypedTuple(counter, rgba);
+ counter++;
+ }
+ }
+ else {
+ for (int j=0; j<numPoints; j++)
+ {
+ rgba[0] = static_cast<unsigned char>(255);
+ rgba[1] = static_cast<unsigned char>(255);
+ rgba[2] = static_cast<unsigned char>(255);
+ rgba[3] = static_cast<unsigned char>(alpha);
+// m_FiberColors->InsertTypedTuple(j, rgba);
+
+ m_FiberColors->InsertTypedTuple(counter, rgba);
+ counter++;
+ }
+ }
+
+ }
+
+// MITK_INFO << m_FiberColors->GetNumberOfTuples();
+ m_UpdateTime3D.Modified();
+ m_UpdateTime2D.Modified();
+}
+
void mitk::FiberBundle::SetFiberColors(float r, float g, float b, float alpha)
{
m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
m_FiberColors->SetNumberOfComponents(4);
m_FiberColors->SetName("FIBER_COLORS");
unsigned char rgba[4] = {0,0,0,0};
for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
{
rgba[0] = static_cast<unsigned char>(r);
rgba[1] = static_cast<unsigned char>(g);
rgba[2] = static_cast<unsigned char>(b);
rgba[3] = static_cast<unsigned char>(alpha);
m_FiberColors->InsertTypedTuple(i, rgba);
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
void mitk::FiberBundle::GenerateFiberIds()
{
if (m_FiberPolyData == nullptr)
return;
vtkSmartPointer<vtkIdFilter> idFiberFilter = vtkSmartPointer<vtkIdFilter>::New();
idFiberFilter->SetInputData(m_FiberPolyData);
idFiberFilter->CellIdsOn();
// idFiberFilter->PointIdsOn(); // point id's are not needed
idFiberFilter->SetCellIdsArrayName(FIBER_ID_ARRAY);
idFiberFilter->FieldDataOn();
idFiberFilter->Update();
m_FiberIdDataSet = idFiberFilter->GetOutput();
}
float mitk::FiberBundle::GetNumEpFractionInMask(ItkUcharImgType* mask, bool different_label)
{
vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
MITK_INFO << "Calculating EP-Fraction";
boost::timer::progress_display disp(m_NumFibers);
unsigned int in_mask = 0;
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = PolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(0));
itk::Index<3> startIndex;
mask->TransformPhysicalPointToIndex(startVertex, startIndex);
itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
itk::Index<3> endIndex;
mask->TransformPhysicalPointToIndex(endVertex, endIndex);
if (mask->GetLargestPossibleRegion().IsInside(startIndex) && mask->GetLargestPossibleRegion().IsInside(endIndex))
{
float v1 = mask->GetPixel(startIndex);
if (v1 < 0.5f)
continue;
float v2 = mask->GetPixel(startIndex);
if (v2 < 0.5f)
continue;
if (!different_label)
++in_mask;
else if (fabs(v1-v2)>0.00001f)
++in_mask;
}
}
return float(in_mask)/m_NumFibers;
}
std::tuple<float, float> mitk::FiberBundle::GetDirectionalOverlap(ItkUcharImgType* mask, mitk::PeakImage::ItkPeakImageType* peak_image)
{
vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
MITK_INFO << "Calculating overlap";
auto spacing = mask->GetSpacing();
boost::timer::progress_display disp(m_NumFibers);
double length_sum = 0;
double in_mask_length = 0;
double aligned_length = 0;
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = PolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
for (int j=0; j<numPoints-1; j++)
{
itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(j));
itk::Index<3> startIndex;
itk::ContinuousIndex<float, 3> startIndexCont;
mask->TransformPhysicalPointToIndex(startVertex, startIndex);
mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(j + 1));
itk::Index<3> endIndex;
itk::ContinuousIndex<float, 3> endIndexCont;
mask->TransformPhysicalPointToIndex(endVertex, endIndex);
mask->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
vnl_vector_fixed< float, 3 > fdir;
fdir[0] = endVertex[0] - startVertex[0];
fdir[1] = endVertex[1] - startVertex[1];
fdir[2] = endVertex[2] - startVertex[2];
fdir.normalize();
std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
for (std::pair< itk::Index<3>, double > segment : segments)
{
if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 )
{
in_mask_length += segment.second;
mitk::PeakImage::ItkPeakImageType::IndexType idx4;
idx4[0] = segment.first[0];
idx4[1] = segment.first[1];
idx4[2] = segment.first[2];
vnl_vector_fixed< float, 3 > peak;
idx4[3] = 0;
peak[0] = peak_image->GetPixel(idx4);
idx4[3] = 1;
peak[1] = peak_image->GetPixel(idx4);
idx4[3] = 2;
peak[2] = peak_image->GetPixel(idx4);
if (std::isnan(peak[0]) || std::isnan(peak[1]) || std::isnan(peak[2]) || peak.magnitude()<0.0001f)
continue;
peak.normalize();
double f = 1.0 - std::acos(std::fabs(static_cast<double>(dot_product(fdir, peak)))) * 2.0/itk::Math::pi;
aligned_length += segment.second * f;
}
length_sum += segment.second;
}
}
}
if (length_sum<=0.0001)
{
MITK_INFO << "Fiber length sum is zero!";
return std::make_tuple(0,0);
}
return std::make_tuple(aligned_length/length_sum, in_mask_length/length_sum);
}
float mitk::FiberBundle::GetOverlap(ItkUcharImgType* mask)
{
vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
MITK_INFO << "Calculating overlap";
auto spacing = mask->GetSpacing();
boost::timer::progress_display disp(m_NumFibers);
double length_sum = 0;
double in_mask_length = 0;
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = PolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
for (int j=0; j<numPoints-1; j++)
{
itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(j));
itk::Index<3> startIndex;
itk::ContinuousIndex<float, 3> startIndexCont;
mask->TransformPhysicalPointToIndex(startVertex, startIndex);
mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(j + 1));
itk::Index<3> endIndex;
itk::ContinuousIndex<float, 3> endIndexCont;
mask->TransformPhysicalPointToIndex(endVertex, endIndex);
mask->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
for (std::pair< itk::Index<3>, double > segment : segments)
{
if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 )
in_mask_length += segment.second;
length_sum += segment.second;
}
}
}
if (length_sum<=0.000001)
{
MITK_INFO << "Fiber length sum is zero!";
return 0;
}
return static_cast<float>(in_mask_length/length_sum);
}
mitk::FiberBundle::Pointer mitk::FiberBundle::RemoveFibersOutside(ItkUcharImgType* mask, bool invert)
{
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
std::vector< float > fib_weights;
MITK_INFO << "Cutting fibers";
boost::timer::progress_display disp(m_NumFibers);
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
int newNumPoints = 0;
if (numPoints>1)
{
for (int j=0; j<numPoints; j++)
{
itk::Point<float, 3> itkP =mitk::imv::GetItkPoint(points->GetPoint(j));
itk::Index<3> idx;
mask->TransformPhysicalPointToIndex(itkP, idx);
bool inside = false;
if ( mask->GetLargestPossibleRegion().IsInside(idx) && mask->GetPixel(idx)!=0 )
inside = true;
if (inside && !invert)
{
vtkIdType id = vtkNewPoints->InsertNextPoint(itkP.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
newNumPoints++;
}
else if ( !inside && invert )
{
vtkIdType id = vtkNewPoints->InsertNextPoint(itkP.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
newNumPoints++;
}
else if (newNumPoints>1)
{
fib_weights.push_back(this->GetFiberWeight(i));
vtkNewCells->InsertNextCell(container);
newNumPoints = 0;
container = vtkSmartPointer<vtkPolyLine>::New();
}
else
{
newNumPoints = 0;
container = vtkSmartPointer<vtkPolyLine>::New();
}
}
if (newNumPoints>1)
{
fib_weights.push_back(this->GetFiberWeight(i));
vtkNewCells->InsertNextCell(container);
}
}
}
vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
newFiberWeights->SetName("FIBER_WEIGHTS");
newFiberWeights->SetNumberOfValues(static_cast<vtkIdType>(fib_weights.size()));
if (vtkNewCells->GetNumberOfCells()<=0)
return nullptr;
for (unsigned int i=0; i<newFiberWeights->GetNumberOfValues(); i++)
newFiberWeights->SetValue(i, fib_weights.at(i));
// vtkSmartPointer<vtkUnsignedCharArray> newFiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
// newFiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
// newFiberColors->SetNumberOfComponents(4);
// newFiberColors->SetName("FIBER_COLORS");
// unsigned char rgba[4] = {0,0,0,0};
// for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
// {
// rgba[0] = (unsigned char) r;
// rgba[1] = (unsigned char) g;
// rgba[2] = (unsigned char) b;
// rgba[3] = (unsigned char) alpha;
// m_FiberColors->InsertTypedTuple(i, rgba);
// }
vtkSmartPointer<vtkPolyData> newPolyData = vtkSmartPointer<vtkPolyData>::New();
newPolyData->SetPoints(vtkNewPoints);
newPolyData->SetLines(vtkNewCells);
mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(newPolyData);
newFib->SetFiberWeights(newFiberWeights);
// newFib->Compress(0.1);
newFib->SetTrackVisHeader(this->GetTrackVisHeader());
return newFib;
}
mitk::FiberBundle::Pointer mitk::FiberBundle::ExtractFiberSubset(DataNode* roi, DataStorage* storage)
{
if (roi==nullptr || !(dynamic_cast<PlanarFigure*>(roi->GetData()) || dynamic_cast<PlanarFigureComposite*>(roi->GetData())) )
return nullptr;
std::vector<unsigned int> tmp = ExtractFiberIdSubset(roi, storage);
if (tmp.size()<=0)
return mitk::FiberBundle::New();
vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
vtkSmartPointer<vtkPolyData> pTmp = GeneratePolyDataByIds(tmp, weights);
mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp);
fib->SetFiberWeights(weights);
fib->SetTrackVisHeader(this->GetTrackVisHeader());
return fib;
}
std::vector<unsigned int> mitk::FiberBundle::ExtractFiberIdSubset(DataNode *roi, DataStorage* storage)
{
std::vector<unsigned int> result;
if (roi==nullptr || roi->GetData()==nullptr)
return result;
mitk::PlanarFigureComposite::Pointer pfc = dynamic_cast<mitk::PlanarFigureComposite*>(roi->GetData());
if (!pfc.IsNull()) // handle composite
{
DataStorage::SetOfObjects::ConstPointer children = storage->GetDerivations(roi);
if (children->size()==0)
return result;
switch (pfc->getOperationType())
{
case 0: // AND
{
MITK_INFO << "AND";
result = this->ExtractFiberIdSubset(children->ElementAt(0), storage);
std::vector<unsigned int>::iterator it;
for (unsigned int i=1; i<children->Size(); ++i)
{
std::vector<unsigned int> inRoi = this->ExtractFiberIdSubset(children->ElementAt(i), storage);
std::vector<unsigned int> rest(std::min(result.size(),inRoi.size()));
it = std::set_intersection(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() );
rest.resize( static_cast<unsigned int>(it - rest.begin()) );
result = rest;
}
break;
}
case 1: // OR
{
MITK_INFO << "OR";
result = ExtractFiberIdSubset(children->ElementAt(0), storage);
std::vector<unsigned int>::iterator it;
for (unsigned int i=1; i<children->Size(); ++i)
{
it = result.end();
std::vector<unsigned int> inRoi = ExtractFiberIdSubset(children->ElementAt(i), storage);
result.insert(it, inRoi.begin(), inRoi.end());
}
// remove duplicates
sort(result.begin(), result.end());
it = unique(result.begin(), result.end());
result.resize( static_cast<unsigned int>(it - result.begin()) );
break;
}
case 2: // NOT
{
MITK_INFO << "NOT";
for(unsigned int i=0; i<this->GetNumFibers(); i++)
result.push_back(i);
std::vector<unsigned int>::iterator it;
for (unsigned int i=0; i<children->Size(); ++i)
{
std::vector<unsigned int> inRoi = ExtractFiberIdSubset(children->ElementAt(i), storage);
std::vector<unsigned int> rest(result.size()-inRoi.size());
it = std::set_difference(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() );
rest.resize( static_cast<unsigned int>(it - rest.begin()) );
result = rest;
}
break;
}
}
}
else if ( dynamic_cast<mitk::PlanarFigure*>(roi->GetData()) ) // actual extraction
{
if ( dynamic_cast<mitk::PlanarPolygon*>(roi->GetData()) )
{
mitk::PlanarFigure::Pointer planarPoly = dynamic_cast<mitk::PlanarFigure*>(roi->GetData());
//create vtkPolygon using controlpoints from planarFigure polygon
vtkSmartPointer<vtkPolygon> polygonVtk = vtkSmartPointer<vtkPolygon>::New();
for (unsigned int i=0; i<planarPoly->GetNumberOfControlPoints(); ++i)
{
itk::Point<double,3> p = planarPoly->GetWorldControlPoint(i);
vtkIdType id = polygonVtk->GetPoints()->InsertNextPoint(p[0], p[1], p[2] );
polygonVtk->GetPointIds()->InsertNextId(id);
}
MITK_INFO << "Extracting with polygon";
boost::timer::progress_display disp(m_NumFibers);
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp ;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
for (int j=0; j<numPoints-1; j++)
{
// Inputs
double p1[3] = {0,0,0};
points->GetPoint(j, p1);
double p2[3] = {0,0,0};
points->GetPoint(j+1, p2);
double tolerance = 0.001;
// Outputs
double t = 0; // Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
double x[3] = {0,0,0}; // The coordinate of the intersection
double pcoords[3] = {0,0,0};
int subId = 0;
int iD = polygonVtk->IntersectWithLine(p1, p2, tolerance, t, x, pcoords, subId);
if (iD!=0)
{
result.push_back(i);
break;
}
}
}
}
else if ( dynamic_cast<mitk::PlanarCircle*>(roi->GetData()) )
{
mitk::PlanarFigure::Pointer planarFigure = dynamic_cast<mitk::PlanarFigure*>(roi->GetData());
Vector3D planeNormal = planarFigure->GetPlaneGeometry()->GetNormal();
planeNormal.Normalize();
//calculate circle radius
mitk::Point3D V1w = planarFigure->GetWorldControlPoint(0); //centerPoint
mitk::Point3D V2w = planarFigure->GetWorldControlPoint(1); //radiusPoint
double radius = V1w.EuclideanDistanceTo(V2w);
radius *= radius;
MITK_INFO << "Extracting with circle";
boost::timer::progress_display disp(m_NumFibers);
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp ;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
for (int j=0; j<numPoints-1; j++)
{
// Inputs
double p1[3] = {0,0,0};
points->GetPoint(j, p1);
double p2[3] = {0,0,0};
points->GetPoint(j+1, p2);
// Outputs
double t = 0; // Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
double x[3] = {0,0,0}; // The coordinate of the intersection
int iD = vtkPlane::IntersectWithLine(p1,p2,planeNormal.GetDataPointer(),V1w.GetDataPointer(),t,x);
if (iD!=0)
{
double dist = (x[0]-V1w[0])*(x[0]-V1w[0])+(x[1]-V1w[1])*(x[1]-V1w[1])+(x[2]-V1w[2])*(x[2]-V1w[2]);
if( dist <= radius)
{
result.push_back(i);
break;
}
}
}
}
}
return result;
}
return result;
}
void mitk::FiberBundle::UpdateFiberGeometry()
{
vtkSmartPointer<vtkCleanPolyData> cleaner = vtkSmartPointer<vtkCleanPolyData>::New();
cleaner->SetInputData(m_FiberPolyData);
cleaner->PointMergingOff();
cleaner->Update();
m_FiberPolyData = cleaner->GetOutput();
m_FiberLengths.clear();
m_MeanFiberLength = 0;
m_MedianFiberLength = 0;
m_LengthStDev = 0;
m_NumFibers = static_cast<unsigned int>(m_FiberPolyData->GetNumberOfCells());
if (m_FiberColors==nullptr || m_FiberColors->GetNumberOfTuples()!=m_FiberPolyData->GetNumberOfPoints())
this->ColorFibersByOrientation();
if (m_FiberWeights->GetNumberOfValues()!=m_NumFibers)
{
m_FiberWeights = vtkSmartPointer<vtkFloatArray>::New();
m_FiberWeights->SetName("FIBER_WEIGHTS");
m_FiberWeights->SetNumberOfValues(m_NumFibers);
this->SetFiberWeights(1);
}
if (m_NumFibers<=0) // no fibers present; apply default geometry
{
m_MinFiberLength = 0;
m_MaxFiberLength = 0;
mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
geometry->SetImageGeometry(false);
float b[] = {0, 1, 0, 1, 0, 1};
geometry->SetFloatBounds(b);
SetGeometry(geometry);
return;
}
double b[6];
m_FiberPolyData->GetBounds(b);
// calculate statistics
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto p = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
float length = 0;
for (int j=0; j<p-1; j++)
{
double p1[3];
points->GetPoint(j, p1);
double p2[3];
points->GetPoint(j+1, p2);
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
length += static_cast<float>(dist);
}
m_FiberLengths.push_back(length);
m_MeanFiberLength += length;
if (i==0)
{
m_MinFiberLength = length;
m_MaxFiberLength = length;
}
else
{
if (length<m_MinFiberLength)
m_MinFiberLength = length;
if (length>m_MaxFiberLength)
m_MaxFiberLength = length;
}
}
m_MeanFiberLength /= m_NumFibers;
std::vector< float > sortedLengths = m_FiberLengths;
std::sort(sortedLengths.begin(), sortedLengths.end());
for (unsigned int i=0; i<m_NumFibers; i++)
m_LengthStDev += (m_MeanFiberLength-sortedLengths.at(i))*(m_MeanFiberLength-sortedLengths.at(i));
if (m_NumFibers>1)
m_LengthStDev /= (m_NumFibers-1);
else
m_LengthStDev = 0;
m_LengthStDev = std::sqrt(m_LengthStDev);
m_MedianFiberLength = sortedLengths.at(m_NumFibers/2);
mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
geometry->SetFloatBounds(b);
this->SetGeometry(geometry);
GetTrackVisHeader();
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
float mitk::FiberBundle::GetFiberWeight(unsigned int fiber) const
{
return m_FiberWeights->GetValue(fiber);
}
void mitk::FiberBundle::SetFiberWeights(float newWeight)
{
for (int i=0; i<m_FiberWeights->GetNumberOfValues(); i++)
m_FiberWeights->SetValue(i, newWeight);
}
void mitk::FiberBundle::SetFiberWeights(vtkSmartPointer<vtkFloatArray> weights)
{
if (m_NumFibers!=weights->GetNumberOfValues())
{
MITK_INFO << "Weights array not equal to number of fibers! " << weights->GetNumberOfValues() << " vs " << m_NumFibers;
return;
}
for (int i=0; i<weights->GetNumberOfValues(); i++)
m_FiberWeights->SetValue(i, weights->GetValue(i));
m_FiberWeights->SetName("FIBER_WEIGHTS");
}
void mitk::FiberBundle::SetFiberWeight(unsigned int fiber, float weight)
{
m_FiberWeights->SetValue(fiber, weight);
}
void mitk::FiberBundle::SetFiberColors(vtkSmartPointer<vtkUnsignedCharArray> fiberColors)
{
for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
{
unsigned char source[4] = {0,0,0,0};
fiberColors->GetTypedTuple(i, source);
unsigned char target[4] = {0,0,0,0};
target[0] = source[0];
target[1] = source[1];
target[2] = source[2];
target[3] = source[3];
m_FiberColors->InsertTypedTuple(i, target);
}
m_UpdateTime3D.Modified();
m_UpdateTime2D.Modified();
}
itk::Matrix< double, 3, 3 > mitk::FiberBundle::TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz)
{
rx = rx*itk::Math::pi/180;
ry = ry*itk::Math::pi/180;
rz = rz*itk::Math::pi/180;
itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
rotX[1][1] = cos(rx);
rotX[2][2] = rotX[1][1];
rotX[1][2] = -sin(rx);
rotX[2][1] = -rotX[1][2];
itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
rotY[0][0] = cos(ry);
rotY[2][2] = rotY[0][0];
rotY[0][2] = sin(ry);
rotY[2][0] = -rotY[0][2];
itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
rotZ[0][0] = cos(rz);
rotZ[1][1] = rotZ[0][0];
rotZ[0][1] = -sin(rz);
rotZ[1][0] = -rotZ[0][1];
itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX;
m = rot*m;
return m;
}
void mitk::FiberBundle::TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform)
{
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (unsigned int i=0; i<m_NumFibers; i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
itk::Point<float, 3> p =mitk::imv::GetItkPoint(points->GetPoint(j));
p = transform->TransformPoint(p);
vtkIdType id = vtkNewPoints->InsertNextPoint(p.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
void mitk::FiberBundle::TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz)
{
vnl_matrix_fixed< double, 3, 3 > rot = mitk::imv::GetRotationMatrixVnl(rx, ry, rz);
mitk::BaseGeometry::Pointer geom = this->GetGeometry();
mitk::Point3D center = geom->GetCenter();
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (unsigned int i=0; i<m_NumFibers; i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
vnl_vector_fixed< double, 3 > dir;
dir[0] = p[0]-center[0];
dir[1] = p[1]-center[1];
dir[2] = p[2]-center[2];
dir = rot*dir;
dir[0] += center[0]+tx;
dir[1] += center[1]+ty;
dir[2] += center[2]+tz;
vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block());
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
void mitk::FiberBundle::RotateAroundAxis(double x, double y, double z)
{
x = x*itk::Math::pi/180;
y = y*itk::Math::pi/180;
z = z*itk::Math::pi/180;
vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity();
rotX[1][1] = cos(x);
rotX[2][2] = rotX[1][1];
rotX[1][2] = -sin(x);
rotX[2][1] = -rotX[1][2];
vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity();
rotY[0][0] = cos(y);
rotY[2][2] = rotY[0][0];
rotY[0][2] = sin(y);
rotY[2][0] = -rotY[0][2];
vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity();
rotZ[0][0] = cos(z);
rotZ[1][1] = rotZ[0][0];
rotZ[0][1] = -sin(z);
rotZ[1][0] = -rotZ[0][1];
mitk::BaseGeometry::Pointer geom = this->GetGeometry();
mitk::Point3D center = geom->GetCenter();
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (unsigned int i=0; i<m_NumFibers; i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
vnl_vector_fixed< double, 3 > dir;
dir[0] = p[0]-center[0];
dir[1] = p[1]-center[1];
dir[2] = p[2]-center[2];
dir = rotZ*rotY*rotX*dir;
dir[0] += center[0];
dir[1] += center[1];
dir[2] += center[2];
vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block());
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
void mitk::FiberBundle::ScaleFibers(double x, double y, double z, bool subtractCenter)
{
MITK_INFO << "Scaling fibers";
boost::timer::progress_display disp(m_NumFibers);
mitk::BaseGeometry* geom = this->GetGeometry();
mitk::Point3D c = geom->GetCenter();
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp ;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
if (subtractCenter)
{
p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2];
}
p[0] *= x;
p[1] *= y;
p[2] *= z;
if (subtractCenter)
{
p[0] += c[0]; p[1] += c[1]; p[2] += c[2];
}
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
void mitk::FiberBundle::TranslateFibers(double x, double y, double z)
{
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (unsigned int i=0; i<m_NumFibers; i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
p[0] += x;
p[1] += y;
p[2] += z;
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
void mitk::FiberBundle::MirrorFibers(unsigned int axis)
{
if (axis>2)
return;
MITK_INFO << "Mirroring fibers";
boost::timer::progress_display disp(m_NumFibers);
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
p[axis] = -p[axis];
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
void mitk::FiberBundle::RemoveDir(vnl_vector_fixed<double,3> dir, double threshold)
{
dir.normalize();
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
++disp ;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
// calculate curvatures
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
bool discard = false;
for (int j=0; j<numPoints-1; j++)
{
double p1[3];
points->GetPoint(j, p1);
double p2[3];
points->GetPoint(j+1, p2);
vnl_vector_fixed< double, 3 > v1;
v1[0] = p2[0]-p1[0];
v1[1] = p2[1]-p1[1];
v1[2] = p2[2]-p1[2];
if (v1.magnitude()>0.001)
{
v1.normalize();
if (fabs(dot_product(v1,dir))>threshold)
{
discard = true;
break;
}
}
}
if (!discard)
{
for (int j=0; j<numPoints; j++)
{
double p1[3];
points->GetPoint(j, p1);
vtkIdType id = vtkNewPoints->InsertNextPoint(p1);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
// UpdateColorCoding();
// UpdateFiberGeometry();
}
bool mitk::FiberBundle::ApplyCurvatureThreshold(float minRadius, bool deleteFibers)
{
if (minRadius<0)
return true;
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
MITK_INFO << "Applying curvature threshold";
boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
++disp ;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
// calculate curvatures
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints-2; j++)
{
double p1[3];
points->GetPoint(j, p1);
double p2[3];
points->GetPoint(j+1, p2);
double p3[3];
points->GetPoint(j+2, p3);
vnl_vector_fixed< float, 3 > v1, v2, v3;
v1[0] = static_cast<float>(p2[0]-p1[0]);
v1[1] = static_cast<float>(p2[1]-p1[1]);
v1[2] = static_cast<float>(p2[2]-p1[2]);
v2[0] = static_cast<float>(p3[0]-p2[0]);
v2[1] = static_cast<float>(p3[1]-p2[1]);
v2[2] = static_cast<float>(p3[2]-p2[2]);
v3[0] = static_cast<float>(p1[0]-p3[0]);
v3[1] = static_cast<float>(p1[1]-p3[1]);
v3[2] = static_cast<float>(p1[2]-p3[2]);
float a = v1.magnitude();
float b = v2.magnitude();
float c = v3.magnitude();
float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle)
vtkIdType id = vtkNewPoints->InsertNextPoint(p1);
container->GetPointIds()->InsertNextId(id);
if (deleteFibers && r<minRadius)
break;
if (r<minRadius)
{
j += 2;
vtkNewCells->InsertNextCell(container);
container = vtkSmartPointer<vtkPolyLine>::New();
}
else if (j==numPoints-3)
{
id = vtkNewPoints->InsertNextPoint(p2);
container->GetPointIds()->InsertNextId(id);
id = vtkNewPoints->InsertNextPoint(p3);
container->GetPointIds()->InsertNextId(id);
vtkNewCells->InsertNextCell(container);
}
}
}
if (vtkNewCells->GetNumberOfCells()<=0)
return false;
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
return true;
}
bool mitk::FiberBundle::RemoveShortFibers(float lengthInMM)
{
MITK_INFO << "Removing short fibers";
if (lengthInMM<=0 || lengthInMM<m_MinFiberLength)
{
MITK_INFO << "No fibers shorter than " << lengthInMM << " mm found!";
return true;
}
if (lengthInMM>m_MaxFiberLength) // can't remove all fibers
{
MITK_WARN << "Process aborted. No fibers would be left!";
return false;
}
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
float min = m_MaxFiberLength;
boost::timer::progress_display disp(m_NumFibers);
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (m_FiberLengths.at(i)>=lengthInMM)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
if (m_FiberLengths.at(i)<min)
min = m_FiberLengths.at(i);
}
}
if (vtkNewCells->GetNumberOfCells()<=0)
return false;
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
return true;
}
bool mitk::FiberBundle::RemoveLongFibers(float lengthInMM)
{
if (lengthInMM<=0 || lengthInMM>m_MaxFiberLength)
return true;
if (lengthInMM<m_MinFiberLength) // can't remove all fibers
return false;
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
MITK_INFO << "Removing long fibers";
boost::timer::progress_display disp(m_NumFibers);
for (unsigned int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (m_FiberLengths.at(i)<=lengthInMM)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
}
if (vtkNewCells->GetNumberOfCells()<=0)
return false;
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
return true;
}
void mitk::FiberBundle::ResampleSpline(float pointDistance, double tension, double continuity, double bias )
{
if (pointDistance<=0)
return;
vtkSmartPointer<vtkPoints> vtkSmoothPoints = vtkSmartPointer<vtkPoints>::New(); //in smoothpoints the interpolated points representing a fiber are stored.
//in vtkcells all polylines are stored, actually all id's of them are stored
vtkSmartPointer<vtkCellArray> vtkSmoothCells = vtkSmartPointer<vtkCellArray>::New(); //cellcontainer for smoothed lines
MITK_INFO << "Smoothing fibers";
vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
newFiberWeights->SetName("FIBER_WEIGHTS");
newFiberWeights->SetNumberOfValues(m_NumFibers);
std::vector< vtkSmartPointer<vtkPolyLine> > resampled_streamlines;
resampled_streamlines.resize(m_NumFibers);
boost::timer::progress_display disp(m_NumFibers);
#pragma omp parallel for
for (int i=0; i<static_cast<int>(m_NumFibers); i++)
{
vtkSmartPointer<vtkPoints> newPoints = vtkSmartPointer<vtkPoints>::New();
float length = 0;
#pragma omp critical
{
length = m_FiberLengths.at(static_cast<unsigned int>(i));
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
for (int j=0; j<numPoints; j++)
newPoints->InsertNextPoint(points->GetPoint(j));
}
int sampling = static_cast<int>(std::ceil(length/pointDistance));
vtkSmartPointer<vtkKochanekSpline> xSpline = vtkSmartPointer<vtkKochanekSpline>::New();
vtkSmartPointer<vtkKochanekSpline> ySpline = vtkSmartPointer<vtkKochanekSpline>::New();
vtkSmartPointer<vtkKochanekSpline> zSpline = vtkSmartPointer<vtkKochanekSpline>::New();
xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity);
ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity);
zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity);
vtkSmartPointer<vtkParametricSpline> spline = vtkSmartPointer<vtkParametricSpline>::New();
spline->SetXSpline(xSpline);
spline->SetYSpline(ySpline);
spline->SetZSpline(zSpline);
spline->SetPoints(newPoints);
vtkSmartPointer<vtkParametricFunctionSource> functionSource = vtkSmartPointer<vtkParametricFunctionSource>::New();
functionSource->SetParametricFunction(spline);
functionSource->SetUResolution(sampling);
functionSource->SetVResolution(sampling);
functionSource->SetWResolution(sampling);
functionSource->Update();
vtkPolyData* outputFunction = functionSource->GetOutput();
vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber
vtkSmartPointer<vtkPolyLine> smoothLine = vtkSmartPointer<vtkPolyLine>::New();
#pragma omp critical
{
for (int j=0; j<tmpSmoothPnts->GetNumberOfPoints(); j++)
{
vtkIdType id = vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j));
smoothLine->GetPointIds()->InsertNextId(id);
}
resampled_streamlines[static_cast<unsigned long>(i)] = smoothLine;
}
}
for (auto container : resampled_streamlines)
{
vtkSmoothCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkSmoothPoints);
m_FiberPolyData->SetLines(vtkSmoothCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
void mitk::FiberBundle::ResampleSpline(float pointDistance)
{
ResampleSpline(pointDistance, 0, 0, 0 );
}
unsigned int mitk::FiberBundle::GetNumberOfPoints() const
{
unsigned int points = 0;
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
points += cell->GetNumberOfPoints();
}
return points;
}
void mitk::FiberBundle::Compress(float error)
{
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
MITK_INFO << "Compressing fibers with max. error " << error << "mm";
unsigned int numRemovedPoints = 0;
boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
newFiberWeights->SetName("FIBER_WEIGHTS");
newFiberWeights->SetNumberOfValues(m_NumFibers);
#pragma omp parallel for
for (int i=0; i<static_cast<int>(m_FiberPolyData->GetNumberOfCells()); i++)
{
std::vector< vnl_vector_fixed< double, 3 > > vertices;
float weight = 1;
#pragma omp critical
{
++disp;
weight = m_FiberWeights->GetValue(i);
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
for (int j=0; j<numPoints; j++)
{
double cand[3];
points->GetPoint(j, cand);
vnl_vector_fixed< double, 3 > candV;
candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
vertices.push_back(candV);
}
}
// calculate curvatures
auto numPoints = vertices.size();
std::vector< int > removedPoints; removedPoints.resize(numPoints, 0);
removedPoints[0]=-1; removedPoints[numPoints-1]=-1;
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
unsigned int remCounter = 0;
bool pointFound = true;
while (pointFound)
{
pointFound = false;
double minError = static_cast<double>(error);
unsigned int removeIndex = 0;
for (unsigned int j=0; j<vertices.size(); j++)
{
if (removedPoints[j]==0)
{
vnl_vector_fixed< double, 3 > candV = vertices.at(j);
int validP = -1;
vnl_vector_fixed< double, 3 > pred;
for (int k=static_cast<int>(j)-1; k>=0; k--)
if (removedPoints[static_cast<unsigned int>(k)]<=0)
{
pred = vertices.at(static_cast<unsigned int>(k));
validP = k;
break;
}
int validS = -1;
vnl_vector_fixed< double, 3 > succ;
for (unsigned int k=j+1; k<numPoints; k++)
if (removedPoints[k]<=0)
{
succ = vertices.at(k);
validS = static_cast<int>(k);
break;
}
if (validP>=0 && validS>=0)
{
double a = (candV-pred).magnitude();
double b = (candV-succ).magnitude();
double c = (pred-succ).magnitude();
double s=0.5*(a+b+c);
double hc=(2.0/c)*sqrt(fabs(s*(s-a)*(s-b)*(s-c)));
if (hc<minError)
{
removeIndex = j;
minError = hc;
pointFound = true;
}
}
}
}
if (pointFound)
{
removedPoints[removeIndex] = 1;
remCounter++;
}
}
for (unsigned int j=0; j<numPoints; j++)
{
if (removedPoints[j]<=0)
{
#pragma omp critical
{
vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
container->GetPointIds()->InsertNextId(id);
}
}
}
#pragma omp critical
{
newFiberWeights->SetValue(vtkNewCells->GetNumberOfCells(), weight);
numRemovedPoints += remCounter;
vtkNewCells->InsertNextCell(container);
}
}
if (vtkNewCells->GetNumberOfCells()>0)
{
MITK_INFO << "Removed points: " << numRemovedPoints;
SetFiberWeights(newFiberWeights);
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
}
void mitk::FiberBundle::ResampleToNumPoints(unsigned int targetPoints)
{
if (targetPoints<2)
mitkThrow() << "Minimum two points required for resampling!";
MITK_INFO << "Resampling fibers (number of points " << targetPoints << ")";
bool unequal_fibs = true;
while (unequal_fibs)
{
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
newFiberWeights->SetName("FIBER_WEIGHTS");
newFiberWeights->SetNumberOfValues(m_NumFibers);
unequal_fibs = false;
+ MITK_INFO << "Start";
+// cv::parallel_for_(cv::Range(0, m_FiberPolyData->GetNumberOfCells()), [&](const cv::Range &range)
+// {
+// for (int i = range.start; i < range.end; i++)
for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
std::vector< vnl_vector_fixed< double, 3 > > vertices;
float weight = 1;
double seg_len = 0;
{
weight = m_FiberWeights->GetValue(i);
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
if (numPoints!=targetPoints)
seg_len = static_cast<double>(this->GetFiberLength(i)/(targetPoints-1));
vtkPoints* points = cell->GetPoints();
for (int j=0; j<numPoints; j++)
{
double cand[3];
points->GetPoint(j, cand);
vnl_vector_fixed< double, 3 > candV;
candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
vertices.push_back(candV);
}
}
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
vnl_vector_fixed< double, 3 > lastV = vertices.at(0);
{
vtkIdType id = vtkNewPoints->InsertNextPoint(lastV.data_block());
container->GetPointIds()->InsertNextId(id);
}
for (unsigned int j=1; j<vertices.size(); j++)
{
vnl_vector_fixed< double, 3 > vec = vertices.at(j) - lastV;
double new_dist = vec.magnitude();
if (new_dist >= seg_len && seg_len>0)
{
vnl_vector_fixed< double, 3 > newV = lastV;
if ( new_dist-seg_len <= mitk::eps )
{
vec.normalize();
newV += vec * seg_len;
}
else
{
// intersection between sphere (radius 'pointDistance', center 'lastV') and line (direction 'd' and point 'p')
vnl_vector_fixed< double, 3 > p = vertices.at(j-1);
vnl_vector_fixed< double, 3 > d = vertices.at(j) - p;
double a = d[0]*d[0] + d[1]*d[1] + d[2]*d[2];
double b = 2 * (d[0] * (p[0] - lastV[0]) + d[1] * (p[1] - lastV[1]) + d[2] * (p[2] - lastV[2]));
double c = (p[0] - lastV[0])*(p[0] - lastV[0]) + (p[1] - lastV[1])*(p[1] - lastV[1]) + (p[2] - lastV[2])*(p[2] - lastV[2]) - seg_len*seg_len;
double v1 =(-b + std::sqrt(b*b-4*a*c))/(2*a);
double v2 =(-b - std::sqrt(b*b-4*a*c))/(2*a);
if (v1>0)
newV = p + d * v1;
else if (v2>0)
newV = p + d * v2;
else
MITK_INFO << "ERROR1 - linear resampling";
j--;
}
//#pragma omp critical
{
vtkIdType id = vtkNewPoints->InsertNextPoint(newV.data_block());
container->GetPointIds()->InsertNextId(id);
}
lastV = newV;
}
else if ( (j==vertices.size()-1 && new_dist>0.0001) || seg_len<=0.0000001)
{
//#pragma omp critical
{
vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
container->GetPointIds()->InsertNextId(id);
}
}
}
//#pragma omp critical
{
newFiberWeights->SetValue(vtkNewCells->GetNumberOfCells(), weight);
vtkNewCells->InsertNextCell(container);
if (container->GetNumberOfPoints()!=targetPoints)
unequal_fibs = true;
}
}
+// });
+// MITK_INFO << "Done";
if (vtkNewCells->GetNumberOfCells()>0)
{
SetFiberWeights(newFiberWeights);
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
}
}
void mitk::FiberBundle::ResampleLinear(double pointDistance)
{
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
MITK_INFO << "Resampling fibers (linear)";
boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
newFiberWeights->SetName("FIBER_WEIGHTS");
newFiberWeights->SetNumberOfValues(m_NumFibers);
std::vector< vtkSmartPointer<vtkPolyLine> > resampled_streamlines;
resampled_streamlines.resize(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
#pragma omp parallel for
for (int i=0; i<static_cast<int>(m_FiberPolyData->GetNumberOfCells()); i++)
{
std::vector< vnl_vector_fixed< double, 3 > > vertices;
#pragma omp critical
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
for (int j=0; j<numPoints; j++)
{
double cand[3];
points->GetPoint(j, cand);
vnl_vector_fixed< double, 3 > candV;
candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
vertices.push_back(candV);
}
}
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
vnl_vector_fixed< double, 3 > lastV = vertices.at(0);
#pragma omp critical
{
vtkIdType id = vtkNewPoints->InsertNextPoint(lastV.data_block());
container->GetPointIds()->InsertNextId(id);
}
for (unsigned int j=1; j<vertices.size(); j++)
{
vnl_vector_fixed< double, 3 > vec = vertices.at(j) - lastV;
double new_dist = vec.magnitude();
if (new_dist >= pointDistance)
{
vnl_vector_fixed< double, 3 > newV = lastV;
if ( new_dist-pointDistance <= mitk::eps )
{
vec.normalize();
newV += vec * pointDistance;
}
else
{
// intersection between sphere (radius 'pointDistance', center 'lastV') and line (direction 'd' and point 'p')
vnl_vector_fixed< double, 3 > p = vertices.at(j-1);
vnl_vector_fixed< double, 3 > d = vertices.at(j) - p;
double a = d[0]*d[0] + d[1]*d[1] + d[2]*d[2];
double b = 2 * (d[0] * (p[0] - lastV[0]) + d[1] * (p[1] - lastV[1]) + d[2] * (p[2] - lastV[2]));
double c = (p[0] - lastV[0])*(p[0] - lastV[0]) + (p[1] - lastV[1])*(p[1] - lastV[1]) + (p[2] - lastV[2])*(p[2] - lastV[2]) - pointDistance*pointDistance;
double v1 =(-b + std::sqrt(b*b-4*a*c))/(2*a);
double v2 =(-b - std::sqrt(b*b-4*a*c))/(2*a);
if (v1>0)
newV = p + d * v1;
else if (v2>0)
newV = p + d * v2;
else
MITK_INFO << "ERROR1 - linear resampling";
j--;
}
#pragma omp critical
{
vtkIdType id = vtkNewPoints->InsertNextPoint(newV.data_block());
container->GetPointIds()->InsertNextId(id);
}
lastV = newV;
}
else if (j==vertices.size()-1 && new_dist>0.0001)
{
#pragma omp critical
{
vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
container->GetPointIds()->InsertNextId(id);
}
}
}
#pragma omp critical
{
resampled_streamlines[static_cast<unsigned int>(i)] = container;
}
}
for (auto container : resampled_streamlines)
{
vtkNewCells->InsertNextCell(container);
}
if (vtkNewCells->GetNumberOfCells()>0)
{
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
this->SetFiberPolyData(m_FiberPolyData, true);
}
}
// reapply selected colorcoding in case PolyData structure has changed
bool mitk::FiberBundle::Equals(mitk::FiberBundle* fib, double eps)
{
if (fib==nullptr)
{
MITK_INFO << "Reference bundle is nullptr!";
return false;
}
if (m_NumFibers!=fib->GetNumFibers())
{
MITK_INFO << "Unequal number of fibers!";
MITK_INFO << m_NumFibers << " vs. " << fib->GetNumFibers();
return false;
}
for (unsigned int i=0; i<m_NumFibers; i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
auto numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i);
auto numPoints2 = cell2->GetNumberOfPoints();
vtkPoints* points2 = cell2->GetPoints();
if (numPoints2!=numPoints)
{
MITK_INFO << "Unequal number of points in fiber " << i << "!";
MITK_INFO << numPoints2 << " vs. " << numPoints;
return false;
}
for (int j=0; j<numPoints; j++)
{
double* p1 = points->GetPoint(j);
double* p2 = points2->GetPoint(j);
if (fabs(p1[0]-p2[0])>eps || fabs(p1[1]-p2[1])>eps || fabs(p1[2]-p2[2])>eps)
{
MITK_INFO << "Unequal points in fiber " << i << " at position " << j << "!";
MITK_INFO << "p1: " << p1[0] << ", " << p1[1] << ", " << p1[2];
MITK_INFO << "p2: " << p2[0] << ", " << p2[1] << ", " << p2[2];
return false;
}
}
}
return true;
}
void mitk::FiberBundle::PrintSelf(std::ostream &os, itk::Indent indent) const
{
os << indent << "Number of fibers: " << this->GetNumFibers() << std::endl;
os << indent << "Min. fiber length: " << this->GetMinFiberLength() << std::endl;
os << indent << "Max. fiber length: " << this->GetMaxFiberLength() << std::endl;
os << indent << "Mean fiber length: " << this->GetMeanFiberLength() << std::endl;
os << indent << "Median fiber length: " << this->GetMedianFiberLength() << std::endl;
os << indent << "STDEV fiber length: " << this->GetLengthStDev() << std::endl;
os << indent << "Number of points: " << this->GetNumberOfPoints() << std::endl;
os << indent << "Extent x: " << this->GetGeometry()->GetExtentInMM(0) << "mm" << std::endl;
os << indent << "Extent y: " << this->GetGeometry()->GetExtentInMM(1) << "mm" << std::endl;
os << indent << "Extent z: " << this->GetGeometry()->GetExtentInMM(2) << "mm" << std::endl;
os << indent << "Diagonal: " << this->GetGeometry()->GetDiagonalLength() << "mm" << std::endl;
os << "\nReference geometry:" << std::endl;
os << indent << "Size: [" << std::defaultfloat << m_TrackVisHeader.dim[0] << " " << m_TrackVisHeader.dim[1] << " " << m_TrackVisHeader.dim[2] << "]" << std::endl;
os << indent << "Voxel size: [" << m_TrackVisHeader.voxel_size[0] << " " << m_TrackVisHeader.voxel_size[1] << " " << m_TrackVisHeader.voxel_size[2] << "]" << std::endl;
os << indent << "Origin: [" << m_TrackVisHeader.origin[0] << " " << m_TrackVisHeader.origin[1] << " " << m_TrackVisHeader.origin[2] << "]" << std::endl;
os << indent << "Matrix: " << std::scientific << std::endl;
os << indent << "[[" << m_TrackVisHeader.vox_to_ras[0][0] << ", " << m_TrackVisHeader.vox_to_ras[0][1] << ", " << m_TrackVisHeader.vox_to_ras[0][2] << ", " << m_TrackVisHeader.vox_to_ras[0][3] << "]" << std::endl;
os << indent << " [" << m_TrackVisHeader.vox_to_ras[1][0] << ", " << m_TrackVisHeader.vox_to_ras[1][1] << ", " << m_TrackVisHeader.vox_to_ras[1][2] << ", " << m_TrackVisHeader.vox_to_ras[1][3] << "]" << std::endl;
os << indent << " [" << m_TrackVisHeader.vox_to_ras[2][0] << ", " << m_TrackVisHeader.vox_to_ras[2][1] << ", " << m_TrackVisHeader.vox_to_ras[2][2] << ", " << m_TrackVisHeader.vox_to_ras[2][3] << "]" << std::endl;
os << indent << " [" << m_TrackVisHeader.vox_to_ras[3][0] << ", " << m_TrackVisHeader.vox_to_ras[3][1] << ", " << m_TrackVisHeader.vox_to_ras[3][2] << ", " << m_TrackVisHeader.vox_to_ras[3][3] << "]]" << std::defaultfloat << std::endl;
if (m_FiberWeights!=nullptr)
{
std::vector< float > weights;
for (int i=0; i<m_FiberWeights->GetSize(); i++)
weights.push_back(m_FiberWeights->GetValue(i));
std::sort(weights.begin(), weights.end());
os << "\nFiber weight statistics" << std::endl;
os << indent << "Min: " << weights.front() << std::endl;
os << indent << "1% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.01)) << std::endl;
os << indent << "5% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.05)) << std::endl;
os << indent << "25% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.25)) << std::endl;
os << indent << "Median: " << weights.at(static_cast<unsigned long>(weights.size()*0.5)) << std::endl;
os << indent << "75% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.75)) << std::endl;
os << indent << "95% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.95)) << std::endl;
os << indent << "99% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.99)) << std::endl;
os << indent << "Max: " << weights.back() << std::endl;
}
else
os << indent << "\n\nNo fiber weight array found." << std::endl;
Superclass::PrintSelf(os, 0);
}
mitk::FiberBundle::TrackVis_header mitk::FiberBundle::GetTrackVisHeader()
{
if (m_TrackVisHeader.hdr_size==0)
{
mitk::Geometry3D::Pointer geom = dynamic_cast<mitk::Geometry3D*>(this->GetGeometry());
SetTrackVisHeader(geom);
}
return m_TrackVisHeader;
}
void mitk::FiberBundle::SetTrackVisHeader(const mitk::FiberBundle::TrackVis_header &TrackVisHeader)
{
m_TrackVisHeader = TrackVisHeader;
}
void mitk::FiberBundle::SetTrackVisHeader(mitk::BaseGeometry* geometry)
{
vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New();
matrix->Identity();
if (geometry==nullptr)
return;
for(int i=0; i<3 ;i++)
{
m_TrackVisHeader.dim[i] = geometry->GetExtent(i);
m_TrackVisHeader.voxel_size[i] = geometry->GetSpacing()[i];
m_TrackVisHeader.origin[i] = geometry->GetOrigin()[i];
matrix = geometry->GetVtkMatrix();
}
for (int i=0; i<4; ++i)
for (int j=0; j<4; ++j)
m_TrackVisHeader.vox_to_ras[i][j] = matrix->GetElement(i, j);
m_TrackVisHeader.n_scalars = 0;
m_TrackVisHeader.n_properties = 0;
sprintf(m_TrackVisHeader.voxel_order,"LPS");
m_TrackVisHeader.image_orientation_patient[0] = 1.0;
m_TrackVisHeader.image_orientation_patient[1] = 0.0;
m_TrackVisHeader.image_orientation_patient[2] = 0.0;
m_TrackVisHeader.image_orientation_patient[3] = 0.0;
m_TrackVisHeader.image_orientation_patient[4] = 1.0;
m_TrackVisHeader.image_orientation_patient[5] = 0.0;
m_TrackVisHeader.pad1[0] = 0;
m_TrackVisHeader.pad1[1] = 0;
m_TrackVisHeader.pad2[0] = 0;
m_TrackVisHeader.pad2[1] = 0;
m_TrackVisHeader.invert_x = 0;
m_TrackVisHeader.invert_y = 0;
m_TrackVisHeader.invert_z = 0;
m_TrackVisHeader.swap_xy = 0;
m_TrackVisHeader.swap_yz = 0;
m_TrackVisHeader.swap_zx = 0;
m_TrackVisHeader.n_count = 0;
m_TrackVisHeader.version = 2;
m_TrackVisHeader.hdr_size = 1000;
std::string id = "TRACK";
strcpy(m_TrackVisHeader.id_string, id.c_str());
}
/* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */
void mitk::FiberBundle::UpdateOutputInformation()
{
}
void mitk::FiberBundle::SetRequestedRegionToLargestPossibleRegion()
{
}
bool mitk::FiberBundle::RequestedRegionIsOutsideOfTheBufferedRegion()
{
return false;
}
bool mitk::FiberBundle::VerifyRequestedRegion()
{
return true;
}
void mitk::FiberBundle::SetRequestedRegion(const itk::DataObject* )
{
}
diff --git a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h
index c6bbdf1..75a2008 100644
--- a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h
+++ b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h
@@ -1,247 +1,252 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center.
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 _MITK_FiberBundle_H
#define _MITK_FiberBundle_H
//includes for MITK datastructure
#include <mitkBaseData.h>
#include <MitkDiffusionCoreExports.h>
#include <mitkImage.h>
#include <mitkDataStorage.h>
#include <mitkPlanarFigure.h>
#include <mitkPixelTypeTraits.h>
#include <mitkPlanarFigureComposite.h>
#include <mitkPeakImage.h>
//includes storing fiberdata
#include <vtkSmartPointer.h>
#include <vtkPolyData.h>
#include <vtkPoints.h>
#include <vtkDataSet.h>
#include <vtkTransform.h>
#include <vtkFloatArray.h>
#include <itkScalableAffineTransform.h>
#include <mitkDiffusionFunctionCollection.h>
#include <mitkLookupTable.h>
+#include <opencv2/ml.hpp>
+#include <opencv2/opencv.hpp>
+#include <opencv2/highgui/highgui.hpp>
+
namespace mitk {
/**
* \brief Base Class for Fiber Bundles; */
class MITKDIFFUSIONCORE_EXPORT FiberBundle : public BaseData
{
public:
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
// fiber colorcodings
static const char* FIBER_ID_ARRAY;
void UpdateOutputInformation() override;
void SetRequestedRegionToLargestPossibleRegion() override;
bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
bool VerifyRequestedRegion() override;
void SetRequestedRegion(const itk::DataObject*) override;
mitkClassMacro( FiberBundle, BaseData )
itkFactorylessNewMacro(Self)
itkCloneMacro(Self)
mitkNewMacro1Param(Self, vtkSmartPointer<vtkPolyData>) // custom constructor
// colorcoding related methods
void ColorSinglePoint(int f_idx, int p_idx, double rgb[3]);
void ColorFibersByFiberWeights(bool opacity, LookupTable::LookupTableType type);
void ColorFibersByCurvature(bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type);
void ColorFibersByLength(bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type);
void ColorFibersByScalarMap(mitk::Image::Pointer, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap, bool interpolate=true);
template <typename TPixel>
void ColorFibersByScalarMap(typename itk::Image<TPixel, 3>::Pointer, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap, bool interpolate=true);
void ColorFibersByOrientation();
void SetFiberOpacity(vtkDoubleArray *FAValArray);
void ResetFiberOpacity();
void SetFiberColors(vtkSmartPointer<vtkUnsignedCharArray> fiberColors);
void SetFiberColors(float r, float g, float b, float alpha=255);
+ void SetSingleFiberColor(float r, float g, float b, unsigned int cellId, float alpha=255);
vtkSmartPointer<vtkUnsignedCharArray> GetFiberColors() const { return m_FiberColors; }
// fiber compression
void Compress(float error = 0.0);
// fiber resampling
void ResampleSpline(float pointDistance=1);
void ResampleSpline(float pointDistance, double tension, double continuity, double bias );
void ResampleLinear(double pointDistance=1);
void ResampleToNumPoints(unsigned int targetPoints);
mitk::FiberBundle::Pointer FilterByWeights(float weight_thr, bool invert=false);
bool RemoveShortFibers(float lengthInMM);
bool RemoveLongFibers(float lengthInMM);
bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers);
void MirrorFibers(unsigned int axis);
void RotateAroundAxis(double x, double y, double z);
void TranslateFibers(double x, double y, double z);
void ScaleFibers(double x, double y, double z, bool subtractCenter=true);
void TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz);
void TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform);
void RemoveDir(vnl_vector_fixed<double,3> dir, double threshold);
template< class TType=float >
void TransformPoint(itk::Point<TType, 3>& point, itk::Matrix< TType, 3, 3>& rot, TType& tx, TType& ty, TType& tz)
{
mitk::Point3D center = this->GetGeometry()->GetCenter();
point[0] -= center[0];
point[1] -= center[1];
point[2] -= center[2];
point = rot*point;
point[0] += center[0]+tx;
point[1] += center[1]+ty;
point[2] += center[2]+tz;
}
template< class TType=float >
void TransformPoint(itk::Point<TType, 3>& point, TType rx, TType ry, TType rz, TType tx, TType ty, TType tz)
{
auto rot = mitk::imv::GetRotationMatrixItk<TType>(rx, ry, rz);
mitk::Point3D center = this->GetGeometry()->GetCenter();
point[0] -= center[0];
point[1] -= center[1];
point[2] -= center[2];
point = rot*point;
point[0] += center[0]+tx;
point[1] += center[1]+ty;
point[2] += center[2]+tz;
}
itk::Matrix< double, 3, 3 > TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz);
// add/subtract fibers
FiberBundle::Pointer AddBundle(FiberBundle* fib);
mitk::FiberBundle::Pointer AddBundles(std::vector< mitk::FiberBundle::Pointer > fibs);
FiberBundle::Pointer SubtractBundle(FiberBundle* fib);
// fiber subset extraction
FiberBundle::Pointer ExtractFiberSubset(DataNode *roi, DataStorage* storage);
std::vector<unsigned int> ExtractFiberIdSubset(DataNode* roi, DataStorage* storage);
FiberBundle::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false);
float GetOverlap(ItkUcharImgType* mask);
std::tuple<float, float> GetDirectionalOverlap(ItkUcharImgType* mask, mitk::PeakImage::ItkPeakImageType* peak_image);
float GetNumEpFractionInMask(ItkUcharImgType* mask, bool different_label);
mitk::FiberBundle::Pointer SubsampleFibers(float factor, bool random_seed);
// get/set data
float GetFiberLength(unsigned int index) const { return m_FiberLengths.at(index); }
vtkSmartPointer<vtkFloatArray> GetFiberWeights() const { return m_FiberWeights; }
float GetFiberWeight(unsigned int fiber) const;
void SetFiberWeights(float newWeight);
void SetFiberWeight(unsigned int fiber, float weight);
void SetFiberWeights(vtkSmartPointer<vtkFloatArray> weights);
void SetFiberPolyData(vtkSmartPointer<vtkPolyData>, bool updateGeometry = true);
vtkSmartPointer<vtkPolyData> GetFiberPolyData() const;
itkGetConstMacro( NumFibers, unsigned int)
//itkGetMacro( FiberSampling, int)
itkGetConstMacro( MinFiberLength, float )
itkGetConstMacro( MaxFiberLength, float )
itkGetConstMacro( MeanFiberLength, float )
itkGetConstMacro( MedianFiberLength, float )
itkGetConstMacro( LengthStDev, float )
itkGetConstMacro( UpdateTime2D, itk::TimeStamp )
itkGetConstMacro( UpdateTime3D, itk::TimeStamp )
void RequestUpdate2D(){ m_UpdateTime2D.Modified(); }
void RequestUpdate3D(){ m_UpdateTime3D.Modified(); }
void RequestUpdate(){ m_UpdateTime2D.Modified(); m_UpdateTime3D.Modified(); }
unsigned int GetNumberOfPoints() const;
// copy fiber bundle
mitk::FiberBundle::Pointer GetDeepCopy();
// compare fiber bundles
bool Equals(FiberBundle* fib, double eps=0.01);
vtkSmartPointer<vtkPolyData> GeneratePolyDataByIds(std::vector<unsigned int> fiberIds, vtkSmartPointer<vtkFloatArray> weights);
// Structure to hold metadata of a TrackVis file
struct TrackVis_header
{
char id_string[6];
short int dim[3];
float voxel_size[3];
float origin[3];
short int n_scalars;
char scalar_name[10][20];
short int n_properties;
char property_name[10][20];
float vox_to_ras[4][4];
char reserved[444];
char voxel_order[4];
char pad2[4];
float image_orientation_patient[6];
char pad1[2];
unsigned char invert_x;
unsigned char invert_y;
unsigned char invert_z;
unsigned char swap_xy;
unsigned char swap_yz;
unsigned char swap_zx;
int n_count;
int version;
int hdr_size;
};
TrackVis_header GetTrackVisHeader();
void SetTrackVisHeader(const TrackVis_header &TrackVisHeader);
void SetTrackVisHeader(BaseGeometry *geometry);
void PrintSelf(std::ostream &os, itk::Indent indent) const override;
protected:
FiberBundle( vtkPolyData* fiberPolyData = nullptr );
~FiberBundle() override;
void GenerateFiberIds();
void UpdateFiberGeometry();
private:
// actual fiber container
vtkSmartPointer<vtkPolyData> m_FiberPolyData;
// contains fiber ids
vtkSmartPointer<vtkDataSet> m_FiberIdDataSet;
unsigned int m_NumFibers;
vtkSmartPointer<vtkUnsignedCharArray> m_FiberColors;
vtkSmartPointer<vtkFloatArray> m_FiberWeights;
std::vector< float > m_FiberLengths;
float m_MinFiberLength;
float m_MaxFiberLength;
float m_MeanFiberLength;
float m_MedianFiberLength;
float m_LengthStDev;
itk::TimeStamp m_UpdateTime2D;
itk::TimeStamp m_UpdateTime3D;
TrackVis_header m_TrackVisHeader;
};
} // namespace mitk
#endif /* _MITK_FiberBundle_H */
diff --git a/Modules/FiberDissection/CMakeLists.txt b/Modules/FiberDissection/CMakeLists.txt
new file mode 100644
index 0000000..9b030ee
--- /dev/null
+++ b/Modules/FiberDissection/CMakeLists.txt
@@ -0,0 +1,5 @@
+MITK_CREATE_MODULE(
+ SUBPROJECTS MITK-Diffusion
+ INCLUDE_DIRS Interactor MachineLearning ${CMAKE_CURRENT_BINARY_DIR}
+ DEPENDS MitkDiffusionCore
+)
diff --git a/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.cpp b/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.cpp
new file mode 100644
index 0000000..e885d79
--- /dev/null
+++ b/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.cpp
@@ -0,0 +1,1207 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#include "mitkStreamlineInteractor.h"
+//#include "mitkStreamlineMapper2D.h"
+
+// MITK includes
+#include <mitkInteractionConst.h>
+#include <mitkInteractionPositionEvent.h>
+#include <mitkInternalEvent.h>
+#include <mitkLookupTableProperty.h>
+#include <mitkOperationEvent.h>
+#include <mitkRotationOperation.h>
+#include <mitkScaleOperation.h>
+#include <mitkSurface.h>
+#include <mitkUndoController.h>
+#include <mitkVtkMapper.h>
+
+// VTK includes
+#include <vtkCamera.h>
+#include <vtkInteractorObserver.h>
+#include <vtkInteractorStyle.h>
+#include <vtkMath.h>
+#include <vtkPointData.h>
+#include <vtkPolyData.h>
+#include <vtkRenderWindowInteractor.h>
+#include <vtkVector.h>
+#include <vtkPolyLine.h>
+#include <vtkVectorOperators.h>
+
+mitk::StreamlineInteractor::StreamlineInteractor()
+{
+ m_ColorForHighlight[0] = 1.0;
+ m_ColorForHighlight[1] = 0.5;
+ m_ColorForHighlight[2] = 0.0;
+ m_ColorForHighlight[3] = 1.0;
+
+ // TODO if we want to get this configurable, the this is the recipe:
+ // - make the 2D mapper add corresponding properties to control "enabled" and "color"
+ // - make the interactor evaluate those properties
+ // - in an ideal world, modify the state machine on the fly and skip mouse move handling
+}
+
+mitk::StreamlineInteractor::~StreamlineInteractor()
+{
+}
+
+void mitk::StreamlineInteractor::ConnectActionsAndFunctions()
+{
+// CONNECT_CONDITION("isoverstreamline", HasPickedHandle);
+ CONNECT_CONDITION("isoverstreamline", CheckSelection);
+ CONNECT_FUNCTION("selectstreamline", SelectStreamline);
+
+ CONNECT_FUNCTION("addnegstreamline", AddStreamlineNegBundle);
+ CONNECT_FUNCTION("addposstreamline", AddStreamlinePosBundle);
+ CONNECT_FUNCTION("addnegtolabelstreamline", AddNegStreamlinetolabelsBundle);
+ CONNECT_FUNCTION("addpostolabelstreamline", AddPosStreamlinetolabelsBundle);
+// CONNECT_FUNCTION("FeedUndoStack", FeedUndoStack);
+}
+
+void mitk::StreamlineInteractor::SetNegativeNode(DataNode *node)
+{
+
+// DataInteractor::SetDataNode(node);
+ m_NegStreamlineNode = node;
+ m_NegStreamline= dynamic_cast<mitk::FiberBundle *>(node->GetData());
+ MITK_INFO << "Negative Node added";
+}
+
+void mitk::StreamlineInteractor::SetToLabelNode(DataNode *node)
+{
+ m_manStreamlineNode = node;
+ DataInteractor::SetDataNode(m_manStreamlineNode);
+ m_manStreamline = dynamic_cast<mitk::FiberBundle *>(node->GetData());
+ MITK_INFO << "Label node added";
+// m_init = false;
+
+}
+
+void mitk::StreamlineInteractor::SetPositiveNode(DataNode *node)
+{
+
+ // DataInteractor::SetDataNode(node);
+ m_PosStreamlineNode = node;
+ m_PosStreamline= dynamic_cast<mitk::FiberBundle *>(node->GetData());
+ MITK_INFO << "Positive Node added";
+}
+
+void mitk::StreamlineInteractor::LabelfromPrediction(bool predlabeling)
+{
+ m_predlabeling = predlabeling;
+
+}
+
+bool mitk::StreamlineInteractor::CheckSelection(const InteractionEvent *interactionEvent)
+{
+ /* Save Colorvector here*/
+
+ const auto *positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent != nullptr)
+ {
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+
+
+ if (picker->GetCellId()==-1 && m_predlabeling==false)
+ {
+// m_manStreamline->SetFiberColors(255, 255, 255);
+// vtkSmartPointer<vtkUnsignedCharArray> FiberColors = m_manStreamline->m_FiberColors;
+
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ return false;
+ }
+ else
+ {
+
+ return true;
+ }
+ }
+ else {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+
+
+ if (picker->GetCellId()==-1 && m_predlabeling==false)
+ {
+// m_manStreamline->SetFiberColors(255, 255, 255);
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ return false;
+ }
+ else
+ {
+
+ return true;
+ }
+
+ }
+
+
+ }
+ else {
+// m_manStreamline->SetFiberColors(255, 255, 255);
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ return false;
+ }
+
+}
+
+void mitk::StreamlineInteractor::SelectStreamline(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ auto *positionEvent = dynamic_cast<InteractionPositionEvent *>(interactionEvent);
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+ // }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+ if (m_predlabeling==false)
+ {
+ vtkIdType pickedCellID = picker->GetCellId();
+ m_manStreamline->SetSingleFiberColor(0.0, 255.0, 0.0, pickedCellID);
+// m_manStreamline->SetFloatProperty("shape.tuberadius", 1.0)
+ }
+ }
+ else {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+ // }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+ if (m_predlabeling==false)
+ {
+ vtkIdType pickedCellID = picker->GetCellId();
+ m_manStreamline->SetSingleFiberColor(0.0, 255.0, 0.0, pickedCellID);
+// m_manStreamline->SetFloatProperty("shape.tuberadius", 1.0);
+ }
+ }
+
+
+ RenderingManager::GetInstance()->RequestUpdateAll();
+}
+
+void mitk::StreamlineInteractor::AddStreamlinePosBundle(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ MITK_INFO << "PositiveBundle clicked";
+ DataInteractor::SetDataNode(m_manStreamlineNode);
+
+ auto positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent == nullptr)
+ {
+ MITK_INFO << "no position";
+ }
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+// m_PickedHandle = PickFrom2D(positionEvent);
+ MITK_INFO << "2D";
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_PosStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_PosStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_PosStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_PosStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_PosStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_PosStreamline->SetFiberColors(0, 255, 0);
+// m_PosStreamline->SetFiberWeights(m_PosStreamline->GetFiberWeights());
+
+ m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_manStreamline->GetFiberPolyData()->RemoveDeletedCells();
+ if (m_predlabeling==false)
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+
+ counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints2);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines2);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+ }
+
+
+
+
+
+ }
+ }
+ else
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_PosStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_PosStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_PosStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_PosStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_PosStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_PosStreamline->SetFiberColors(0, 255, 0);
+// m_PosStreamline->SetFiberWeights(m_PosStreamline->GetFiberWeights());
+
+
+ m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_manStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ if (m_predlabeling==false)
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+
+ counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints2);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines2);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+ }
+
+ }
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
+void mitk::StreamlineInteractor::AddStreamlineNegBundle(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ MITK_INFO << "NegativeBundle clicked";
+
+ DataInteractor::SetDataNode(m_manStreamlineNode);
+
+ auto positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent == nullptr)
+ {
+ MITK_INFO << "no position";
+ }
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+// m_PickedHandle = PickFrom2D(positionEvent);
+ MITK_INFO << "2D";
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_NegStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_NegStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_NegStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_NegStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_NegStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_NegStreamline->SetFiberColors(255, 0, 0);
+// m_NegStreamline->SetFiberWeights(m_NegStreamline->GetFiberWeights());
+
+ m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_manStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ if (m_predlabeling==false)
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+
+ counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints2);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines2);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+ }
+
+
+
+
+
+ }
+ }
+ else
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+// if (picker == nullptr)
+// {
+
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_NegStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = m_NegStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_NegStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_NegStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_NegStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_NegStreamline->SetFiberColors(255, 0, 0);
+
+ m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_manStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ if (m_predlabeling==false)
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+
+ counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints2);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines2);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+ }
+
+ }
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
+void mitk::StreamlineInteractor::AddNegStreamlinetolabelsBundle(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ MITK_INFO << "TolabelBundle clicked";
+ DataInteractor::SetDataNode(m_NegStreamlineNode);
+
+
+ auto positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent == nullptr)
+ {
+ MITK_INFO << "no position";
+ }
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+// m_PickedHandle = PickFrom2D(positionEvent);
+
+ MITK_INFO << "2D";
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_NegStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_manStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+// m_manStreamline->SetFiberWeights(m_manStreamline->GetFiberWeights());
+
+ m_NegStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_NegStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+
+
+
+
+ }
+ }
+ else
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+// if (picker == nullptr)
+// {
+
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_NegStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_manStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+
+ m_NegStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_NegStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ }
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
+void mitk::StreamlineInteractor::AddPosStreamlinetolabelsBundle(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ MITK_INFO << "TolabelBundle clicked";
+ DataInteractor::SetDataNode(m_PosStreamlineNode);
+
+
+ auto positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent == nullptr)
+ {
+ MITK_INFO << "no position";
+ }
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+// m_PickedHandle = PickFrom2D(positionEvent);
+
+ MITK_INFO << "2D";
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_PosStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_manStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+// m_manStreamline->SetFiberWeights(m_manStreamline->GetFiberWeights());
+
+ m_PosStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_PosStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+
+
+
+
+ }
+ }
+ else
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+// if (picker == nullptr)
+// {
+
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_PosStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_manStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+
+ m_PosStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_PosStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ }
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
diff --git a/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.h b/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.h
new file mode 100644
index 0000000..3b43f1e
--- /dev/null
+++ b/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.h
@@ -0,0 +1,123 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#ifndef mitkStreamlineInteractor_h
+#define mitkStreamlineInteractor_h
+
+
+#include "MitkFiberDissectionExports.h"
+
+// MITK includes
+#include <mitkDataInteractor.h>
+#include <mitkDataNode.h>
+#include <mitkGeometry3D.h>
+#include <mitkFiberBundle.h>
+
+// VTK includes
+#include <vtkCellPicker.h>
+#include <vtkSmartPointer.h>
+
+// System includes
+#include <memory>
+
+
+namespace mitk
+{
+ class InteractionPositionEvent;
+
+ //! Data interactor to pick streamlines via interaction
+ //! with a mitk::Streamline.
+ //!
+ //!
+ //! To determine what parts of the object are clicked during interaction,
+ //! the mappers (2D: custom mapper, 3D: regular surface mapper) are asked
+ //! for their VTK objects, picking is performed, and the picked point is
+ //! forwarded to the Streamline object for interpretation.
+ //!
+ //! The interactor fills the undo/redo stack with operations on the modified geometry.
+ //!
+ //! \sa Streamline
+ class MITKFIBERDISSECTION_EXPORT StreamlineInteractor : public DataInteractor
+ {
+ public:
+ mitkClassMacro(StreamlineInteractor, DataInteractor);
+ itkFactorylessNewMacro(Self);
+ itkCloneMacro(Self);
+
+ //! The node holding the Fiberbundle for visual feedback.
+ //! This is the node that the interactor is primarily working on
+ //! (calls DataInteractor::SetDataNode).
+
+ void SetNegativeNode(DataNode *node);
+ void SetToLabelNode(DataNode *node);
+ void SetPositiveNode(DataNode *node);
+ void LabelfromPrediction(bool predlabeling);
+
+ protected:
+
+ void AddStreamlineNegBundle(StateMachineAction *, InteractionEvent *interactionEvent);
+
+ void AddStreamlinePosBundle(StateMachineAction *, InteractionEvent *interactionEvent);
+
+ void AddNegStreamlinetolabelsBundle(StateMachineAction *, InteractionEvent *interactionEvent);
+
+ void AddPosStreamlinetolabelsBundle(StateMachineAction *, InteractionEvent *interactionEvent);
+
+ bool CheckSelection(const InteractionEvent *interactionEvent);
+
+ void SelectStreamline(StateMachineAction *, InteractionEvent *);
+
+
+ std::map<BaseRenderer *, vtkSmartPointer<vtkCellPicker>> m_Picker;
+
+ private:
+ StreamlineInteractor();
+ ~StreamlineInteractor() override;
+
+ //! Setup the relation between the XML state machine and this object's methods.
+ void ConnectActionsAndFunctions() override;
+
+ //! State machine condition: successful Streamline picking
+ //! \return true when any part of the Streamline has been picked.
+// bool HasPickedHandle(const InteractionEvent *);
+
+// void DecideInteraction(StateMachineAction *, InteractionEvent *interactionEvent);
+
+// //! Pick a Streamline handle from a 2D event (passing by the 2D mapper)
+// Streamline::HandleType PickFrom2D(const InteractionPositionEvent *positionEvent);
+
+// //! Pick a Streamline handle from a 3D event
+// //! (passing by the general surface mapper and the Streamline object)
+// Streamline::HandleType PickFrom3D(const InteractionPositionEvent *positionEvent);
+
+// void UpdateHandleHighlight();
+
+ //! the Streamline used for visual feedback and picking
+ mitk::FiberBundle::Pointer m_NegStreamline;
+ mitk::FiberBundle::Pointer m_PosStreamline;
+ mitk::FiberBundle::Pointer m_manStreamline;
+ bool m_predlabeling;
+// mitk::FiberBundle::Pointer m_visualStreamline;
+ mitk::DataNode::Pointer m_NegStreamlineNode;
+ mitk::DataNode::Pointer m_PosStreamlineNode;
+ mitk::DataNode::Pointer m_manStreamlineNode;
+// mitk::DataNode::Pointer m_visualStreamlineNode;
+
+
+
+ vtkSmartPointer<vtkPolyData> m_extracted_streamline;
+
+ double m_ColorForHighlight[4];
+
+ };
+}
+#endif
diff --git a/Modules/FiberDissection/Interactor/mitkStreamlineInteractorBrush.cpp b/Modules/FiberDissection/Interactor/mitkStreamlineInteractorBrush.cpp
new file mode 100644
index 0000000..335500e
--- /dev/null
+++ b/Modules/FiberDissection/Interactor/mitkStreamlineInteractorBrush.cpp
@@ -0,0 +1,1207 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#include "mitkStreamlineInteractorBrush.h"
+//#include "mitkStreamlineMapper2D.h"
+
+// MITK includes
+#include <mitkInteractionConst.h>
+#include <mitkInteractionPositionEvent.h>
+#include <mitkInternalEvent.h>
+#include <mitkLookupTableProperty.h>
+#include <mitkOperationEvent.h>
+#include <mitkRotationOperation.h>
+#include <mitkScaleOperation.h>
+#include <mitkSurface.h>
+#include <mitkUndoController.h>
+#include <mitkVtkMapper.h>
+
+// VTK includes
+#include <vtkCamera.h>
+#include <vtkInteractorObserver.h>
+#include <vtkInteractorStyle.h>
+#include <vtkMath.h>
+#include <vtkPointData.h>
+#include <vtkPolyData.h>
+#include <vtkRenderWindowInteractor.h>
+#include <vtkVector.h>
+#include <vtkPolyLine.h>
+#include <vtkVectorOperators.h>
+
+mitk::StreamlineInteractorBrush::StreamlineInteractorBrush()
+{
+ m_ColorForHighlight[0] = 1.0;
+ m_ColorForHighlight[1] = 0.5;
+ m_ColorForHighlight[2] = 0.0;
+ m_ColorForHighlight[3] = 1.0;
+
+ // TODO if we want to get this configurable, the this is the recipe:
+ // - make the 2D mapper add corresponding properties to control "enabled" and "color"
+ // - make the interactor evaluate those properties
+ // - in an ideal world, modify the state machine on the fly and skip mouse move handling
+}
+
+mitk::StreamlineInteractorBrush::~StreamlineInteractorBrush()
+{
+}
+
+void mitk::StreamlineInteractorBrush::ConnectActionsAndFunctions()
+{
+// CONNECT_CONDITION("isoverstreamline", HasPickedHandle);
+ CONNECT_CONDITION("isoverstreamline", CheckSelection);
+ CONNECT_FUNCTION("selectstreamline", SelectStreamline);
+
+ CONNECT_FUNCTION("addnegstreamline", AddStreamlineNegBundle);
+ CONNECT_FUNCTION("addposstreamline", AddStreamlinePosBundle);
+ CONNECT_FUNCTION("addnegtolabelstreamline", AddNegStreamlinetolabelsBundle);
+ CONNECT_FUNCTION("addpostolabelstreamline", AddPosStreamlinetolabelsBundle);
+// CONNECT_FUNCTION("FeedUndoStack", FeedUndoStack);
+}
+
+void mitk::StreamlineInteractorBrush::SetNegativeNode(DataNode *node)
+{
+
+// DataInteractor::SetDataNode(node);
+ m_NegStreamlineNode = node;
+ m_NegStreamline= dynamic_cast<mitk::FiberBundle *>(node->GetData());
+ MITK_INFO << "Negative Node added";
+}
+
+void mitk::StreamlineInteractorBrush::SetToLabelNode(DataNode *node)
+{
+ m_manStreamlineNode = node;
+ DataInteractor::SetDataNode(m_manStreamlineNode);
+ m_manStreamline = dynamic_cast<mitk::FiberBundle *>(node->GetData());
+ MITK_INFO << "Label node added";
+// m_init = false;
+
+}
+
+void mitk::StreamlineInteractorBrush::SetPositiveNode(DataNode *node)
+{
+
+ // DataInteractor::SetDataNode(node);
+ m_PosStreamlineNode = node;
+ m_PosStreamline= dynamic_cast<mitk::FiberBundle *>(node->GetData());
+ MITK_INFO << "Positive Node added";
+}
+
+void mitk::StreamlineInteractorBrush::LabelfromPrediction(bool predlabeling)
+{
+ m_predlabeling = predlabeling;
+
+}
+
+bool mitk::StreamlineInteractorBrush::CheckSelection(const InteractionEvent *interactionEvent)
+{
+ /* Save Colorvector here*/
+
+ const auto *positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent != nullptr)
+ {
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+
+
+ if (picker->GetCellId()==-1 && m_predlabeling==false)
+ {
+// m_manStreamline->SetFiberColors(255, 255, 255);
+// vtkSmartPointer<vtkUnsignedCharArray> FiberColors = m_manStreamline->m_FiberColors;
+
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ return false;
+ }
+ else
+ {
+
+ return true;
+ }
+ }
+ else {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+
+
+ if (picker->GetCellId()==-1 && m_predlabeling==false)
+ {
+// m_manStreamline->SetFiberColors(255, 255, 255);
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ return false;
+ }
+ else
+ {
+
+ return true;
+ }
+
+ }
+
+
+ }
+ else {
+// m_manStreamline->SetFiberColors(255, 255, 255);
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ return false;
+ }
+
+}
+
+void mitk::StreamlineInteractorBrush::SelectStreamline(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ auto *positionEvent = dynamic_cast<InteractionPositionEvent *>(interactionEvent);
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+ // }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+ if (m_predlabeling==false)
+ {
+ vtkIdType pickedCellID = picker->GetCellId();
+ m_manStreamline->SetSingleFiberColor(0.0, 255.0, 0.0, pickedCellID);
+// m_manStreamline->SetFloatProperty("shape.tuberadius", 1.0)
+ }
+ }
+ else {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+ // }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+ if (m_predlabeling==false)
+ {
+ vtkIdType pickedCellID = picker->GetCellId();
+ m_manStreamline->SetSingleFiberColor(0.0, 255.0, 0.0, pickedCellID);
+// m_manStreamline->SetFloatProperty("shape.tuberadius", 1.0);
+ }
+ }
+
+
+ RenderingManager::GetInstance()->RequestUpdateAll();
+}
+
+void mitk::StreamlineInteractorBrush::AddStreamlinePosBundle(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ MITK_INFO << "PositiveBundle clicked";
+ DataInteractor::SetDataNode(m_manStreamlineNode);
+
+ auto positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent == nullptr)
+ {
+ MITK_INFO << "no position";
+ }
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+// m_PickedHandle = PickFrom2D(positionEvent);
+ MITK_INFO << "2D";
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_PosStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_PosStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_PosStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_PosStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_PosStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_PosStreamline->SetFiberColors(0, 255, 0);
+// m_PosStreamline->SetFiberWeights(m_PosStreamline->GetFiberWeights());
+
+ m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_manStreamline->GetFiberPolyData()->RemoveDeletedCells();
+ if (m_predlabeling==false)
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+
+ counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints2);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines2);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+ }
+
+
+
+
+
+ }
+ }
+ else
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_PosStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_PosStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_PosStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_PosStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_PosStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_PosStreamline->SetFiberColors(0, 255, 0);
+// m_PosStreamline->SetFiberWeights(m_PosStreamline->GetFiberWeights());
+
+
+ m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_manStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ if (m_predlabeling==false)
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+
+ counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints2);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines2);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+ }
+
+ }
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
+void mitk::StreamlineInteractorBrush::AddStreamlineNegBundle(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ MITK_INFO << "NegativeBundle clicked";
+
+ DataInteractor::SetDataNode(m_manStreamlineNode);
+
+ auto positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent == nullptr)
+ {
+ MITK_INFO << "no position";
+ }
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+// m_PickedHandle = PickFrom2D(positionEvent);
+ MITK_INFO << "2D";
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_NegStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_NegStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_NegStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_NegStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_NegStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_NegStreamline->SetFiberColors(255, 0, 0);
+// m_NegStreamline->SetFiberWeights(m_NegStreamline->GetFiberWeights());
+
+ m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_manStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ if (m_predlabeling==false)
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+
+ counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints2);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines2);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+ }
+
+
+
+
+
+ }
+ }
+ else
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+// if (picker == nullptr)
+// {
+
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_NegStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = m_NegStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_NegStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_NegStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_NegStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_NegStreamline->SetFiberColors(255, 0, 0);
+
+ m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_manStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ if (m_predlabeling==false)
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+
+ counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints2);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines2);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+ }
+
+ }
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
+void mitk::StreamlineInteractorBrush::AddNegStreamlinetolabelsBundle(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ MITK_INFO << "TolabelBundle clicked";
+ DataInteractor::SetDataNode(m_NegStreamlineNode);
+
+
+ auto positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent == nullptr)
+ {
+ MITK_INFO << "no position";
+ }
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+// m_PickedHandle = PickFrom2D(positionEvent);
+
+ MITK_INFO << "2D";
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_NegStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_manStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+// m_manStreamline->SetFiberWeights(m_manStreamline->GetFiberWeights());
+
+ m_NegStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_NegStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+
+
+
+
+ }
+ }
+ else
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+// if (picker == nullptr)
+// {
+
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_NegStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_manStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+
+ m_NegStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_NegStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ }
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
+void mitk::StreamlineInteractorBrush::AddPosStreamlinetolabelsBundle(StateMachineAction *, InteractionEvent *interactionEvent)
+{
+ MITK_INFO << "TolabelBundle clicked";
+ DataInteractor::SetDataNode(m_PosStreamlineNode);
+
+
+ auto positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
+ if (positionEvent == nullptr)
+ {
+ MITK_INFO << "no position";
+ }
+
+ if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
+ {
+// m_PickedHandle = PickFrom2D(positionEvent);
+
+ MITK_INFO << "2D";
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D);
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else {
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_PosStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_manStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+// m_manStreamline->SetFiberWeights(m_manStreamline->GetFiberWeights());
+
+ m_PosStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_PosStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+
+
+
+
+ }
+ }
+ else
+ {
+ BaseRenderer *renderer = positionEvent->GetSender();
+
+ auto &picker = m_Picker[renderer];
+// if (picker == nullptr)
+// {
+
+
+ picker = vtkSmartPointer<vtkCellPicker>::New();
+ picker->SetTolerance(0.01);
+ auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D);
+
+
+ auto vtk_mapper = dynamic_cast<VtkMapper *>(mapper);
+ if (vtk_mapper)
+ { // doing this each time is bizarre
+ picker->AddPickList(vtk_mapper->GetVtkProp(renderer));
+ picker->PickFromListOn();
+ }
+// }
+
+ auto displayPosition = positionEvent->GetPointerPositionOnScreen();
+
+ picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer());
+
+ vtkIdType pickedCellID = picker->GetCellId();
+
+
+ if (picker->GetCellId()==-1)
+ {
+ MITK_INFO << "Nothing picked";
+ }
+ else
+ {
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ unsigned int counter = 0;
+ for ( int i=0; i<m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ // weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vtkCell* cell = m_PosStreamline->GetFiberPolyData()->GetCell(pickedCellID);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ // m_manStreamline = mitk::FiberBundle::New(vNewPolyData);
+ m_manStreamline->GetFiberPolyData()->SetPoints(vNewPoints);
+ m_manStreamline->GetFiberPolyData()->SetLines(vNewLines);
+ m_manStreamline->SetFiberColors(255, 255, 255);
+
+ m_PosStreamline->GetFiberPolyData()->DeleteCell(pickedCellID);
+ m_PosStreamline->GetFiberPolyData()->RemoveDeletedCells();
+
+ }
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
diff --git a/Modules/FiberDissection/Interactor/mitkStreamlineInteractorBrush.h b/Modules/FiberDissection/Interactor/mitkStreamlineInteractorBrush.h
new file mode 100644
index 0000000..deb5b8f
--- /dev/null
+++ b/Modules/FiberDissection/Interactor/mitkStreamlineInteractorBrush.h
@@ -0,0 +1,123 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#ifndef mitkStreamlineInteractorBrush_h
+#define mitkStreamlineInteractorBrush_h
+
+
+#include "MitkFiberDissectionExports.h"
+
+// MITK includes
+#include <mitkDataInteractor.h>
+#include <mitkDataNode.h>
+#include <mitkGeometry3D.h>
+#include <mitkFiberBundle.h>
+
+// VTK includes
+#include <vtkCellPicker.h>
+#include <vtkSmartPointer.h>
+
+// System includes
+#include <memory>
+
+
+namespace mitk
+{
+ class InteractionPositionEvent;
+
+ //! Data interactor to pick streamlines via interaction
+ //! with a mitk::Streamline.
+ //!
+ //!
+ //! To determine what parts of the object are clicked during interaction,
+ //! the mappers (2D: custom mapper, 3D: regular surface mapper) are asked
+ //! for their VTK objects, picking is performed, and the picked point is
+ //! forwarded to the Streamline object for interpretation.
+ //!
+ //! The interactor fills the undo/redo stack with operations on the modified geometry.
+ //!
+ //! \sa Streamline
+ class MITKFIBERDISSECTION_EXPORT StreamlineInteractorBrush : public DataInteractor
+ {
+ public:
+ mitkClassMacro(StreamlineInteractorBrush, DataInteractor);
+ itkFactorylessNewMacro(Self);
+ itkCloneMacro(Self);
+
+ //! The node holding the Fiberbundle for visual feedback.
+ //! This is the node that the interactor is primarily working on
+ //! (calls DataInteractor::SetDataNode).
+
+ void SetNegativeNode(DataNode *node);
+ void SetToLabelNode(DataNode *node);
+ void SetPositiveNode(DataNode *node);
+ void LabelfromPrediction(bool predlabeling);
+
+ protected:
+
+ void AddStreamlineNegBundle(StateMachineAction *, InteractionEvent *interactionEvent);
+
+ void AddStreamlinePosBundle(StateMachineAction *, InteractionEvent *interactionEvent);
+
+ void AddNegStreamlinetolabelsBundle(StateMachineAction *, InteractionEvent *interactionEvent);
+
+ void AddPosStreamlinetolabelsBundle(StateMachineAction *, InteractionEvent *interactionEvent);
+
+ bool CheckSelection(const InteractionEvent *interactionEvent);
+
+ void SelectStreamline(StateMachineAction *, InteractionEvent *);
+
+
+ std::map<BaseRenderer *, vtkSmartPointer<vtkCellPicker>> m_Picker;
+
+ private:
+ StreamlineInteractorBrush();
+ ~StreamlineInteractorBrush() override;
+
+ //! Setup the relation between the XML state machine and this object's methods.
+ void ConnectActionsAndFunctions() override;
+
+ //! State machine condition: successful Streamline picking
+ //! \return true when any part of the Streamline has been picked.
+// bool HasPickedHandle(const InteractionEvent *);
+
+// void DecideInteraction(StateMachineAction *, InteractionEvent *interactionEvent);
+
+// //! Pick a Streamline handle from a 2D event (passing by the 2D mapper)
+// Streamline::HandleType PickFrom2D(const InteractionPositionEvent *positionEvent);
+
+// //! Pick a Streamline handle from a 3D event
+// //! (passing by the general surface mapper and the Streamline object)
+// Streamline::HandleType PickFrom3D(const InteractionPositionEvent *positionEvent);
+
+// void UpdateHandleHighlight();
+
+ //! the Streamline used for visual feedback and picking
+ mitk::FiberBundle::Pointer m_NegStreamline;
+ mitk::FiberBundle::Pointer m_PosStreamline;
+ mitk::FiberBundle::Pointer m_manStreamline;
+ bool m_predlabeling;
+// mitk::FiberBundle::Pointer m_visualStreamline;
+ mitk::DataNode::Pointer m_NegStreamlineNode;
+ mitk::DataNode::Pointer m_PosStreamlineNode;
+ mitk::DataNode::Pointer m_manStreamlineNode;
+// mitk::DataNode::Pointer m_visualStreamlineNode;
+
+
+
+ vtkSmartPointer<vtkPolyData> m_extracted_streamline;
+
+ double m_ColorForHighlight[4];
+
+ };
+}
+#endif
diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp
new file mode 100644
index 0000000..309c41f
--- /dev/null
+++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp
@@ -0,0 +1,981 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center.
+
+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 "mitkStreamlineFeatureExtractor.h"
+
+#define _USE_MATH_DEFINES
+#include <math.h>
+#include <boost/progress.hpp>
+#include <vnl/vnl_sparse_matrix.h>
+#include <mitkIOUtil.h>
+
+namespace mitk{
+
+StreamlineFeatureExtractor::StreamlineFeatureExtractor()
+ : m_NumPoints(40)
+{
+
+}
+
+StreamlineFeatureExtractor::~StreamlineFeatureExtractor()
+{
+
+}
+
+void StreamlineFeatureExtractor::SetTractogramPrediction(const mitk::FiberBundle::Pointer &TractogramPrediction)
+{
+ m_TractogramPrediction= TractogramPrediction;
+}
+
+void StreamlineFeatureExtractor::SetTractogramGroundtruth(const mitk::FiberBundle::Pointer &TractogramGroundtruth)
+{
+ m_TractogramGroundtruth= TractogramGroundtruth;
+}
+
+void StreamlineFeatureExtractor::SetTractogramPlus(const mitk::FiberBundle::Pointer &TractogramPlus)
+{
+ m_TractogramPlus = TractogramPlus;
+}
+
+void StreamlineFeatureExtractor::SetTractogramMinus(const mitk::FiberBundle::Pointer &TractogramMinus)
+{
+ m_TractogramMinus = TractogramMinus;
+}
+
+void StreamlineFeatureExtractor::SetTractogramPrototypes(const mitk::FiberBundle::Pointer &TractogramPrototypes, bool standard)
+{
+ if (standard)
+ {
+ MITK_INFO << "Use Standard Prototypes...";
+ m_inputPrototypes = mitk::IOUtil::Load<mitk::FiberBundle>("/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/mitk_diff/prototypes_599671_40.trk");
+ }
+ else {
+ MITK_INFO << "Use individual Prototypes...";
+ m_inputPrototypes = TractogramPrototypes;
+ }
+
+
+}
+
+void StreamlineFeatureExtractor::SetActiveCycle(int &activeCycle)
+{
+ m_activeCycle= activeCycle;
+}
+
+
+void StreamlineFeatureExtractor::SetTractogramTest(const mitk::FiberBundle::Pointer &TractogramTest, std::string TractogramTestName)
+{
+// std::string path = "/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/mitk_diff/storage/";
+// path.append(TractogramTestName);
+ MITK_INFO << TractogramTestName;
+ m_TractogramTest= TractogramTest;
+// auto s = std::to_string(m_NumPoints);
+// m_DistancesTestName= path.append("_distances" + std::to_string(m_NumPoints) + "_" + std::to_string(m_activeCycle) + ".csv");
+}
+
+std::vector<vnl_matrix<float> > StreamlineFeatureExtractor::ResampleFibers(mitk::FiberBundle::Pointer tractogram)
+{
+ MITK_INFO << "Infunction";
+// mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy();
+// temp_fib->ResampleToNumPoints(m_NumPoints);
+ MITK_INFO << "Resampling Done";
+
+ std::vector< vnl_matrix<float> > out_fib(tractogram->GetFiberPolyData()->GetNumberOfCells());
+//#pragma omp parallel for
+ for (int i=0; i<tractogram->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = tractogram->GetFiberPolyData()->GetCell(i);
+ int numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vnl_matrix<float> streamline;
+ streamline.set_size(3, m_NumPoints);
+ streamline.fill(0.0);
+
+ for (int j=0; j<numPoints; j++)
+ {
+ double cand[3];
+ points->GetPoint(j, cand);
+
+ vnl_vector_fixed< float, 3 > candV;
+ candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
+ streamline.set_column(j, candV);
+ }
+
+// out_fib.push_back(streamline);
+ out_fib.at(i)=streamline;
+ }
+// });
+
+
+
+ return out_fib;
+}
+
+std::vector<vnl_matrix<float> > StreamlineFeatureExtractor::CalculateDmdf(std::vector<vnl_matrix<float> > tractogram,
+ std::vector<vnl_matrix<float> > prototypes)
+{
+
+ std::vector< vnl_matrix<float> > dist_vec(tractogram.size());//
+ MITK_INFO << "Start Calculating Dmdf";
+// cv::parallel_for_(cv::Range(0, tractogram.size()), [&](const cv::Range &range)
+// {
+// for (int i = range.start; i < range.end; i++)
+#pragma omp parallel for
+ for (unsigned int i=0; i<tractogram.size(); i++)
+ {
+ vnl_matrix<float> distances;
+ distances.set_size(1, prototypes.size());
+ distances.fill(0.0);
+ for (unsigned int j=0; j<prototypes.size(); j++)
+ {
+ vnl_matrix<float> single_distances;
+ single_distances.set_size(1, tractogram.at(0).cols());
+ single_distances.fill(0.0);
+ vnl_matrix<float> single_distances_flip;
+ single_distances_flip.set_size(1, tractogram.at(0).cols());
+ single_distances_flip.fill(0.0);
+ for (unsigned int ik=0; ik<tractogram.at(0).cols(); ik++)
+ {
+ double cur_dist;
+ double cur_dist_flip;
+
+ cur_dist = sqrt(pow(tractogram.at(i).get(0,ik) - prototypes.at(j).get(0,ik), 2.0) +
+ pow(tractogram.at(i).get(1,ik) - prototypes.at(j).get(1,ik), 2.0) +
+ pow(tractogram.at(i).get(2,ik) - prototypes.at(j).get(2,ik), 2.0));
+
+ cur_dist_flip = sqrt(pow(tractogram.at(i).get(0,ik) - prototypes.at(j).get(0,prototypes.at(0).cols()-(ik+1)), 2.0) +
+ pow(tractogram.at(i).get(1,ik) - prototypes.at(j).get(1,prototypes.at(0).cols()-(ik+1)), 2.0) +
+ pow(tractogram.at(i).get(2,ik) - prototypes.at(j).get(2,prototypes.at(0).cols()-(ik+1)), 2.0));
+
+ single_distances.put(0,ik, cur_dist);
+ single_distances_flip.put(0,ik, cur_dist_flip);
+
+ }
+
+ if (single_distances_flip.mean()> single_distances.mean())
+ {
+ distances.put(0,j, single_distances.mean());
+ }
+ else {
+ distances.put(0,j, single_distances_flip.mean());
+ }
+ }
+ dist_vec.at(i) = distances;
+ }
+// });
+ MITK_INFO << "Done Calculation";
+ MITK_INFO << dist_vec.at(0).size();
+
+ return dist_vec;
+}
+
+std::vector<vnl_matrix<float> > StreamlineFeatureExtractor::MergeTractogram(std::vector<vnl_matrix<float> > prototypes,
+ std::vector<vnl_matrix<float> > positive_local_prototypes,
+ std::vector<vnl_matrix<float> > negative_local_prototypes)
+{
+ unsigned int pos_locals;
+ unsigned int neg_locals;
+
+ if (positive_local_prototypes.size() >= 50)
+ {
+ pos_locals= 50;
+ }
+ else {
+ pos_locals= positive_local_prototypes.size();
+ }
+
+ if (negative_local_prototypes.size() >= 50)
+ {
+ neg_locals = 50;
+ }
+ else {
+ neg_locals= negative_local_prototypes.size();
+ }
+
+
+
+ std::vector< vnl_matrix<float> > merged_prototypes;
+
+ for (unsigned int k=0; k<prototypes.size(); k++)
+ {
+ merged_prototypes.push_back(prototypes.at(k));
+ }
+
+ for (unsigned int k=0; k<positive_local_prototypes.size(); k++)
+ {
+ merged_prototypes.push_back(positive_local_prototypes.at(k));
+ }
+
+ for (unsigned int k=0; k<negative_local_prototypes.size(); k++)
+ {
+ merged_prototypes.push_back(negative_local_prototypes.at(k));
+ }
+
+ MITK_INFO << "Number of prototypes:";
+ MITK_INFO << prototypes.size();
+ MITK_INFO << "Number of positive local prototypes:";
+ MITK_INFO << pos_locals;
+ MITK_INFO << "Number of negative local prototypes:";
+ MITK_INFO << neg_locals;
+
+ return merged_prototypes;
+
+}
+
+
+std::vector<unsigned int> StreamlineFeatureExtractor::Sort(std::vector<float> sortingVector, int lengths, int start)
+{
+ std::vector<unsigned int> index;
+ std::priority_queue<std::pair<float, int>> q;
+
+ for (unsigned int i = 0; i < sortingVector.size(); ++i)
+ {
+ q.push(std::pair<float, int>(sortingVector[i], i));
+ }
+
+
+ for (int i = 0; i < lengths; ++i)
+ {
+ int ki = q.top().second;
+ if (i>=start)
+ {
+ index.push_back(ki);
+ }
+ q.pop();
+ }
+ return index;
+}
+
+
+std::vector<std::vector<unsigned int>> StreamlineFeatureExtractor::GetData()
+{
+ MITK_INFO << "Start Function Get Data";
+
+ /*Vector which saves Prediction and Fibers to label based on uncertainty*/
+ std::vector<std::vector<unsigned int>> index_vec;
+
+// int labels_arr [m_DistancesPlus.size()+m_DistancesMinus.size()];
+ cv::Mat data;
+ cv::Mat labels_arr_vec;
+
+ int size_plus = 0;
+
+
+ /*Create Trainingdata: Go through positive and negative Bundle and save distances as cv::Mat and create vector with labels*/
+ for ( unsigned int i=0; i<m_DistancesPlus.size(); i++)
+ {
+ float data_arr [m_DistancesPlus.at(0).size()];
+// labels_arr[i]=1;
+ labels_arr_vec.push_back(1);
+
+ for ( unsigned int j=0; j<m_DistancesPlus.at(0).cols(); j++)
+ {
+ data_arr[j] = m_DistancesPlus.at(i).get(0,j);
+ }
+ cv::Mat curdata(1, m_DistancesPlus.at(0).size(), CV_32F, data_arr);
+ data.push_back(curdata);
+ size_plus++;
+
+ }
+
+ for ( unsigned int i=m_DistancesPlus.size(); i<m_DistancesPlus.size()+m_DistancesMinus.size(); i++)
+ {
+ int it = i - size_plus;
+ float data_arr [m_DistancesMinus.at(0).size()];
+// labels_arr[i]=0;
+ labels_arr_vec.push_back(0);
+
+ for ( unsigned int j=0; j<m_DistancesMinus.at(0).cols(); j++)
+ {
+ data_arr[j] = m_DistancesMinus.at(it).get(0,j);
+ }
+ cv::Mat curdata(1, m_DistancesPlus.at(0).size(), CV_32F, data_arr);
+ data.push_back(curdata);
+
+ }
+ MITK_INFO << data.cols;
+ MITK_INFO << data.rows;
+
+ /*Calculate weights*/
+ int zerosgt = labels_arr_vec.rows - cv::countNonZero(labels_arr_vec);
+ int onesgt = cv::countNonZero(labels_arr_vec);
+ float plusval = labels_arr_vec.rows / (2.0 * onesgt ) ;
+ float minusval = labels_arr_vec.rows / (2.0 * zerosgt );
+ float w[2] = {minusval, plusval};
+ cv::Mat newweight = cv::Mat(1,2, CV_32F, w);
+ MITK_INFO << "Weights";
+ MITK_INFO << newweight;
+
+
+ /*Shuffle Data*/
+ std::vector <int> seeds;
+ for (int cont = 0; cont < labels_arr_vec.rows; cont++)
+ {
+ seeds.push_back(cont);
+ }
+
+ cv::randShuffle(seeds);
+ cv::Mat labels_shuffled;
+ cv::Mat samples_shuffled;
+
+
+
+
+ for (int cont = 0; cont < labels_arr_vec.rows; cont++)
+ {
+ labels_shuffled.push_back(labels_arr_vec.row(seeds[cont]));
+ }
+
+ for (int cont = 0; cont < labels_arr_vec.rows; cont++)
+ {
+ samples_shuffled.push_back(data.row(seeds[cont]));
+ }
+
+
+// std::ofstream labelsfile;
+// labelsfile.open("/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/mitk_diff/storage/Labels_" + std::to_string(m_activeCycle) + ".csv");
+// labelsfile<< cv::format(labels_shuffled, cv::Formatter::FMT_CSV) << std::endl;
+// labelsfile.close();
+
+// std::ofstream featuresfile;
+// featuresfile.open("/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/mitk_diff/storage/Features_" + std::to_string(m_activeCycle) + ".csv");
+// featuresfile<< cv::format(samples_shuffled, cv::Formatter::FMT_CSV) << std::endl;
+// featuresfile.close();
+
+ /*Create Dataset and initialize Classifier*/
+ cv::Ptr<cv::ml::TrainData> m_traindata = cv::ml::TrainData::create(samples_shuffled, cv::ml::ROW_SAMPLE, labels_shuffled);
+
+
+
+
+ statistic_model= cv::ml::RTrees::create();
+ auto criteria = cv::TermCriteria();
+ criteria.type = cv::TermCriteria::MAX_ITER;
+// criteria.epsilon = 1e-8;
+ criteria.maxCount = 400;
+
+ statistic_model->setMaxDepth(10); //set to three
+// statistic_model->setMinSampleCount(m_traindata->getNTrainSamples()*0.01);
+ statistic_model->setMinSampleCount(2);
+ statistic_model->setTruncatePrunedTree(false);
+ statistic_model->setUse1SERule(false);
+ statistic_model->setUseSurrogates(false);
+ statistic_model->setTermCriteria(criteria);
+ statistic_model->setCVFolds(1);
+ statistic_model->setPriors(newweight);
+
+
+ /*Train Classifier*/
+ MITK_INFO << "Start Training";
+ statistic_model->train(m_traindata);
+
+
+ /*Predict on Test Data*/
+ MITK_INFO << "Predicting";
+
+ /*Create Dataset as cv::Mat*/
+ cv::Mat dataTest;
+ for ( unsigned int i=0; i<m_DistancesTest.size(); i++)
+ {
+ float data_arr [m_DistancesTest.at(0).size()];
+
+ for ( unsigned int j=0; j<m_DistancesTest.at(0).cols(); j++)
+ {
+ data_arr[j] = m_DistancesTest.at(i).get(0,j);
+ }
+ cv::Mat curdata(1, m_DistancesTest.at(0).size(), CV_32F, data_arr);
+ dataTest.push_back(curdata);
+ }
+
+
+ std::vector<unsigned int> indexPrediction;
+ std::vector<float> e(m_DistancesTest.size());
+ std::vector<int> pred(m_DistancesTest.size());
+
+
+ /*For every Sample/Streamline get Prediction and entropy (=based on counts of Random Forest)*/
+ MITK_INFO << "Predicting on all cores";
+#pragma omp parallel for
+ for (unsigned int i=0; i<m_DistancesTest.size(); i++)
+ {
+
+
+ int val = statistic_model->predict(dataTest.row(i));
+ pred.at(i)=val;
+
+ #pragma omp critical
+ if (val==1)
+ {
+ indexPrediction.push_back(i);
+ }
+
+
+ cv::Mat vote;
+ statistic_model->getVotes(dataTest.row(i), vote, 0);
+ e.at(i) = ( -(vote.at<int>(1,0)*1.0)/ (vote.at<int>(1,0)+vote.at<int>(1,1)) * log2((vote.at<int>(1,0)*1.0)/ (vote.at<int>(1,0)+vote.at<int>(1,1))) -
+ (vote.at<int>(1,1)*1.0)/ (vote.at<int>(1,0)+vote.at<int>(1,1))* log2((vote.at<int>(1,1)*1.0)/ (vote.at<int>(1,0)+vote.at<int>(1,1))));
+
+ if (isnan(e.at(i)))
+ {
+ e.at(i)=0;
+ }
+
+ }
+ MITK_INFO << "Done";
+
+ /*Save entropy values for analysis*/
+ std::ofstream entropyfile;
+ entropyfile.open("/home/r948e/mycsv/entropydata_" + std::to_string(m_activeCycle) + ".csv");
+ for (unsigned int i = 0; i < e.size(); i++)
+ {
+ entropyfile << e.at(i) << ' ';
+ }
+ entropyfile.close();
+
+ std::ofstream predictionfile;
+ predictionfile.open("/home/r948e/mycsv/predictiondata_" + std::to_string(m_activeCycle) + ".csv");
+ for (unsigned int i = 0; i < pred.size(); i++)
+ {
+ predictionfile << pred.at(i) << ' ';
+ }
+ predictionfile.close();
+
+
+
+
+ MITK_INFO << "--------------";
+ MITK_INFO << "Prediction vector size:";
+ MITK_INFO << indexPrediction.size();
+ MITK_INFO << "Entropy vector size:";
+ entropy_vector = e;
+ MITK_INFO << e.size();
+
+ MITK_INFO << "--------------";
+
+ /*Get index of most unertain data (lengths defines how many data is saved)*/
+// int lengths=500;
+ int lengths = std::count_if(e.begin(), e.end(),[&](auto const& val){ return val >= 0.95; });
+ if (lengths>1500)
+ {
+ lengths=1500;
+ }
+// else if (lengths>3000)
+// {
+// lengths=3000;
+// }
+
+ int lengthsCertain = std::count_if(e.begin(), e.end(),[&](auto const& val){ return val < 0.1; });
+
+ std::vector<unsigned int> indexUnc = Sort(e, lengths, 0);
+
+ std::vector<unsigned int> indexCertain = Sort(e, e.size() , e.size()-lengthsCertain );
+
+// std::vector<unsigned int> indexCertainBetween = Sort(e, e.size()-lengthsCertain , lengths);
+
+ MITK_INFO << "Index Certainty Vector size";
+ MITK_INFO << indexCertain.size();
+
+// for (unsigned int i=indexCertain.size(); i>=0; --i)
+ std::vector<unsigned int> indexCertainNeg;
+ std::vector<unsigned int> indexCertainPos;
+
+ for (unsigned int i=0; i<indexCertain.size(); i++)
+ {
+ if(pred.at(indexCertain.at(i))==0 )
+ {
+ indexCertainNeg.push_back(indexCertain.at(i));
+ }
+ else {
+ indexCertainPos.push_back(indexCertain.at(i));
+ }
+
+ }
+
+
+ // for (unsigned int i=indexCertain.size(); i>=0; --i)
+// std::vector<unsigned int> indexCertainBetweenNeg;
+// std::vector<unsigned int> indexCertainBetweenPos;
+
+// for (unsigned int i=0; i<indexCertainBetween.size(); i++)
+// {
+// if(pred.at(indexCertainBetween.at(i))==0 )
+// {
+// indexCertainBetweenNeg.push_back(indexCertainBetween.at(i));
+// }
+// else {
+// indexCertainBetweenPos.push_back(indexCertainBetween.at(i));
+// }
+
+// }
+
+ MITK_INFO << "Index Uncertainty Vector size";
+ MITK_INFO << indexUnc.size();
+ MITK_INFO << "Index Certainty Vector size";
+ MITK_INFO << indexCertainPos.size();
+ MITK_INFO << indexCertainNeg.size();
+ MITK_INFO << indexCertainNeg.size() +indexCertainPos.size();
+ MITK_INFO << "Index Certainty between Vector size";
+// MITK_INFO << indexCertainBetweenPos.size();
+// MITK_INFO << indexCertainBetweenNeg.size();
+// MITK_INFO << indexCertainBetweenNeg.size() +indexCertainBetweenPos.size();
+
+
+// vnl_matrix<float> distances_matrix;
+
+// distances_matrix.set_size(lengths, lengths);
+// distances_matrix.fill(0.0);
+
+// std::vector<float> distances_matrix_mean;
+
+
+// for (int i=0; i<lengths; i++)
+// {
+// for (int k=0; k<lengths; k++)
+// {
+// /*From the length.size() Samples with the highest Entropey calculate the differen between the Features*/
+// vnl_matrix<float> diff = m_DistancesTest.at(indexUnc.at(i)) - m_DistancesTest.at(indexUnc.at(k));
+
+// /*Into the eucledean difference matrix, put the distance in Feature Space between every sample pair*/
+// distances_matrix.put(i,k,diff.absolute_value_sum()/m_DistancesTest.at(0).size());
+
+// }
+// /*For every Sample/Streamline get the mean eucledean distance to all other Samples => one value for every Sample*/
+//// distances_matrix_mean.push_back(distances_matrix.get_row(i).mean());
+//// MITK_INFO << meanval.at(i);
+
+// }
+
+
+
+// /*Index to find values in distancematrix*/
+// std::vector<unsigned int> myidx;
+// /*Index to find actual streamlines using indexUnc*/
+// std::vector<unsigned int> indexUncDist;
+// /*Start with the Streamline of the highest entropy, which is in distance_matrix at idx 0*/
+// myidx.push_back(0);
+// indexUncDist.push_back(indexUnc.at(myidx.at(0)));
+
+// /*Vecotr that stores minvalues of current iteration*/
+// vnl_matrix<float> cur_vec;
+// cur_vec.set_size(1,lengths);
+// cur_vec.fill(0.0);
+// for (int i=0; i<lengths; i++)
+// {
+
+//// unsigned int cur_i = indexUnc.at(myidx.at(i));
+
+// /*Save mean distance of all used Samples*/
+// vnl_matrix<float> sum_matrix;
+// sum_matrix.set_size(myidx.size(), lengths);
+// sum_matrix.fill(0);
+// for (unsigned int ii=0; ii<myidx.size(); ii++)
+// {
+
+// sum_matrix.set_row(ii, distances_matrix.get_column(myidx.at(ii)));
+// }
+
+// for (unsigned int k=0; k<sum_matrix.columns(); k++)
+// {
+// cur_vec.put(0,k, sum_matrix.get_column(k).min_value());
+// }
+// myidx.push_back(cur_vec.arg_max());
+
+
+// indexUncDist.push_back(indexUnc.at(myidx.at(i+1)));
+// sum_matrix.clear();
+
+// }
+
+// MITK_INFO << "Dist_stop";
+
+
+ /*Save Prediction*/
+ index_vec.push_back(indexPrediction);
+ /*Save index of uncertainty measures*/
+ index_vec.push_back(indexUnc);
+ /*Save index of uncertainty measures influenced by distance*/
+// index_vec.push_back(indexUncDist);
+ /*Save index of certain measures*/
+ index_vec.push_back(indexCertainNeg);
+ /*Save index of certain measures*/
+// index_vec.push_back(indexCertainPos);
+ /*Save index of certain measures*/
+// index_vec.push_back(indexCertainBetweenNeg);
+ /*Save index of certain measures*/
+// index_vec.push_back(indexCertainBetweenPos);
+
+ return index_vec;
+
+}
+
+std::vector<std::vector<unsigned int>> StreamlineFeatureExtractor::GetDistanceData(float &value)
+{
+ /*Vector which saves Fibers to be labeled based on fft subset uncertainty*/
+ std::vector<std::vector<unsigned int>> index_vec;
+
+ /*Get index of most unertain data (lengths defines how many data is saved)*/
+// int lengths=500;
+ MITK_INFO << entropy_vector.size();
+ int lengths = std::count_if(entropy_vector.begin(), entropy_vector.end(),[&](auto const& val){ return val >= value; });
+ if (lengths>1500)
+ {
+ lengths=1500;
+ }
+ MITK_INFO << lengths;
+ /*Maybe shuffling of length so not the most uncertain values are chosen*/
+ std::vector<unsigned int> indexUnc = Sort(entropy_vector, lengths, 0);
+
+ vnl_matrix<float> distances_matrix;
+
+ distances_matrix.set_size(lengths, lengths);
+ distances_matrix.fill(0.0);
+
+ std::vector<float> distances_matrix_mean;
+
+
+ for (int i=0; i<lengths; i++)
+ {
+ for (int k=0; k<lengths; k++)
+ {
+ /*From the length.size() Samples with the highest Entropey calculate the differen between the Features*/
+ vnl_matrix<float> diff = m_DistancesTest.at(indexUnc.at(i)) - m_DistancesTest.at(indexUnc.at(k));
+
+ /*Into the eucledean difference matrix, put the distance in Feature Space between every sample pair*/
+ distances_matrix.put(i,k,diff.absolute_value_sum()/m_DistancesTest.at(0).size());
+
+ }
+ /*For every Sample/Streamline get the mean eucledean distance to all other Samples => one value for every Sample*/
+// distances_matrix_mean.push_back(distances_matrix.get_row(i).mean());
+// MITK_INFO << meanval.at(i);
+
+ }
+
+ MITK_INFO << "Distance Matrix Calculated";
+
+ /*Index to find values in distancematrix*/
+ std::vector<unsigned int> myidx;
+ /*Index to find actual streamlines using indexUnc*/
+ std::vector<unsigned int> indexUncDist;
+ /*Start with the Streamline of the highest entropy, which is in distance_matrix at idx 0*/
+ myidx.push_back(0);
+ indexUncDist.push_back(indexUnc.at(myidx.at(0)));
+
+ /*Vecotr that stores minvalues of current iteration*/
+ vnl_matrix<float> cur_vec;
+ cur_vec.set_size(1,lengths);
+ cur_vec.fill(0.0);
+ for (int i=0; i<lengths; i++)
+ {
+
+// unsigned int cur_i = indexUnc.at(myidx.at(i));
+
+ /*Save mean distance of all used Samples*/
+ vnl_matrix<float> sum_matrix;
+ sum_matrix.set_size(myidx.size(), lengths);
+ sum_matrix.fill(0);
+ for (unsigned int ii=0; ii<myidx.size(); ii++)
+ {
+
+ sum_matrix.set_row(ii, distances_matrix.get_column(myidx.at(ii)));
+ }
+
+ for (unsigned int k=0; k<sum_matrix.columns(); k++)
+ {
+ cur_vec.put(0,k, sum_matrix.get_column(k).min_value());
+ }
+ myidx.push_back(cur_vec.arg_max());
+
+
+ indexUncDist.push_back(indexUnc.at(myidx.at(i+1)));
+ sum_matrix.clear();
+
+ }
+
+ MITK_INFO << "Dist_stop";
+
+ index_vec.push_back(indexUncDist);
+
+ return index_vec;
+}
+
+mitk::FiberBundle::Pointer StreamlineFeatureExtractor::CreatePrediction(std::vector<unsigned int> &index, bool removefrompool)
+{
+ mitk::FiberBundle::Pointer Prediction;
+ MITK_INFO << "Create Bundle";
+
+ vtkSmartPointer<vtkPolyData> FibersData;
+ FibersData = vtkSmartPointer<vtkPolyData>::New();
+ FibersData->SetPoints(vtkSmartPointer<vtkPoints>::New());
+ FibersData->SetLines(vtkSmartPointer<vtkCellArray>::New());
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+// vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
+// weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers());
+
+ unsigned int indexSize = index.size();
+ unsigned int counter = 0;
+ MITK_INFO << "Start Loop";
+ for (unsigned int i=0; i<indexSize; i++)
+ {
+
+ vtkCell* cell = m_TractogramTest->GetFiberPolyData()->GetCell(index[i]);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+// weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+ if (removefrompool)
+ {
+ for (unsigned int i=0; i<indexSize; i++)
+ {
+ m_TractogramTest->GetFiberPolyData()->DeleteCell(index[i]);
+ }
+ }
+
+
+
+
+ MITK_INFO << "Counter";
+ MITK_INFO << counter;
+
+
+ vNewPolyData->SetLines(vNewLines);
+ vNewPolyData->SetPoints(vNewPoints);
+
+ FibersData = vtkSmartPointer<vtkPolyData>::New();
+ FibersData->SetPoints(vtkSmartPointer<vtkPoints>::New());
+ FibersData->SetLines(vtkSmartPointer<vtkCellArray>::New());
+ FibersData->SetPoints(vNewPoints);
+ FibersData->SetLines(vNewLines);
+
+ Prediction = mitk::FiberBundle::New(vNewPolyData);
+
+// Bundle->SetFiberColors(255, 255, 255);
+ MITK_INFO << "Cells Prediciton";
+ MITK_INFO << Prediction->GetFiberPolyData()->GetNumberOfCells();
+ MITK_INFO << "Cells Tractorgram";
+ MITK_INFO << m_TractogramTest->GetFiberPolyData()->GetNumberOfCells();
+
+ return Prediction;
+}
+
+std::vector<int> StreamlineFeatureExtractor::CreateLabels(std::vector<vnl_matrix<float> > Testdata,
+ std::vector<vnl_matrix<float> > Prediction)
+{
+// vnl_vector<int> labels;
+// vnl_vector.set_size(Testdata.size());
+// vnl_vector.fill(0);
+ std::vector<int> labels(Testdata.size(), 0);
+
+
+#pragma omp parallel for
+ for (unsigned int i=0; i<Prediction.size(); i++)
+ {
+ for (unsigned int k=0; k<Testdata.size(); k++)
+ {
+ if (Testdata.at(k)==Prediction.at(i))
+ {
+ labels.at(k)=1;
+ }
+ }
+ }
+
+
+ return labels;
+
+
+
+
+}
+
+void StreamlineFeatureExtractor::GenerateData()
+{
+ MITK_INFO << "Update";
+
+// mitk::FiberBundle::Pointer inputPrototypes = mitk::IOUtil::Load<mitk::FiberBundle>("/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/data/Synt_tract_40_prototypes.trk");
+
+ std::vector<vnl_matrix<float> > T_Prototypes;
+ std::vector<vnl_matrix<float> > T_TractogramPlus;
+ std::vector<vnl_matrix<float> > T_TractogramMinus;
+ std::vector<vnl_matrix<float> > T_TractogramTest;
+ std::vector<vnl_matrix<float> > T_mergedPrototypes;
+
+
+ MITK_INFO << "Resample Input Prototypes";
+ T_Prototypes = ResampleFibers(m_inputPrototypes);
+ MITK_INFO << "Resample Input Tractogram Minus";
+ T_TractogramMinus= ResampleFibers(m_TractogramMinus);
+ MITK_INFO << "Resample Input Tractogram Plus";
+ T_TractogramPlus= ResampleFibers(m_TractogramPlus);
+
+ /* Merge T_Prototypes, T_TractogramMinus and T_TractogramPlus for extra Features*/
+ MITK_INFO << "Merging Prototypes";
+ T_mergedPrototypes = MergeTractogram(T_Prototypes, T_TractogramPlus, T_TractogramMinus);
+
+
+
+
+ MITK_INFO << "Calculate Features";
+ MITK_INFO << "Calculate Minus Features";
+ m_DistancesMinus = CalculateDmdf(T_TractogramMinus, T_mergedPrototypes);
+ MITK_INFO << "Calculate Plus Features";
+ m_DistancesPlus = CalculateDmdf(T_TractogramPlus, T_mergedPrototypes);
+
+ MITK_INFO << "Resample Test Data";
+ T_TractogramTest= ResampleFibers(m_TractogramTest);
+ MITK_INFO << "Calculate Features of Test Data";
+ m_DistancesTest= CalculateDmdf(T_TractogramTest, T_mergedPrototypes);
+
+
+
+
+ MITK_INFO << "Done with Datacreation";
+ m_index =GetData();
+
+}
+
+vnl_vector<float> StreamlineFeatureExtractor::ValidationPipe()
+{
+ std::vector<vnl_matrix<float> > T_Prototypes;
+ std::vector<vnl_matrix<float> > T_TractogramPrediction;
+ std::vector<vnl_matrix<float> > T_TractogramGroundtruth;
+ std::vector<vnl_matrix<float> > T_TractogramTest;
+ std::vector<vnl_matrix<float> > DistancesPrediction;
+ std::vector<vnl_matrix<float> > DistancesGroundtruth;
+ std::vector<vnl_matrix<float> > DistancesTest;
+ std::vector<int> LabelsPrediction;
+ std::vector<int> LabelsGroundtruth;
+
+ MITK_INFO << "Start Resampling";
+ T_Prototypes = ResampleFibers(m_inputPrototypes);
+ T_TractogramPrediction= ResampleFibers(m_TractogramPrediction);
+ T_TractogramGroundtruth= ResampleFibers(m_TractogramGroundtruth);
+ T_TractogramTest= ResampleFibers(m_TractogramTest);
+
+
+
+ MITK_INFO << "Calculate Features";
+ DistancesPrediction = CalculateDmdf(T_TractogramPrediction, T_Prototypes);
+ DistancesGroundtruth = CalculateDmdf(T_TractogramGroundtruth, T_Prototypes);
+ DistancesTest = CalculateDmdf(T_TractogramTest, T_Prototypes);
+
+ LabelsGroundtruth = CreateLabels(DistancesTest, DistancesGroundtruth);
+ LabelsPrediction = CreateLabels(DistancesTest, DistancesPrediction);
+
+ std::ofstream LabelsPredictionFile;
+ LabelsPredictionFile.open("/home/r948e/mycsv/predictionlabels_" + std::to_string(m_activeCycle) + ".csv");
+ for (unsigned int i = 0; i < LabelsPrediction.size(); i++)
+ {
+ LabelsPredictionFile << LabelsPrediction.at(i) << ' ';
+ }
+ LabelsPredictionFile.close();
+
+ std::ofstream LabelsGroundtruthFile;
+ LabelsGroundtruthFile.open("/home/r948e/mycsv/groundtruthlabels_" + std::to_string(m_activeCycle) + ".csv");
+ for (unsigned int i = 0; i < LabelsGroundtruth.size(); i++)
+ {
+ LabelsGroundtruthFile << LabelsGroundtruth.at(i) << ' ';
+ }
+ LabelsGroundtruthFile.close();
+
+ float FP = 0.0;
+ float FN = 0.0;
+ float TP = 0.0;
+ float TN = 0.0;
+ std::vector<int> indexfp;
+//#pragma omp parallel for
+ for (unsigned int i=0; i<LabelsGroundtruth.size(); i++)
+ {
+ if (LabelsGroundtruth.at(i)==1 && LabelsPrediction.at(i)==1)
+ {
+ TP +=1;
+ }
+ else if (LabelsGroundtruth.at(i)==1 && LabelsPrediction.at(i)==0)
+ {
+ FN +=1;
+ }
+ else if (LabelsGroundtruth.at(i)==0 && LabelsPrediction.at(i)==1)
+ {
+ FP +=1;
+ indexfp.push_back(i);
+ }
+ else if (LabelsGroundtruth.at(i)==0 && LabelsPrediction.at(i)==0)
+ {
+ TN +=1;
+ }
+ }
+
+ float Precision;
+ float Recall;
+ float F1_score;
+
+ MITK_INFO << "TP";
+ MITK_INFO << TP;
+ MITK_INFO << "FP";
+ MITK_INFO << FP;
+ MITK_INFO << "TN";
+ MITK_INFO << TN;
+ MITK_INFO << "FN";
+ MITK_INFO << FN;
+ Precision = TP/(TP + FP);
+ MITK_INFO << "Precision";
+ MITK_INFO << Precision;
+ Recall = TP/(TP + FN);
+ MITK_INFO << "Recall";
+ MITK_INFO << Recall;
+ F1_score = (2*Precision*Recall)/(Precision+Recall);
+ MITK_INFO << "F1_score";
+ MITK_INFO << F1_score;
+
+
+
+ vnl_vector<float> metrics(7);
+
+ metrics.put(0, TP);
+ metrics.put(1, FP);
+ metrics.put(2, TN);
+ metrics.put(3, FN);
+ metrics.put(4, Precision);
+ metrics.put(5, Recall);
+ metrics.put(6, F1_score);
+
+
+
+
+ return metrics;
+
+}
+
+
+}
+
+
+
diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h
new file mode 100644
index 0000000..c39865e
--- /dev/null
+++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h
@@ -0,0 +1,129 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center.
+
+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 StreamlineFeatureExtractor_h
+#define StreamlineFeatureExtractor_h
+
+
+#include "MitkFiberDissectionExports.h"
+// MITK
+#include <mitkPlanarEllipse.h>
+#include <mitkFiberBundle.h>
+
+// ITK
+#include <itkProcessObject.h>
+
+// VTK
+#include <vtkSmartPointer.h>
+#include <vtkPolyData.h>
+#include <vtkCellArray.h>
+#include <vtkPoints.h>
+#include <vtkPolyLine.h>
+
+// OpenCV
+#include <opencv2/ml.hpp>
+#include <opencv2/opencv.hpp>
+#include <opencv2/highgui/highgui.hpp>
+
+namespace mitk{
+
+/**
+* \brief */
+
+class MITKFIBERDISSECTION_EXPORT StreamlineFeatureExtractor
+{
+public:
+
+
+ StreamlineFeatureExtractor();
+ ~StreamlineFeatureExtractor();
+
+ typedef itk::Image< float, 3 > FloatImageType;
+ typedef itk::Image< unsigned char, 3 > UcharImageType;
+
+ void Update(){
+ this->GenerateData();
+ }
+
+// void Validate(){
+// this->ValidationPipe();
+// }
+
+
+
+ void SetTractogramGroundtruth(const mitk::FiberBundle::Pointer &Tractogram);
+ void SetTractogramPrediction(const mitk::FiberBundle::Pointer &Tractogram);
+ void SetTractogramPlus(const mitk::FiberBundle::Pointer &Tractogram);
+ void SetTractogramMinus(const mitk::FiberBundle::Pointer &Tractogram);
+ void SetTractogramTest(const mitk::FiberBundle::Pointer &Tractogram, std::string TractogramTestName);
+ void SetTractogramPrototypes(const mitk::FiberBundle::Pointer &TractogramPrototypes, bool standard);
+ void SetActiveCycle(int &activeCycle);
+ void SetInitRandom(int &initRandom);
+// void SetRandomThreshold(int &threshold);
+ vnl_vector<float> ValidationPipe();
+
+
+ void CreateClassifier();
+ std::vector<std::vector<unsigned int>> GetData();
+
+// void CreatePrediction(std::vector<unsigned int> &index);
+ mitk::FiberBundle::Pointer CreatePrediction(std::vector<unsigned int> &index, bool removefrompool);
+ std::vector<std::vector<unsigned int>> GetDistanceData(float &value);
+
+ mitk::FiberBundle::Pointer m_Prediction;
+ mitk::FiberBundle::Pointer m_ToLabel;
+
+ std::vector<std::vector<unsigned int>> m_index;
+ std::vector<float> entropy_vector;
+ cv::Ptr<cv::ml::RTrees> statistic_model;
+
+
+protected:
+
+ void GenerateData();
+// void ValidationPipe();
+
+ std::vector<int> CreateLabels(std::vector<vnl_matrix<float> > Testdata,
+ std::vector<vnl_matrix<float> > Prediction);
+ std::vector< vnl_matrix<float> > ResampleFibers(FiberBundle::Pointer tractogram);
+ std::vector<vnl_matrix<float> > CalculateDmdf(std::vector<vnl_matrix<float> > tractogram,
+ std::vector<vnl_matrix<float> > prototypes);
+ std::vector< vnl_matrix<float> > MergeTractogram(std::vector<vnl_matrix<float> > prototypes,
+ std::vector<vnl_matrix<float> > positive_local_prototypes,
+ std::vector<vnl_matrix<float> > negative_local_prototypes);
+ std::vector<unsigned int> Sort(std::vector<float> sortingVector, int lengths, int start);
+
+
+
+
+ unsigned int m_NumPoints;
+ int m_activeCycle;
+ int m_initRandom;
+ int m_thresh;
+ mitk::FiberBundle::Pointer m_TractogramPrediction;
+ mitk::FiberBundle::Pointer m_TractogramGroundtruth;
+ mitk::FiberBundle::Pointer m_TractogramPlus;
+ mitk::FiberBundle::Pointer m_TractogramMinus;
+ mitk::FiberBundle::Pointer m_TractogramTest;
+ mitk::FiberBundle::Pointer m_inputPrototypes;
+ std::string m_DistancesTestName;
+ std::vector<vnl_matrix<float> > m_DistancesPlus;
+ std::vector<vnl_matrix<float> > m_DistancesMinus;
+ std::vector<vnl_matrix<float> > m_DistancesTest;
+ cv::Ptr<cv::ml::TrainData> m_traindata;
+};
+}
+
+#endif
diff --git a/Modules/FiberDissection/files.cmake b/Modules/FiberDissection/files.cmake
new file mode 100644
index 0000000..397bf16
--- /dev/null
+++ b/Modules/FiberDissection/files.cmake
@@ -0,0 +1,27 @@
+set(H_FILES
+
+ #Interactor
+ Interactor/mitkStreamlineInteractor.h
+ Interactor/mitkStreamlineInteractorBrush.h
+
+ #MachineLearning
+ MachineLearning/mitkStreamlineFeatureExtractor.h
+)
+
+set(CPP_FILES
+
+ #Interactor
+ Interactor/mitkStreamlineInteractor.cpp
+ Interactor/mitkStreamlineInteractorBrush.cpp
+
+ #MachineLearning
+ MachineLearning/mitkStreamlineFeatureExtractor.cpp
+)
+
+set(RESOURCE_FILES
+ # "Interactions" prefix forced by mitk::StateMachine
+ Interactions/Streamline3DStates.xml
+ Interactions/Streamline3DConfig.xml
+ Interactions/StreamlineBrush3DStates.xml
+ Interactions/StreamlineBrush3DConfig.xml
+)
diff --git a/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml b/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml
new file mode 100644
index 0000000..e01f2f2
--- /dev/null
+++ b/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml
@@ -0,0 +1,19 @@
+<config>
+ <event_variant class="MousePressEvent" name="AddNegStreamlineClick">
+ <attribute name="EventButton" value="RightMouseButton"/>
+ <attribute name="Modifiers" value="shift"/>
+ </event_variant>addtolabelstreamline
+ <event_variant class="MousePressEvent" name="AddPosStreamlineClick">
+ <attribute name="EventButton" value="RightMouseButton"/>
+ <attribute name="Modifiers" value="alt"/>
+ </event_variant>
+ <event_variant class="MousePressEvent" name="AddNegStreamlinetolabelClick">
+ <attribute name="EventButton" value="RightMouseButton"/>
+ <attribute name="Modifiers" value="ctrl,shift"/>
+ </event_variant>
+ <event_variant class="MousePressEvent" name="AddPosStreamlinetolabelClick">
+ <attribute name="EventButton" value="RightMouseButton"/>
+ <attribute name="Modifiers" value="ctrl,alt"/>
+ </event_variant>
+ <event_variant class="MouseMoveEvent" name="CheckSelected"/>
+</config>
diff --git a/Modules/FiberDissection/resource/Interactions/Streamline3DStates.xml b/Modules/FiberDissection/resource/Interactions/Streamline3DStates.xml
new file mode 100644
index 0000000..5b4f97f
--- /dev/null
+++ b/Modules/FiberDissection/resource/Interactions/Streamline3DStates.xml
@@ -0,0 +1,20 @@
+<statemachine NAME="StreamlineInteractor3D">
+ <state name="start" startstate="true" >
+ <transition event_class="MouseMoveEvent" event_variant="CheckSelected" target="start">
+ <condition name="isoverstreamline"/>
+ <action name="selectstreamline"/>
+ </transition>
+ <transition event_class="InteractionPositionEvent" event_variant="AddNegStreamlineClick" target="start">
+ <action name="addnegstreamline"/>
+ </transition>
+ <transition event_class="InteractionPositionEvent" event_variant="AddPosStreamlineClick" target="start">
+ <action name="addposstreamline"/>
+ </transition>
+ <transition event_class="InteractionPositionEvent" event_variant="AddNegStreamlinetolabelClick" target="start">
+ <action name="addnegtolabelstreamline"/>
+ </transition>
+ <transition event_class="InteractionPositionEvent" event_variant="AddPosStreamlinetolabelClick" target="start">
+ <action name="addpostolabelstreamline"/>
+ </transition>
+ </state>
+</statemachine>
diff --git a/Modules/FiberDissection/resource/Interactions/StreamlineBrush3DConfig.xml b/Modules/FiberDissection/resource/Interactions/StreamlineBrush3DConfig.xml
new file mode 100644
index 0000000..0890749
--- /dev/null
+++ b/Modules/FiberDissection/resource/Interactions/StreamlineBrush3DConfig.xml
@@ -0,0 +1,19 @@
+<config>
+ <event_variant class="MouseMoveEvent" name="AddNegStreamlineClick">
+ <attribute name="EventButton" value="RightMouseButton"/>
+ <attribute name="Modifiers" value="shift"/>
+ </event_variant>addtolabelstreamline
+ <event_variant class="MouseMoveEvent" name="AddPosStreamlineClick">
+ <attribute name="EventButton" value="RightMouseButton"/>
+ <attribute name="Modifiers" value="alt"/>
+ </event_variant>
+ <event_variant class="MouseMoveEvent" name="AddNegStreamlinetolabelClick">
+ <attribute name="EventButton" value="RightMouseButton"/>
+ <attribute name="Modifiers" value="ctrl,shift"/>
+ </event_variant>
+ <event_variant class="MouseMoveEvent" name="AddPosStreamlinetolabelClick">
+ <attribute name="EventButton" value="RightMouseButton"/>
+ <attribute name="Modifiers" value="ctrl,alt"/>
+ </event_variant>
+ <event_variant class="MouseMoveEvent" name="CheckSelected"/>
+</config>
diff --git a/Modules/FiberDissection/resource/Interactions/StreamlineBrush3DStates.xml b/Modules/FiberDissection/resource/Interactions/StreamlineBrush3DStates.xml
new file mode 100644
index 0000000..5b4f97f
--- /dev/null
+++ b/Modules/FiberDissection/resource/Interactions/StreamlineBrush3DStates.xml
@@ -0,0 +1,20 @@
+<statemachine NAME="StreamlineInteractor3D">
+ <state name="start" startstate="true" >
+ <transition event_class="MouseMoveEvent" event_variant="CheckSelected" target="start">
+ <condition name="isoverstreamline"/>
+ <action name="selectstreamline"/>
+ </transition>
+ <transition event_class="InteractionPositionEvent" event_variant="AddNegStreamlineClick" target="start">
+ <action name="addnegstreamline"/>
+ </transition>
+ <transition event_class="InteractionPositionEvent" event_variant="AddPosStreamlineClick" target="start">
+ <action name="addposstreamline"/>
+ </transition>
+ <transition event_class="InteractionPositionEvent" event_variant="AddNegStreamlinetolabelClick" target="start">
+ <action name="addnegtolabelstreamline"/>
+ </transition>
+ <transition event_class="InteractionPositionEvent" event_variant="AddPosStreamlinetolabelClick" target="start">
+ <action name="addpostolabelstreamline"/>
+ </transition>
+ </state>
+</statemachine>
diff --git a/Modules/ModuleList.cmake b/Modules/ModuleList.cmake
index ac97051..926de49 100644
--- a/Modules/ModuleList.cmake
+++ b/Modules/ModuleList.cmake
@@ -1,8 +1,9 @@
set(MITK_MODULES
DiffusionCore
FiberTracking
Connectomics
MriSimulation
DiffusionIO
DiffusionCmdApps
+ FiberDissection
)
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt
index 8462ed4..6a48682 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt
@@ -1,10 +1,10 @@
# The project name must correspond to the directory name of your plug-in
# and must not contain periods.
project(org_mitk_gui_qt_diffusionimaging_fiberprocessing)
mitk_create_plugin(
SUBPROJECTS MITK-Diffusion
EXPORT_DIRECTIVE DIFFUSIONIMAGING_FIBERPROCESSING_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkFiberTracking MitkMriSimulation MitkChart MitkMultilabel MitkModelFit
+ MODULE_DEPENDS MitkFiberTracking MitkMriSimulation MitkChart MitkMultilabel MitkModelFit MitkQtWidgetsExt MitkFiberDissection
)
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt.user b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt.user
new file mode 100644
index 0000000..ab39197
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt.user
@@ -0,0 +1,434 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE QtCreatorProject>
+<!-- Written by QtCreator 6.0.2, 2022-07-14T14:22:18. -->
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diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/files.cmake
index 0f586c9..3a42839 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/files.cmake
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/files.cmake
@@ -1,63 +1,70 @@
set(SRC_CPP_FILES
)
set(INTERNAL_CPP_FILES
mitkPluginActivator.cpp
QmitkFiberQuantificationView.cpp
QmitkFiberProcessingView.cpp
QmitkFiberClusteringView.cpp
+ QmitkInteractiveFiberDissectionView.cpp
QmitkFiberFitView.cpp
QmitkTractometryView.cpp
Perspectives/QmitkFiberProcessingPerspective.cpp
)
set(UI_FILES
src/internal/QmitkFiberQuantificationViewControls.ui
src/internal/QmitkFiberProcessingViewControls.ui
src/internal/QmitkFiberClusteringViewControls.ui
+ src/internal/QmitkInteractiveFiberDissectionViewControls.ui
src/internal/QmitkFiberFitViewControls.ui
src/internal/QmitkTractometryViewControls.ui
)
set(MOC_H_FILES
src/internal/mitkPluginActivator.h
src/internal/QmitkFiberQuantificationView.h
src/internal/QmitkFiberProcessingView.h
src/internal/QmitkFiberClusteringView.h
+ src/internal/QmitkInteractiveFiberDissectionView.h
src/internal/QmitkFiberFitView.h
src/internal/QmitkTractometryView.h
src/internal/Perspectives/QmitkFiberProcessingPerspective.h
)
set(CACHED_RESOURCE_FILES
plugin.xml
resources/FiberBundleOperations.png
resources/FiberQuantification.png
resources/FiberClustering.png
resources/FiberFit.png
resources/Tractometry.png
resources/circle.png
resources/polygon.png
+ resources/eraze.png
+ resources/brush.png
+ resources/highlighter.png
)
set(QRC_FILES
resources/QmitkFiberprocessing.qrc
+ resources/QmitkInteractiveFiberDissection.qrc
)
set(CPP_FILES )
foreach(file ${SRC_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/${file})
endforeach(file ${SRC_CPP_FILES})
foreach(file ${INTERNAL_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/internal/${file})
endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml
index 4150004..4a46258 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml
@@ -1,163 +1,171 @@
<?xml version="1.0" encoding="UTF-8"?>
<?BlueBerry version="0.1"?>
<plugin>
<extension point="org.blueberry.ui.views">
<view id="org.mitk.views.fiberquantification"
name="Fiber Quantification"
category="Fiber processing"
class="QmitkFiberQuantificationView"
icon="resources/FiberQuantification.png">
<keywordReference id="org.mitk.views.fiberquantification.Keyword"/>
</view>
+ <view id="org.mitk.views.interactivefiberdissection"
+ name="Interactive Fiber Dissection"
+ category="Fiber processing"
+ class="QmitkInteractiveFiberDissectionView"
+ icon="resources/FiberBundleOperations.png">
+ <keywordReference id="org.mitk.views.interactivefiberdissection.Keyword"/>
+ </view>
+
<view id="org.mitk.views.fiberprocessing"
name="Fiber Processing"
category="Fiber processing"
class="QmitkFiberProcessingView"
icon="resources/FiberBundleOperations.png">
<keywordReference id="org.mitk.views.fiberprocessing.Keyword"/>
</view>
<view id="org.mitk.views.fiberclustering"
name="Fiber Clustering"
category="Fiber processing"
class="QmitkFiberClusteringView"
icon="resources/FiberClustering.png">
<keywordReference id="org.mitk.views.fiberclustering.Keyword"/>
</view>
<view id="org.mitk.views.fiberfit"
name="Fiber Fit"
category="Fiber processing"
class="QmitkFiberFitView"
icon="resources/FiberFit.png">
<keywordReference id="org.mitk.views.fiberfit.Keyword"/>
</view>
<view id="org.mitk.views.tractometry"
name="Tractometry"
category="Fiber processing"
class="QmitkTractometryView"
icon="resources/Tractometry.png">
<keywordReference id="org.mitk.views.tractometry.Keyword"/>
</view>
</extension>
<extension point="org.blueberry.ui.perspectives">
<perspective id="org.mitk.perspectives.fiberprocessings"
name="Fiber Processing"
class="QmitkFiberProcessingPerspective"
icon="resources/FiberBundleOperations.png">
<description>This perspective contains all views necessary to post process fibers.</description>
<keywordReference id="org.mitk.perspectives.fiberprocessings.Keyword"/>
</perspective>
</extension>
<extension point="org.blueberry.ui.keywords">
<keyword label="cluster" id="org.mitk.views.fiberclustering.Keyword"/>
<keyword label="fiber" id="org.mitk.views.fiberclustering.Keyword"/>
<keyword label="quickbundles" id="org.mitk.views.fiberclustering.Keyword"/>
<keyword label="clustering" id="org.mitk.views.fiberclustering.Keyword"/>
<keyword label="fit" id="org.mitk.views.fiberfit.Keyword"/>
<keyword label="sift" id="org.mitk.views.fiberfit.Keyword"/>
<keyword label="life" id="org.mitk.views.fiberfit.Keyword"/>
<keyword label="fiber" id="org.mitk.views.fiberfit.Keyword"/>
<keyword label="processing" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="extract" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="remove" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="fiber" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="bundle" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="color" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="mirror" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="threshold" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="prune" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="select" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="segment" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="dissect" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="modify" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="join" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="merge" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="add" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="subtract" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="difference" id="org.mitk.views.fiberprocessing.Keyword"/>
<keyword label="fiber" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="quantification" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="statistics" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="length" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="number" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="principal" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="direction" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="peak" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="main" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="tract" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="density" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="image" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="TDI" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="envelope" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="hull" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="endpoints" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="end" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="endings" id="org.mitk.views.fiberquantification.Keyword"/>
<keyword label="cluster" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="fiber" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="quickbundles" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="clustering" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="fit" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="sift" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="life" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="fiber" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="processing" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="extract" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="remove" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="fiber" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="bundle" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="color" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="mirror" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="threshold" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="prune" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="select" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="segment" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="dissect" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="modify" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="join" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="merge" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="add" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="subtract" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="difference" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="fiber" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="quantification" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="statistics" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="length" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="number" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="principal" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="direction" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="peak" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="main" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="tract" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="density" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="image" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="TDI" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="envelope" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="hull" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="endpoints" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="end" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
<keyword label="endings" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/QmitkInteractiveFiberDissection.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/QmitkInteractiveFiberDissection.qrc
new file mode 100644
index 0000000..047b9e6
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/QmitkInteractiveFiberDissection.qrc
@@ -0,0 +1,9 @@
+<RCC>
+ <qresource prefix="/QmitkInteractiveFiberDissection">
+ <file>FiberBundle.png</file>
+ <file>circle.png</file>
+ <file>polygon.png</file>
+ <file>eraze.png</file>
+ <file>highlighter.png</file>
+ </qresource>
+</RCC>
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png
new file mode 100644
index 0000000..4fdb238
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png
new file mode 100644
index 0000000..d4ac1c0
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/highlighter.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/highlighter.png
new file mode 100644
index 0000000..4fa7514
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/highlighter.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp
index 038ed58..4ad19e7 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp
@@ -1,52 +1,53 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center.
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 "QmitkFiberProcessingPerspective.h"
#include "berryIViewLayout.h"
void QmitkFiberProcessingPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
{
/////////////////////////////////////////////////////
// all di-app perspectives should have the following:
/////////////////////////////////////////////////////
QString editorArea = layout->GetEditorArea();
layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
layout->AddStandaloneView("org.mitk.views.datamanager",
false, berry::IPageLayout::LEFT, 0.3f, editorArea);
layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
berry::IFolderLayout::Pointer left =
layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
/////////////////////////////////////////////
// here goes the perspective specific stuff
/////////////////////////////////////////////
left->AddView("org.mitk.views.fiberprocessing");
left->AddView("org.mitk.views.fiberquantification");
+ left->AddView("org.mitk.views.interactivefiberdissection");
left->AddView("org.mitk.views.fiberclustering");
left->AddView("org.mitk.views.fiberfit");
left->AddView("org.mitk.views.tractometry");
}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp
new file mode 100644
index 0000000..4cf6a57
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp
@@ -0,0 +1,1767 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center.
+
+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 <berryISelectionService.h>
+#include <berryIWorkbenchPart.h>
+#include <berryIWorkbenchWindow.h>
+
+// Qmitk
+#include "QmitkInteractiveFiberDissectionView.h"
+#include <QmitkRenderWindow.h> //Pointset
+#include <QmitkPointListWidget.h> //Pointset
+
+#include <QMessageBox>
+
+#include <mitkNodePredicateProperty.h>
+#include <mitkImageCast.h>
+#include <mitkPointSet.h>
+#include <mitkImageAccessByItk.h>
+#include <mitkDataNodeObject.h>
+#include <mitkTensorImage.h>
+#include "mitkNodePredicateDataType.h"
+#include <mitkNodePredicateProperty.h>
+#include <mitkNodePredicateAnd.h>
+#include <mitkNodePredicateNot.h>
+#include <mitkNodePredicateOr.h>
+//#include <mitkStreamlineFeatureExtractor.h>
+
+#include <mitkInteractionConst.h>
+#include "usModuleRegistry.h"
+//#include <itkFiberCurvatureFilter.h>
+
+
+#include <itkResampleImageFilter.h>
+#include <itkGaussianInterpolateImageFunction.h>
+#include <itkImageRegionIteratorWithIndex.h>
+#include <itkTractsToFiberEndingsImageFilter.h>
+#include <itkTractDensityImageFilter.h>
+#include <itkImageRegion.h>
+#include <itkTractsToRgbaImageFilter.h>
+#include <itkFiberExtractionFilter.h>
+
+#include <mitkInteractionEventObserver.h>
+#include <vtkCellPicker.h>
+
+#include <boost/algorithm/string.hpp>
+#include <boost/lexical_cast.hpp>
+
+#include <vnl/vnl_sparse_matrix.h>
+
+const std::string QmitkInteractiveFiberDissectionView::VIEW_ID = "org.mitk.views.interactivefiberdissection";
+const std::string id_DataManager = "org.mitk.views.datamanager";
+using namespace mitk;
+
+QmitkInteractiveFiberDissectionView::QmitkInteractiveFiberDissectionView()
+ : QmitkAbstractView()
+ , m_Controls( 0 )
+ , m_IterationCounter(0)
+ , m_RandomExtractionCounter(0)
+ , m_activeCycleCounter(0)
+ , m_createdStreamlineCounter(0)
+ , m_StreamlineInteractor(nullptr)
+{
+
+}
+
+// Destructor
+QmitkInteractiveFiberDissectionView::~QmitkInteractiveFiberDissectionView()
+{
+ //disable interactor
+ if (m_StreamlineInteractor != nullptr)
+ {
+// m_StreamlineInteractor->SetStreamlineNode(nullptr);
+ m_StreamlineInteractor->EnableInteraction(false);
+ }
+}
+
+
+void QmitkInteractiveFiberDissectionView::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::QmitkInteractiveFiberDissectionViewControls;
+ m_Controls->setupUi( parent );
+ m_Controls->m_selectedPointSetWidget->SetDataStorage(GetDataStorage());//pointset
+ m_Controls->m_selectedPointSetWidget->SetNodePredicate(mitk::NodePredicateAnd::New(//pointset
+ mitk::TNodePredicateDataType<mitk::PointSet>::New(),//pointset
+ mitk::NodePredicateNot::New(mitk::NodePredicateOr::New(//pointset
+ mitk::NodePredicateProperty::New("helper object"),//pointset
+ mitk::NodePredicateProperty::New("hidden object")))));//pointset
+
+ m_Controls->m_selectedPointSetWidget->SetSelectionIsOptional(true);//pointset
+ m_Controls->m_selectedPointSetWidget->SetAutoSelectNewNodes(true);//pointset
+ m_Controls->m_selectedPointSetWidget->SetEmptyInfo(QString("Please select a point set"));//pointset
+ m_Controls->m_selectedPointSetWidget->SetPopUpTitel(QString("Select point set"));//pointsett
+
+ m_Controls->m_BundleBox->SetDataStorage(this->GetDataStorage());
+ mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isBundle= mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
+ m_Controls->m_BundleBox->SetPredicate( isBundle );
+
+ m_Controls->m_PrototypeBox->SetDataStorage(this->GetDataStorage());
+ mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isPrototype = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
+ m_Controls->m_PrototypeBox->SetPredicate( isPrototype );
+
+ m_Controls->m_PredictionBox->SetDataStorage(this->GetDataStorage());
+ mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isPrediction = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
+ m_Controls->m_PredictionBox->SetPredicate( isPrediction );
+
+ m_Controls->m_GroundtruthBox->SetDataStorage(this->GetDataStorage());
+ mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isGroundtruth = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
+ m_Controls->m_GroundtruthBox->SetPredicate( isGroundtruth );
+
+ m_Controls->m_TestBundleBox->SetDataStorage(this->GetDataStorage());
+ mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isTestBundle = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
+ m_Controls->m_TestBundleBox->SetPredicate( isTestBundle);
+
+
+
+
+ connect(m_Controls->m_ErazorButton, SIGNAL(toggled(bool)), this, SLOT( RemovefromBundle(bool) ) );
+ connect(m_Controls->m_BrushButton, SIGNAL(toggled(bool)), this, SLOT( RemovefromBundleBrush(bool) ) );
+
+ connect(m_Controls->m_StreamlineCreation, SIGNAL( clicked() ), this, SLOT( CreateStreamline()));
+
+ connect(m_Controls->m_AddRandomFibers, SIGNAL( clicked() ), this, SLOT( ExtractRandomFibersFromTractogram() ) ); //need
+
+ connect(m_Controls->m_TrainClassifier, SIGNAL( clicked() ), this, SLOT( StartAlgorithm( )));
+
+ connect(m_Controls->m_CreatePrediction, SIGNAL( clicked() ), this, SLOT( CreatePredictionNode( )));
+
+ connect(m_Controls->m_certainData, SIGNAL( clicked() ), this, SLOT( CreateCertainNode( )));
+
+ connect(m_Controls->m_AddUncertainFibers, SIGNAL( clicked() ), this, SLOT( CreateUncertaintySampleNode( )));
+
+ connect(m_Controls->m_AddDistanceFibers, SIGNAL( clicked() ), this, SLOT( CreateDistanceSampleNode( )));
+
+ connect(m_Controls->m_unclabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromUncertainty(bool) ) ); //need
+
+ connect(m_Controls->m_unclabelingBrush, SIGNAL(toggled(bool)), this, SLOT( RemovefromUncertaintyBrush(bool) ) ); //need
+
+ connect(m_Controls->m_distlabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromDistance(bool) ) ); //need
+
+ connect(m_Controls->m_predlabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromPrediction(bool) ) ); //need
+
+ connect(m_Controls->m_predlabelingBrush, SIGNAL(toggled(bool)), this, SLOT( RemovefromPredictionBrush(bool) ) ); //need
+
+ connect(m_Controls->m_sellabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromSelection(bool) ) ); //need
+
+ connect(m_Controls->m_ResampleButton, SIGNAL( clicked() ), this, SLOT( ResampleTractogram( ) ) );
+
+ connect(m_Controls->m_RandomPrototypesButton, SIGNAL( clicked() ), this, SLOT( RandomPrototypes( ) ) );
+
+ connect(m_Controls->m_SFFPrototypesButton, SIGNAL( clicked() ), this, SLOT( SFFPrototypes( ) ) );
+
+ connect(m_Controls->m_validate, SIGNAL( clicked() ), this, SLOT( StartValidation( ) ) );
+
+ connect(m_Controls->m_automaticLabelling, SIGNAL( clicked() ), this, SLOT( AutomaticLabelling( ) ) );
+
+ connect(m_Controls->m_RemoveCertainData, SIGNAL( clicked() ), this, SLOT( RemoveCertainData( ) ) );
+
+ connect(m_Controls->m_resetClassifier, SIGNAL( clicked() ), this, SLOT( ResetClassifier( ) ) );
+
+
+
+ connect(m_Controls->m_addPointSetPushButton, &QPushButton::clicked,//pointset
+ this, &QmitkInteractiveFiberDissectionView::OnAddPointSetClicked);//pointset
+ connect(m_Controls->m_selectedPointSetWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged,//pointset
+ this, &QmitkInteractiveFiberDissectionView::OnCurrentSelectionChanged);//pointset
+
+
+
+
+ auto renderWindowPart = this->GetRenderWindowPart();//pointset
+ if (nullptr != renderWindowPart)//pointset
+ this->RenderWindowPartActivated(renderWindowPart);//pointset
+ this->OnCurrentSelectionChanged(m_Controls->m_selectedPointSetWidget->GetSelectedNodes());//pointset
+
+ }
+
+ UpdateGui();
+}
+
+
+void QmitkInteractiveFiberDissectionView::SetFocus()
+{
+ m_Controls->toolBoxx->setFocus();
+ //m_Controls->m_addPointSetPushButton->setFocus();//pointset
+ UpdateGui();
+}
+
+void QmitkInteractiveFiberDissectionView::UpdateGui()
+{
+ m_Controls->m_FibLabel->setText("<font color='red'>nothing selected</font>");
+ m_Controls->m_InputData->setTitle("Please Select Input Data");
+
+ // disable alle frames
+
+ m_Controls->m_ErazorButton->setCheckable(true);
+ m_Controls->m_ErazorButton->setEnabled(false);
+ m_Controls->m_BrushButton->setCheckable(true);
+ m_Controls->m_BrushButton->setEnabled(false);
+ m_Controls->m_unclabeling->setCheckable(true);
+ m_Controls->m_unclabeling->setEnabled(false);
+ m_Controls->m_predlabeling->setCheckable(true);
+ m_Controls->m_predlabeling->setEnabled(false);
+ m_Controls->m_unclabelingBrush->setCheckable(true);
+ m_Controls->m_unclabelingBrush->setEnabled(false);
+ m_Controls->m_predlabelingBrush->setCheckable(true);
+ m_Controls->m_predlabelingBrush->setEnabled(false);
+ m_Controls->m_distlabeling->setCheckable(true);
+ m_Controls->m_distlabeling->setEnabled(false);
+ m_Controls->m_sellabeling->setCheckable(true);
+ m_Controls->m_sellabeling->setEnabled(false);
+
+
+
+ m_Controls->m_addPointSetPushButton->setEnabled(false);
+ m_Controls->m_StreamlineCreation->setEnabled(false);
+ m_Controls->m_TrainClassifier->setEnabled(false);
+ m_Controls->m_CreatePrediction->setEnabled(false);
+ m_Controls->m_CreateUncertantyMap->setEnabled(false);
+ m_Controls->m_Numtolabel->setEnabled(false);
+ m_Controls->m_Numtolabel2->setEnabled(false);
+ m_Controls->m_addPointSetPushButton->setEnabled(false);
+ m_Controls->m_AddRandomFibers->setEnabled(false);
+ m_Controls->m_AddDistanceFibers->setEnabled(false);
+ m_Controls->m_AddUncertainFibers->setEnabled(false);
+// m_Controls->m_PrototypeBox->setEditable(false);
+// m_Controls->m_useStandardP->
+
+ mitk::DataNode::Pointer curtestnode = m_Controls->m_TestBundleBox->GetSelectedNode();
+ bool testnodeSelected = curtestnode.IsNotNull();
+ MITK_INFO << testnodeSelected;
+ bool fibSelected = !m_SelectedFB.empty();
+ bool multipleFibsSelected = (m_SelectedFB.size()>1);
+ bool sthSelected = m_SelectedImageNode.IsNotNull();
+ bool psSelected = m_SelectedPS.IsNotNull();
+// bool nfibSelected = !m_newfibersBundleNode.empty();
+// bool posSelected = !m_positiveBundleNode.empty();
+ bool nfibSelected = m_newfibersBundleNode.IsNotNull();
+// bool posSelected = !m_positiveBundleNode.IsNotNull();
+// bool negSelected = !m_negativeBundleNode.IsNotNull();
+ bool posSelected = this->GetDataStorage()->Exists(m_positiveBundleNode);
+ bool negSelected = this->GetDataStorage()->Exists(m_negativeBundleNode);
+ bool indexSelected = !m_index.empty();
+ bool uncertaintySelected = this->GetDataStorage()->Exists(m_UncertaintyLabelNode);
+// bool distanceSelected = this->GetDataStorage()->Exists(m_DistanceLabelNode);
+ bool predictionSelected = this->GetDataStorage()->Exists(m_PredictionNode);
+
+
+
+ // toggle visibility of elements according to selected method
+
+
+ // are fiber bundles selected?
+ if ( testnodeSelected )
+ {
+ m_Controls->m_addPointSetPushButton->setEnabled(true);
+ m_Controls->m_AddRandomFibers->setEnabled(true);
+ m_Controls->m_sellabeling->setEnabled(true);
+ }
+
+ if (fibSelected)
+ {
+ m_Controls->m_FibLabel->setText(QString(m_SelectedFB.at(0)->GetName().c_str()));
+ // more than two bundles needed to join/subtract
+ if (multipleFibsSelected )
+ {
+ m_Controls->m_FibLabel->setText("multiple bundles selected");
+ }
+
+
+
+ }
+
+
+ // is image selected
+ if ((sthSelected) || (testnodeSelected))
+ {
+ m_Controls->m_addPointSetPushButton->setEnabled(true);
+ }
+
+ if (psSelected)
+ {
+ m_Controls->m_StreamlineCreation->setEnabled(true);
+ }
+
+ if (nfibSelected && posSelected)
+ {
+ m_Controls->m_ErazorButton->setEnabled(true);
+ m_Controls->m_BrushButton->setEnabled(true);
+ }
+
+
+ if (posSelected && negSelected)
+ {
+ m_Controls->m_TrainClassifier->setEnabled(true);
+ }
+
+ if (indexSelected)
+ {
+ m_Controls->m_CreatePrediction->setEnabled(true);
+ m_Controls->m_AddUncertainFibers->setEnabled(true);
+ m_Controls->m_Numtolabel->setEnabled(true);
+ m_Controls->m_AddDistanceFibers->setEnabled(true);
+ m_Controls->m_Numtolabel2->setEnabled(true);
+ }
+
+ if (uncertaintySelected)
+ {
+ m_Controls->m_unclabeling->setEnabled(true);
+ m_Controls->m_unclabelingBrush->setEnabled(true);
+ }
+
+ if (predictionSelected)
+ {
+ m_Controls->m_predlabeling->setEnabled(true);
+ m_Controls->m_predlabelingBrush->setEnabled(true);
+ }
+
+// if (distanceSelected)
+// {
+ m_Controls->m_distlabeling->setEnabled(true);
+// }
+
+// if (m_Controls->m_useStandardP->isChecked())
+// {
+// m_Controls->m_PrototypeBox->setEditable(true);
+// }
+
+
+
+
+
+
+}
+
+void QmitkInteractiveFiberDissectionView::OnEndInteraction()
+{
+
+}
+
+void QmitkInteractiveFiberDissectionView::ResampleTractogram()
+{
+ mitk::DataNode::Pointer node = m_Controls->m_BundleBox->GetSelectedNode();
+ auto tractogram = dynamic_cast<mitk::FiberBundle *>(node->GetData());
+ mitk::FiberBundle::Pointer tempfib = tractogram->GetDeepCopy();
+
+ std::vector<int> myvec;
+ for (unsigned int k=0; k<tempfib->GetNumFibers(); k++)
+ {
+ myvec.push_back(k);
+ }
+// auto rng = std::default_random_engine {};
+ std::random_shuffle(std::begin(myvec), std::end(myvec));
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
+
+ /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/
+ unsigned int counter = 0;
+
+ for (unsigned int i=0; i<tempfib->GetNumFibers(); i++)
+ {
+ vtkCell* cell = tempfib->GetFiberPolyData()->GetCell(myvec.at(i));
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ weights->InsertValue(counter, tempfib->GetFiberWeight(myvec.at(i)));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+ vNewPolyData->SetLines(vNewLines);
+ vNewPolyData->SetPoints(vNewPoints);
+
+ mitk::FiberBundle::Pointer ShuffledBundle = mitk::FiberBundle::New(vNewPolyData);
+ ShuffledBundle->SetFiberWeights(weights);
+
+ ShuffledBundle->ResampleToNumPoints(40);
+ MITK_INFO << "Resampling Done";
+
+ mitk::DataNode::Pointer newnode = mitk::DataNode::New();
+ newnode->SetData( ShuffledBundle );
+ newnode->SetName( node->GetName() + "_" + std::to_string(40) );
+ this->GetDataStorage()->Add(newnode);
+ UpdateGui();
+}
+
+void QmitkInteractiveFiberDissectionView::RandomPrototypes()
+{
+
+
+ MITK_INFO << "Number of Fibers to use as Prototypes: ";
+ MITK_INFO << m_Controls->m_NumPrototypes->value();
+
+ mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_BundleBox->GetSelectedNode()->GetData());
+
+ MITK_INFO << fib->GetNumFibers();
+ std::vector<int> myvec;
+ for (unsigned int k=0; k<fib->GetNumFibers(); k++)
+ {
+ myvec.push_back(k);
+ }
+// auto rng = std::default_random_engine {};
+ std::random_shuffle(std::begin(myvec), std::end(myvec));
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
+
+ /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/
+ unsigned int counter = 0;
+
+ for (int i=0; i<m_Controls->m_NumPrototypes->value(); i++)
+ {
+ vtkCell* cell = fib->GetFiberPolyData()->GetCell(myvec.at(i));
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ weights->InsertValue(counter, fib->GetFiberWeight(myvec.at(i)));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vNewPolyData->SetLines(vNewLines);
+ vNewPolyData->SetPoints(vNewPoints);
+
+ mitk::FiberBundle::Pointer PrototypesBundle = mitk::FiberBundle::New(vNewPolyData);
+ PrototypesBundle->SetFiberWeights(weights);
+
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(PrototypesBundle);
+ node->SetName("Random_Prototypes");
+
+// MITK_INFO << "Number of Streamlines in first function";
+// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells();
+ m_Controls->m_PrototypeBox->SetAutoSelectNewItems (true);
+ this->GetDataStorage()->Add(node);
+ m_Controls->m_PrototypeBox->SetAutoSelectNewItems (false);
+ m_Controls->m_useStandardP->setChecked(false);
+ node->SetVisibility(false);
+
+
+}
+
+void QmitkInteractiveFiberDissectionView::SFFPrototypes()
+{
+
+
+ MITK_INFO << "Number of Fibers to use as Prototypes: ";
+ MITK_INFO << m_Controls->m_NumPrototypes->value();
+ MITK_INFO << "Start Creating Prototypes based on SFF";
+
+ mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_BundleBox->GetSelectedNode()->GetData());
+
+ /* Get Subset of Tractogram*/
+ int size_subset = std::max(1.0, ceil(3.0 * m_Controls->m_NumPrototypes->value() * std::log(m_Controls->m_NumPrototypes->value())));
+
+ MITK_INFO << fib->GetNumFibers();
+ std::vector<int> myvec;
+ for (unsigned int k=0; k<fib->GetNumFibers(); k++)
+ {
+ myvec.push_back(k);
+ }
+
+// std::random_shuffle(std::begin(myvec), std::end(myvec));
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
+
+
+ unsigned int counter = 0;
+
+ for (int i=0; i<size_subset; i++)
+ {
+ vtkCell* cell = fib->GetFiberPolyData()->GetCell(myvec.at(i));
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ weights->InsertValue(counter, fib->GetFiberWeight(myvec.at(i)));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+ vNewPolyData->SetLines(vNewLines);
+ vNewPolyData->SetPoints(vNewPoints);
+
+ mitk::FiberBundle::Pointer temp_fib = mitk::FiberBundle::New(vNewPolyData);
+ temp_fib->SetFiberWeights(weights);
+
+ MITK_INFO << temp_fib->GetFiberPolyData()->GetNumberOfCells();
+ /* Create std::vector <vnl_matrix> of the SubsetBundle*/
+ std::vector< vnl_matrix<float> > out_fib(temp_fib->GetFiberPolyData()->GetNumberOfCells());
+
+ for (int i=0; i<temp_fib->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i);
+ int numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vnl_matrix<float> streamline;
+ streamline.set_size(3, cell->GetNumberOfPoints());
+ streamline.fill(0.0);
+
+ for (int j=0; j<numPoints; j++)
+ {
+ double cand[3];
+ points->GetPoint(j, cand);
+
+ vnl_vector_fixed< float, 3 > candV;
+ candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
+ streamline.set_column(j, candV);
+ }
+
+ // out_fib.push_back(streamline);
+ out_fib.at(i)=streamline;
+ }
+
+
+ /* Calculate the distancematrix of Subset*/
+ std::vector< vnl_matrix<float> > dist_vec(out_fib.size());//
+ cv::parallel_for_(cv::Range(0, out_fib.size()), [&](const cv::Range &range)
+ {
+ for (int i = range.start; i < range.end; i++)
+
+ // for (unsigned int i=0; i<tractogram.size(); i++)
+ {
+
+ vnl_matrix<float> distances;
+ distances.set_size(1, out_fib.size());
+ distances.fill(0.0);
+
+
+ for (unsigned int j=0; j<out_fib.size(); j++)
+ {
+ vnl_matrix<float> single_distances;
+ single_distances.set_size(1, out_fib.at(0).cols());
+ single_distances.fill(0.0);
+ vnl_matrix<float> single_distances_flip;
+ single_distances_flip.set_size(1, out_fib.at(0).cols());
+ single_distances_flip.fill(0.0);
+ for (unsigned int ik=0; ik<out_fib.at(0).cols(); ik++)
+ {
+ double cur_dist;
+ double cur_dist_flip;
+
+ cur_dist = sqrt(pow(out_fib.at(i).get(0,ik) - out_fib.at(j).get(0,ik), 2.0) +
+ pow(out_fib.at(i).get(1,ik) - out_fib.at(j).get(1,ik), 2.0) +
+ pow(out_fib.at(i).get(2,ik) - out_fib.at(j).get(2,ik), 2.0));
+
+ cur_dist_flip = sqrt(pow(out_fib.at(i).get(0,ik) - out_fib.at(j).get(0,out_fib.at(0).cols()-(ik+1)), 2.0) +
+ pow(out_fib.at(i).get(1,ik) - out_fib.at(j).get(1,out_fib.at(0).cols()-(ik+1)), 2.0) +
+ pow(out_fib.at(i).get(2,ik) - out_fib.at(j).get(2,out_fib.at(0).cols()-(ik+1)), 2.0));
+
+ single_distances.put(0,ik, cur_dist);
+ single_distances_flip.put(0,ik, cur_dist_flip);
+
+ }
+
+ if (single_distances_flip.mean()> single_distances.mean())
+ {
+ distances.put(0,j, single_distances.mean());
+ }
+ else {
+ distances.put(0,j, single_distances_flip.mean());
+ }
+
+
+
+ }
+ // dist_vec.push_back(distances);
+ dist_vec.at(i) = distances;
+ }
+ });
+
+
+ /*Index to find values in distancematrix*/
+ std::vector<unsigned int> myidx;
+ /*Index to find actual streamlines using indexUnc*/
+ std::vector<unsigned int> indexUncDist;
+ /*Start with the Streamline of the highest entropy, which is in distance_matrix at idx 0*/
+ myidx.push_back(0);
+
+ /*Vecotr that stores minvalues of current iteration*/
+ vnl_matrix<float> cur_vec;
+ cur_vec.set_size(1, size_subset);
+ cur_vec.fill(0.0);
+ for (int i=0; i<m_Controls->m_NumPrototypes->value(); i++)
+ {
+
+ // unsigned int cur_i = indexUnc.at(myidx.at(i));
+
+ /*Save mean distance of all used Samples*/
+
+ vnl_matrix<float> sum_matrix;
+ sum_matrix.set_size(myidx.size(), size_subset);
+ sum_matrix.fill(0);
+ for (unsigned int ii=0; ii<myidx.size(); ii++)
+ {
+
+ sum_matrix.set_row(ii, dist_vec.at(myidx.at(ii)).get_row(0));
+ }
+
+ for (unsigned int k=0; k<sum_matrix.columns(); k++)
+ {
+ cur_vec.put(0,k, sum_matrix.get_column(k).min_value());
+ }
+ myidx.push_back(cur_vec.arg_max());
+ sum_matrix.clear();
+
+ }
+ vtkSmartPointer<vtkPolyData> vNewPolyData2 = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines2 = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints2 = vtkSmartPointer<vtkPoints>::New();
+
+ vtkSmartPointer<vtkFloatArray> weights2 = vtkSmartPointer<vtkFloatArray>::New();
+
+ /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/
+ counter = 0;
+
+ for (int i=0; i<m_Controls->m_NumPrototypes->value(); i++)
+ {
+
+ vtkCell* cell = fib->GetFiberPolyData()->GetCell(myidx.at(i));
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints2->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ weights2->InsertValue(counter, fib->GetFiberWeight(myvec.at(i)));
+ vNewLines2->InsertNextCell(container);
+ counter++;
+
+ }
+
+ vNewPolyData2->SetLines(vNewLines2);
+ vNewPolyData2->SetPoints(vNewPoints2);
+
+ mitk::FiberBundle::Pointer PrototypesBundle = mitk::FiberBundle::New(vNewPolyData2);
+ PrototypesBundle->SetFiberWeights(weights2);
+ MITK_INFO << PrototypesBundle->GetFiberPolyData()->GetNumberOfCells();
+
+
+
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(PrototypesBundle);
+ node->SetName("SFF_Prototypes");
+
+//// MITK_INFO << "Number of Streamlines in first function";
+//// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells();
+ m_Controls->m_PrototypeBox->SetAutoSelectNewItems (true);
+ this->GetDataStorage()->Add(node);
+ m_Controls->m_PrototypeBox->SetAutoSelectNewItems (false);
+ m_Controls->m_useStandardP->setChecked(false);
+ node->SetVisibility(false);
+
+
+
+}
+
+void QmitkInteractiveFiberDissectionView::OnAddPointSetClicked()//pointset
+{
+ // ask for the name of the point set
+ bool ok = false;
+ QString name = QInputDialog::getText(QApplication::activeWindow(),
+ tr("Add point set..."), tr("Enter name for the new point set"), QLineEdit::Normal, tr("PointSet").arg(++m_IterationCounter), &ok);
+// QString name = "PointSet";
+ if (!ok || name.isEmpty())
+ {
+ return;
+ }
+ mitk::PointSet::Pointer pointSet = mitk::PointSet::New();
+ mitk::DataNode::Pointer pointSetNode = mitk::DataNode::New();
+ pointSetNode->SetData(pointSet);
+ pointSetNode->SetProperty("name", mitk::StringProperty::New(name.toStdString()));
+ pointSetNode->SetProperty("opacity", mitk::FloatProperty::New(1));
+ pointSetNode->SetColor(1.0, 1.0, 0.0);
+ m_testnode = m_Controls->m_TestBundleBox->GetSelectedNode();
+ this->GetDataStorage()->Add(pointSetNode, m_testnode);
+
+
+ m_Controls->m_selectedPointSetWidget->SetCurrentSelectedNode(pointSetNode);
+}
+
+void QmitkInteractiveFiberDissectionView::OnCurrentSelectionChanged(QmitkSingleNodeSelectionWidget::NodeList /*nodes*/)//pointset
+{
+
+ m_Controls->m_poinSetListWidget->SetPointSetNode(m_Controls->m_selectedPointSetWidget->GetSelectedNode());
+ m_SelectedPS = m_Controls->m_selectedPointSetWidget->GetSelectedNode();
+
+// m_Controls->m_trainbundleWidget->SetPointSetNode(m_Controls->m_trainbundleWidget->GetSelectedNode());
+// m_trainbundle = m_Controls->m_trainbundleWidget->GetSelectedNode();
+
+
+ UpdateGui();
+
+}
+
+void QmitkInteractiveFiberDissectionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer>& nodes)
+{
+
+ m_SelectedFB.clear();
+
+ if (nodes.empty() || nodes.front().IsNull())
+ {
+ m_SelectedImageNode = nullptr;
+ }
+ else
+ {
+ m_SelectedImageNode = nodes.front();
+ }
+
+
+
+ for (auto node: nodes)
+ {
+ if (dynamic_cast<mitk::Image*>(node->GetData()))
+ m_SelectedImage = dynamic_cast<mitk::Image*>(node->GetData());
+ else if ( dynamic_cast<mitk::FiberBundle*>(node->GetData()) )
+ m_SelectedFB.push_back(node);
+ }
+
+
+
+ UpdateGui();
+}
+
+void QmitkInteractiveFiberDissectionView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart)//pointset
+{
+ if (nullptr != m_Controls)
+ {
+ m_Controls->m_poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController());
+ m_Controls->m_poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController());
+ m_Controls->m_poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController());
+ }
+}
+
+void QmitkInteractiveFiberDissectionView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart)//pointset
+{
+ if (nullptr != m_Controls)
+ {
+ m_Controls->m_poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController());
+ m_Controls->m_poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController());
+ m_Controls->m_poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController());
+ }
+}
+
+void QmitkInteractiveFiberDissectionView::CreateStreamline()
+{
+
+ if (m_positiveBundleNode.IsNull())
+ {
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+
+ m_positiveFibersData = vtkSmartPointer<vtkPolyData>::New();
+ m_positiveFibersData->SetPoints(vtkSmartPointer<vtkPoints>::New());
+ m_positiveFibersData->SetLines(vtkSmartPointer<vtkCellArray>::New());
+ m_positiveBundle = mitk::FiberBundle:: New(m_positiveFibersData);
+
+ node->SetData( m_positiveBundle );
+ node->SetData(m_negativeBundle);
+// node->SetFloatProperty("shape.tuberadius", 0.5);
+// mitk::RenderingManager::GetInstance()->RequestUpdateAll();
+ m_positiveBundleNode = node;
+ this->GetDataStorage()->Add(m_positiveBundleNode);
+ MITK_INFO << "Create Bundle";
+ }
+
+ if (!m_positiveBundleNode.IsNull())
+ {
+
+ this->GetDataStorage()->Remove(m_positiveBundleNode);
+ MITK_INFO << "Adding fibers";
+ MITK_INFO << m_positiveBundle->GetFiberPolyData()->GetNumberOfCells();
+ m_positiveFibersData = m_positiveBundle->GetFiberPolyData();
+ }
+
+
+
+
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+
+
+ unsigned int counter = 0;
+ for (unsigned int i=0; i<m_positiveFibersData->GetNumberOfCells(); ++i)
+ {
+ MITK_INFO<< "New Line";
+ vtkCell* cell = m_positiveFibersData->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; ++j)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+
+ vNewLines->InsertNextCell(container);
+ counter++;
+ }
+
+ mitk::PointSet::Pointer pointSet = dynamic_cast<mitk::PointSet *>(m_SelectedPS->GetData());
+
+
+ vnl_matrix<float> streamline;
+ streamline.set_size(3, pointSet->GetSize());
+ streamline.fill(0.0);
+
+
+ mitk::PointSet::PointsIterator begin = pointSet->Begin();
+ mitk::PointSet::PointsIterator end = pointSet->End();
+ unsigned int i;
+ mitk::PointSet::PointsContainer::Iterator it;
+
+ for (it = begin, i = 0; it != end; ++it, ++i)
+ {
+ PointSet::PointType pt = pointSet->GetPoint(it->Index());
+ vnl_vector_fixed< float, 3 > candV;
+ candV[0]=pt[0]; candV[1]=pt[1]; candV[2]=pt[2];
+ streamline.set_column(i, candV);
+ }
+
+ // build Fiber
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+
+
+ for (unsigned int j=0; j<streamline.cols(); j++)
+ {
+ double p[3];
+ p[0] = streamline.get(0,j);
+ p[1] = streamline.get(1,j);
+ p[2] = streamline.get(2,j);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ MITK_INFO<< "Last Line from current pointset";
+ vNewLines->InsertNextCell(container);
+
+ vNewPolyData->SetPoints(vNewPoints);
+ vNewPolyData->SetLines(vNewLines);
+
+ m_positiveFibersData = vtkSmartPointer<vtkPolyData>::New();
+ m_positiveFibersData->SetPoints(vtkSmartPointer<vtkPoints>::New());
+ m_positiveFibersData->SetLines(vtkSmartPointer<vtkCellArray>::New());
+ m_positiveFibersData->SetPoints(vNewPoints);
+ m_positiveFibersData->SetLines(vNewLines);
+
+ m_positiveBundle = mitk::FiberBundle::New(vNewPolyData);
+ m_positiveBundle->ResampleToNumPoints(40);
+ MITK_INFO << "Resampling Done";
+
+
+ m_positiveBundle->SetFiberColors(0, 255, 0);
+
+
+
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(m_positiveBundle);
+ node->SetName("+Bundle");
+// node->SetFloatProperty("shape.tuberadius", 0.5);
+// mitk::RenderingManager::GetInstance()->RequestUpdateAll();
+
+ m_positiveBundleNode= node;
+
+
+
+ MITK_INFO << "The + Bundle has Streamlines:";
+ auto m_PosStreamline= dynamic_cast<mitk::FiberBundle *>(m_positiveBundleNode->GetData());
+ MITK_INFO << m_PosStreamline->GetFiberPolyData()->GetNumberOfCells();
+
+ this->GetDataStorage()->Add(m_positiveBundleNode);
+// m_Controls->m_selectedPointSetWidget->m_ToggleAddPoint->setEnabled(false);
+
+ UpdateGui();
+ m_createdStreamlineCounter +=1;
+
+}
+
+void QmitkInteractiveFiberDissectionView::ExtractRandomFibersFromTractogram()
+{
+ m_testnode = m_Controls->m_TestBundleBox->GetSelectedNode();
+ m_testnode->SetVisibility(false);
+// m_SelectedFB.at(0)->SetVisibility(false);
+ m_Controls->m_ErazorButton->setChecked(false);
+ m_Controls->m_BrushButton->setChecked(false);
+
+
+ MITK_INFO << "Number of Fibers to extract from Tractogram: ";
+ MITK_INFO << m_Controls->m_NumRandomFibers->value();
+ if (this->GetDataStorage()->Exists(m_newfibersBundleNode))
+ {
+ MITK_INFO << "To Label Bundle Exists";
+ mitk::FiberBundle::Pointer Stack = dynamic_cast<mitk::FiberBundle *>(m_newfibersBundleNode->GetData());
+ this->GetDataStorage()->Remove(m_newfibersBundleNode);
+
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+
+ m_newfibersFibersData = vtkSmartPointer<vtkPolyData>::New();
+ m_newfibersFibersData->SetPoints(vtkSmartPointer<vtkPoints>::New());
+ m_newfibersBundle = mitk::FiberBundle:: New(m_newfibersFibersData);
+ m_newfibersFibersData->SetLines(vtkSmartPointer<vtkCellArray>::New());
+
+// node->SetData( m_newfibersBundle );
+// m_newfibersBundleNode = node ;
+
+ MITK_INFO << "Create Bundle";
+ }
+
+ mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_testnode->GetData());
+ // mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
+// mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle *>(m_trainbundle->GetData());
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
+// weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers());
+
+// MITK_INFO << fib->GetNumFibers();
+// std::vector<int> myvec;
+// for (unsigned int k=0; k<fib->GetNumFibers(); k++)
+// {
+// myvec.push_back(k);
+// }
+// std::random_shuffle(std::begin(myvec), std::end(myvec));
+
+ /* Check weather all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/
+ unsigned int counter = 0;
+// int thresh1;
+// int thresh2;
+// thresh2 = m_Controls->m_NumRandomFibers->value()*(m_RandomExtractionCounter+1);
+// thresh1 = m_Controls->m_NumRandomFibers->value()*(m_RandomExtractionCounter);
+// if (thresh1>fib->GetFiberPolyData()->GetNumberOfCells())
+// {
+// thresh1=fib->GetFiberPolyData()->GetNumberOfCells();
+// }
+// if (thresh2>fib->GetFiberPolyData()->GetNumberOfCells())
+// {
+// thresh2=fib->GetFiberPolyData()->GetNumberOfCells();
+// }
+
+// if (thresh1!=fib->GetFiberPolyData()->GetNumberOfCells())
+ if (m_Controls->m_NumRandomFibers->value()!=fib->GetFiberPolyData()->GetNumberOfCells())
+ {
+// for ( int i=thresh1; i<thresh2; i++)
+ for ( int i=0; i<m_Controls->m_NumRandomFibers->value(); i++)
+ {
+ vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+
+ counter++;
+
+ }
+
+ for ( int i=0; i<m_Controls->m_NumRandomFibers->value(); i++)
+ {
+ fib->GetFiberPolyData()->DeleteCell(i);
+ }
+ fib->GetFiberPolyData()->RemoveDeletedCells();
+
+ MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells();
+
+// m_SelectedFB.at(0)->SetData(fib);
+
+ vNewPolyData->SetLines(vNewLines);
+ vNewPolyData->SetPoints(vNewPoints);
+
+ m_newfibersFibersData = vtkSmartPointer<vtkPolyData>::New();
+ m_newfibersFibersData->SetPoints(vtkSmartPointer<vtkPoints>::New());
+ m_newfibersFibersData->SetLines(vtkSmartPointer<vtkCellArray>::New());
+ m_newfibersFibersData->SetPoints(vNewPoints);
+ m_newfibersFibersData->SetLines(vNewLines);
+
+ m_newfibersBundle = mitk::FiberBundle::New(vNewPolyData);
+ m_newfibersBundle->SetFiberColors(255, 255, 255);
+ m_newfibersBundle->SetFiberWeights(weights);
+
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(m_newfibersBundle);
+ node->SetName("ToLabel");
+// node->SetData(m_negativeBundle);
+// node->SetFloatProperty("shape.tuberadius", 0.5);
+// mitk::RenderingManager::GetInstance()->RequestUpdateAll();
+
+ m_newfibersBundleNode = node;
+
+// MITK_INFO << "Number of Streamlines in first function";
+// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells();
+ this->GetDataStorage()->Add(m_newfibersBundleNode);
+
+ mitk::FiberBundle::Pointer m_negativeBundle = mitk::FiberBundle::New();
+ mitk::DataNode::Pointer node2 = mitk::DataNode::New();
+ node2->SetName("-Bundle");
+ node2->SetData(m_negativeBundle);
+// node->SetFloatProperty("shape.tuberadius", 0.5);
+// mitk::RenderingManager::GetInstance()->RequestUpdateAll();
+ m_negativeBundleNode = node2;
+ this->GetDataStorage()->Add(m_negativeBundleNode);
+
+ m_RandomExtractionCounter++;
+ }
+
+// m_Controls->m_ErazorButton->setChecked(true);
+
+
+ UpdateGui();
+
+
+}
+
+void QmitkInteractiveFiberDissectionView::RemovefromBundle( bool checked )
+{
+ if (checked)
+ {
+ m_Controls->m_BrushButton->setChecked(false);
+
+// if (m_StreamlineInteractor.IsNull())
+// {
+ this->CreateStreamlineInteractorBrush();
+ this->CreateStreamlineInteractor();
+// }
+ m_StreamlineInteractor->EnableInteraction(true);
+ m_StreamlineInteractor->LabelfromPrediction(false);
+ m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode);
+ m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode);
+ m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode);
+ m_StreamlineInteractor->EnableInteraction(true);
+
+// m_StreamlineInteractor->EnableInteraction(true);
+// m_StreamlineInteractor->LabelfromPrediction(false);
+// m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode);
+// m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode);
+// m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode);
+// }
+// else
+// {
+// m_StreamlineInteractor->EnableInteraction(true);
+// m_StreamlineInteractor->LabelfromPrediction(false);
+// m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode);
+// m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode);
+// }
+ }
+ else
+ {
+ m_StreamlineInteractor->EnableInteraction(false);
+// m_StreamlineInteractor = nullptr;
+ }
+
+
+ UpdateGui();
+}
+
+void QmitkInteractiveFiberDissectionView::RemovefromBundleBrush( bool checked )
+{
+ if (checked)
+ {
+ m_Controls->m_ErazorButton->setChecked(false);
+
+// if (m_StreamlineInteractorBrush.IsNull())
+// {
+ this->CreateStreamlineInteractor();
+ this->CreateStreamlineInteractorBrush();
+// }
+
+
+ m_StreamlineInteractorBrush->EnableInteraction(true);
+ m_StreamlineInteractorBrush->LabelfromPrediction(false);
+ m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode);
+ m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode);
+ m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode);
+ m_StreamlineInteractorBrush->EnableInteraction(true);
+// m_StreamlineInteractorBrush->EnableInteraction(true);
+// m_StreamlineInteractorBrush->LabelfromPrediction(false);
+// m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode);
+// m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode);
+// m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode);
+// }
+// else
+// {
+// m_StreamlineInteractorBrush->EnableInteraction(true);
+// m_StreamlineInteractorBrush->LabelfromPrediction(false);
+// m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode);
+// m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode);
+// }
+ }
+ else
+ {
+ m_StreamlineInteractorBrush->EnableInteraction(false);
+// m_StreamlineInteractor = nullptr;
+ }
+
+
+ UpdateGui();
+}
+
+void QmitkInteractiveFiberDissectionView::CreateStreamlineInteractor()
+{
+
+ m_StreamlineInteractor = mitk::StreamlineInteractor::New();
+
+ m_StreamlineInteractor->LoadStateMachine("Streamline3DStates.xml", us::ModuleRegistry::GetModule("MitkFiberDissection"));
+ m_StreamlineInteractor->SetEventConfig("Streamline3DConfig.xml", us::ModuleRegistry::GetModule("MitkFiberDissection"));
+
+// m_StreamlineInteractor->SetRotationEnabled(rotationEnabled);
+}
+
+void QmitkInteractiveFiberDissectionView::CreateStreamlineInteractorBrush()
+{
+
+ m_StreamlineInteractorBrush = mitk::StreamlineInteractorBrush::New();
+
+ m_StreamlineInteractorBrush->LoadStateMachine("StreamlineBrush3DStates.xml", us::ModuleRegistry::GetModule("MitkFiberDissection"));
+ m_StreamlineInteractorBrush->SetEventConfig("StreamlineBrush3DConfig.xml", us::ModuleRegistry::GetModule("MitkFiberDissection"));
+
+// m_StreamlineInteractor->SetRotationEnabled(rotationEnabled);
+}
+
+void QmitkInteractiveFiberDissectionView::StartAlgorithm()
+{
+
+ m_negativeBundle = dynamic_cast<mitk::FiberBundle*>(m_negativeBundleNode->GetData());
+ m_positiveBundle = dynamic_cast<mitk::FiberBundle*>(m_positiveBundleNode->GetData());
+
+
+ this->GetDataStorage()->Remove(m_UncertaintyLabelNode);
+ this->GetDataStorage()->Remove(m_DistanceLabelNode);
+
+
+ MITK_INFO << "Clean Test Data";
+
+// this->CleanTestArray();
+ m_testnode = m_Controls->m_TestBundleBox->GetSelectedNode();
+// mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
+ mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_testnode->GetData());
+
+ MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells();
+ fib->GetFiberPolyData()->RemoveDeletedCells();
+ MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells();
+
+
+ m_Controls->m_unclabeling->setChecked(false);
+ m_Controls->m_distlabeling->setChecked(false);
+ m_Controls->m_unclabelingBrush->setChecked(false);
+ m_Controls->m_predlabeling->setChecked(false);
+ m_Controls->m_predlabelingBrush->setChecked(false);
+ m_uncCounter = 0;
+
+// classifier.reset();
+ MITK_INFO << "Extract Features";
+
+ classifier = std::make_shared<mitk::StreamlineFeatureExtractor>();
+ classifier->SetActiveCycle(m_activeCycleCounter);
+ classifier->SetTractogramPlus(m_positiveBundle);
+ classifier->SetTractogramMinus(m_negativeBundle);
+ classifier->SetTractogramPrototypes(dynamic_cast<mitk::FiberBundle*>(m_Controls->m_PrototypeBox->GetSelectedNode()->GetData()), m_Controls->m_useStandardP->isChecked());
+// classifier->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName());
+ classifier->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_testnode->GetData()), m_testnode->GetName());
+// classifier->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_trainbundle->GetData()), m_trainbundle->GetName());
+
+
+
+ classifier->Update();
+
+ m_index = classifier->m_index;
+ MITK_INFO << "Number of Cycles";
+ MITK_INFO << m_activeCycleCounter;
+ m_activeCycleCounter += 1;
+
+
+ MITK_INFO << "Algorithm run succesfully";
+// mitk::DataNode::Pointer node = mitk::DataNode::New();
+// this->GetDataStorage()->Add(node);
+ m_Controls->m_CreatePrediction->setEnabled(true);
+ UpdateGui();
+
+}
+
+void QmitkInteractiveFiberDissectionView::CreatePredictionNode()
+{
+ MITK_INFO << "Create Prediction";
+
+ m_Prediction = classifier->CreatePrediction(m_index.at(0), false);
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(m_Prediction);
+ auto s = std::to_string(m_activeCycleCounter);
+ node->SetName("Prediction"+s);
+ m_PredictionNode = node;
+ this->GetDataStorage()->Add(m_PredictionNode);
+ UpdateGui();
+}
+
+void QmitkInteractiveFiberDissectionView::CreateCertainNode()
+{
+ MITK_INFO << "Create Certain Data";
+
+
+ m_CertainMinus = classifier->CreatePrediction(m_index.at(2), false);
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(m_CertainMinus);
+ auto s = std::to_string(m_activeCycleCounter);
+ node->SetName("m_CertainMinus"+s);
+ m_CertainMinusNode = node;
+ this->GetDataStorage()->Add(m_CertainMinusNode);
+
+// m_CertainPlus = classifier->CreatePrediction(m_index.at(4));
+// mitk::DataNode::Pointer node2= mitk::DataNode::New();
+// node2->SetData(m_CertainPlus);
+// node2->SetName("m_CertainPlus"+s);
+// m_CertainPlusNode = node2;
+// this->GetDataStorage()->Add(m_CertainPlusNode);
+
+
+// m_CertainBetweenMinus = classifier->CreatePrediction(m_index.at(4));
+// mitk::DataNode::Pointer node3 = mitk::DataNode::New();
+// node3->SetData(m_CertainBetweenMinus);
+// node3->SetName("m_CertainBetweenMinus"+s);
+// m_CertainBetweenMinusNode = node3;
+// this->GetDataStorage()->Add(m_CertainBetweenMinusNode);
+
+// m_CertainBetweenPlus = classifier->CreatePrediction(m_index.at(6));
+// mitk::DataNode::Pointer node4= mitk::DataNode::New();
+// node4->SetData(m_CertainBetweenPlus);
+// node4->SetName("m_CertainBetweenPlus"+s);
+// m_CertainBetweenPlusNode = node4;
+// this->GetDataStorage()->Add(m_CertainBetweenPlusNode);
+
+}
+
+void QmitkInteractiveFiberDissectionView::RemoveCertainData()
+{
+// mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
+ mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_testnode->GetData());
+ MITK_INFO << "Length of certain negativ data:";
+ MITK_INFO << m_index.at(2).size();
+ MITK_INFO << "Length of Testdata";
+ MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells();
+ for (unsigned int i=0; i< m_index.at(2).size(); i++)
+ {
+ fib->GetFiberPolyData()->DeleteCell(m_index.at(2).at(i));
+ }
+// fib->GetFiberPolyData()->RemoveDeletedCells();
+
+ MITK_INFO << "Length of Testdata";
+ MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells();
+}
+
+void QmitkInteractiveFiberDissectionView::CreateUncertaintySampleNode()
+{
+ this->GetDataStorage()->Remove(m_UncertaintyLabelNode);
+ MITK_INFO << "Create Fibers to label based on Uncertainty";
+
+ std::vector<unsigned int> vec = m_index.at(1);
+ std::vector<unsigned int> myvec = {vec.begin() + m_uncCounter, vec.begin() + m_uncCounter + m_Controls->m_Numtolabel->value()};
+ m_uncCounter = m_uncCounter + m_Controls->m_Numtolabel->value();
+ MITK_INFO << m_index.at(1).size();
+ MITK_INFO << myvec.size();
+
+
+ m_UncertaintyLabel = classifier->CreatePrediction(myvec, true);
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(m_UncertaintyLabel);
+ float d = 5.0;
+
+ auto s = std::to_string(m_activeCycleCounter);
+ node->SetName("UncertaintyLabel"+s);
+ m_UncertaintyLabelNode = node;
+ m_UncertaintyLabelNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(d));
+ this->GetDataStorage()->Add(m_UncertaintyLabelNode);
+ UpdateGui();
+}
+
+void QmitkInteractiveFiberDissectionView::CreateDistanceSampleNode()
+{
+// MITK_INFO << "Create Fibers to label based on Distance in Features-Space";
+// std::vector<unsigned int> myvec = m_index.at(2);
+// myvec.resize(m_Controls->m_Numtolabel2->value());
+// MITK_INFO << m_index.at(2).size();
+// MITK_INFO << myvec.size();
+
+ float myval = m_Controls->m_subsetfft->value() * 0.01;
+ MITK_INFO << myval;
+ std::vector<std::vector<unsigned int>> curidx;
+ curidx = classifier->GetDistanceData(myval);
+ std::vector<unsigned int> myvec = curidx.at(0);
+ myvec.resize(m_Controls->m_Numtolabel2->value());
+ MITK_INFO << m_index.at(2).size();
+ MITK_INFO << myvec.size();
+ m_DistanceLabel = classifier->CreatePrediction(myvec, true);
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(m_DistanceLabel);
+ auto s = std::to_string(m_activeCycleCounter);
+ node->SetName("DistanceLabel"+s);
+ m_DistanceLabelNode = node;
+ this->GetDataStorage()->Add(m_DistanceLabelNode);
+ UpdateGui();
+}
+
+void QmitkInteractiveFiberDissectionView::RemovefromUncertainty( bool checked )
+{
+ if (checked)
+ {
+ m_Controls->m_unclabelingBrush->setChecked(false);
+ m_Controls->m_predlabelingBrush->setChecked(false);
+ m_Controls->m_predlabeling->setChecked(false);
+
+
+ m_UncertaintyLabel->SetFiberColors(255, 255, 255);
+ this->CreateStreamlineInteractor();
+ m_StreamlineInteractor->EnableInteraction(true);
+ m_StreamlineInteractor->LabelfromPrediction(false);
+ m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode);
+ m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode);
+ m_StreamlineInteractor->SetToLabelNode(m_UncertaintyLabelNode);
+ }
+ else
+ {
+ m_StreamlineInteractor->EnableInteraction(false);
+// m_StreamlineInteractor = nullptr;
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+}
+
+void QmitkInteractiveFiberDissectionView::RemovefromUncertaintyBrush( bool checked )
+{
+ if (checked)
+ {
+ m_Controls->m_unclabeling->setChecked(false);
+ m_Controls->m_predlabelingBrush->setChecked(false);
+ m_Controls->m_predlabeling->setChecked(false);
+
+ m_UncertaintyLabel->SetFiberColors(255, 255, 255);
+ this->CreateStreamlineInteractorBrush();
+ m_StreamlineInteractorBrush->EnableInteraction(true);
+ m_StreamlineInteractorBrush->LabelfromPrediction(false);
+ m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode);
+ m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode);
+ m_StreamlineInteractorBrush->SetToLabelNode(m_UncertaintyLabelNode);
+ }
+ else
+ {
+ m_StreamlineInteractorBrush->EnableInteraction(false);
+// m_StreamlineInteractor = nullptr;
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+}
+
+void QmitkInteractiveFiberDissectionView::RemovefromDistance( bool checked )
+{
+ if (checked)
+ {
+
+ m_DistanceLabel->SetFiberColors(255, 255, 255);
+ m_StreamlineInteractor->EnableInteraction(true);
+ m_StreamlineInteractor->LabelfromPrediction(false);
+ m_StreamlineInteractor->SetToLabelNode(m_DistanceLabelNode);
+ }
+ else
+ {
+ m_StreamlineInteractor->EnableInteraction(false);
+// m_StreamlineInteractor = nullptr;
+ }
+ RenderingManager::GetInstance()->RequestUpdateAll();
+}
+
+void QmitkInteractiveFiberDissectionView::RemovefromPrediction( bool checked )
+{
+ if (checked)
+ {
+ m_Controls->m_predlabelingBrush->setChecked(false);
+ m_Controls->m_unclabelingBrush->setChecked(false);
+ m_Controls->m_unclabeling->setChecked(false);
+
+// m_Prediction->SetFiberColors(255, 255, 255);
+ this->CreateStreamlineInteractor();
+ m_StreamlineInteractor->EnableInteraction(true);
+ m_StreamlineInteractor->LabelfromPrediction(true);
+ m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode);
+ m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode);
+ m_StreamlineInteractor->SetToLabelNode(m_PredictionNode);
+ }
+ else
+ {
+ m_StreamlineInteractor->EnableInteraction(false);
+// m_StreamlineInteractor = nullptr;
+// this->CleanTestArray();
+ }
+
+}
+
+void QmitkInteractiveFiberDissectionView::RemovefromPredictionBrush( bool checked )
+{
+ if (checked)
+ {
+ m_Controls->m_predlabeling->setChecked(false);
+ m_Controls->m_unclabelingBrush->setChecked(false);
+ m_Controls->m_unclabeling->setChecked(false);
+
+// m_Prediction->SetFiberColors(255, 255, 255);
+ this->CreateStreamlineInteractorBrush();
+ m_StreamlineInteractorBrush->EnableInteraction(true);
+ m_StreamlineInteractorBrush->LabelfromPrediction(true);
+ m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode);
+ m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode);
+ m_StreamlineInteractorBrush->SetToLabelNode(m_PredictionNode);
+ }
+ else
+ {
+ m_StreamlineInteractorBrush->EnableInteraction(false);
+// m_StreamlineInteractor = nullptr;
+// this->CleanTestArray();
+ }
+
+}
+
+void QmitkInteractiveFiberDissectionView::RemovefromSelection( bool checked )
+{
+ if (checked)
+ {
+
+ // m_Prediction->SetFiberColors(255, 255, 255);
+ m_StreamlineInteractor->EnableInteraction(true);
+ m_StreamlineInteractor->LabelfromPrediction(true);
+// m_StreamlineInteractor->SetToLabelNode(m_SelectedFB.at(0));
+ m_StreamlineInteractor->SetToLabelNode(m_testnode);
+ }
+ else
+ {
+ m_StreamlineInteractor->EnableInteraction(false);
+ // m_StreamlineInteractor = nullptr;
+ }
+}
+
+void QmitkInteractiveFiberDissectionView::StartValidation()
+{
+
+
+
+
+ validater.reset();
+// mitk::DataNode::Pointer prednode = m_Controls->m_BundleBox->GetSelectedNode();
+// mitk::FiberBundle::Pointer pred = dynamic_cast<mitk::FiberBundle *>(prednode->GetData());
+// mitk::DataNode::Pointer gtnode = m_Controls->m_BundleBox->GetSelectedNode();
+// mitk::FiberBundle::Pointer gt = dynamic_cast<mitk::FiberBundle *>(gtnode->GetData());
+// mitk::FiberBundle::Pointer pred = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_PredictionBox->GetSelectedNode()->GetData());
+// mitk::FiberBundle::Pointer gt = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData());
+
+ validater= std::make_shared<mitk::StreamlineFeatureExtractor>();
+ validater->SetTractogramPrototypes(dynamic_cast<mitk::FiberBundle*>(m_Controls->m_PrototypeBox->GetSelectedNode()->GetData()), m_Controls->m_useStandardP->isChecked());
+ MITK_INFO << "Prototypes loaded";
+ validater->SetTractogramPrediction(dynamic_cast<mitk::FiberBundle*>(m_Controls->m_PredictionBox->GetSelectedNode()->GetData()));
+ MITK_INFO << "Prediction loaded";
+ validater->SetTractogramGroundtruth(dynamic_cast<mitk::FiberBundle*>(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData()));
+ MITK_INFO << "Groundtruth loaded";
+
+ validater->SetActiveCycle(m_activeCycleCounter);
+// validater->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName());
+ validater->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_testnode->GetData()), m_testnode->GetName());
+// classifier->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_trainbundle->GetData()), m_trainbundle->GetName());
+
+
+
+ MITK_INFO << "Testdata loaded";
+ vnl_vector<float> metrics;
+ metrics = validater->ValidationPipe();
+
+ m_metrics.push_back(metrics);
+
+
+ std::ofstream metricsfile;
+ metricsfile.open("/home/r948e/mycsv/metrics_" + std::to_string(m_activeCycleCounter) + ".csv");
+ for (unsigned int i = 0; i < m_metrics.size(); i++)
+ {
+ metricsfile << m_metrics.at(i) << std::endl;
+ }
+
+ metricsfile.close();
+
+
+ MITK_INFO << "Validation run succesfully";
+
+ UpdateGui();
+
+}
+
+void QmitkInteractiveFiberDissectionView::AutomaticLabelling()
+{
+// mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
+// mitk::FiberBundle::Pointer fib_true = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData());
+// vtkCell* cell;
+// vtkCell* cell2;
+// for (int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
+// {
+// cell = fib->GetFiberPolyData()->GetCell(i);
+// for (int k=0; k<fib->GetFiberPolyData()->GetNumberOfCells(); k++ )
+// {
+// cell2 = fib_true->GetFiberPolyData()->GetCell(i);
+// if (cell==cell2)
+// MITK_INFO << "Same";
+// }
+// }
+
+ mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_PredictionNode->GetData());
+ mitk::FiberBundle::Pointer fib_true = dynamic_cast<mitk::FiberBundle*>(m_positiveBundleNode->GetData());
+
+ vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
+ vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
+
+ vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
+
+ /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/
+ unsigned int counter = 0;
+
+ for (int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ weights->InsertValue(counter, fib->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+ for (int i=0; i<fib_true->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ vtkCell* cell = fib_true->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+
+ vtkIdType id = vNewPoints->InsertNextPoint(p);
+ container->GetPointIds()->InsertNextId(id);
+ }
+ weights->InsertValue(counter, fib_true->GetFiberWeight(i));
+ vNewLines->InsertNextCell(container);
+ counter++;
+
+ }
+
+
+
+ vNewPolyData->SetLines(vNewLines);
+ vNewPolyData->SetPoints(vNewPoints);
+
+ mitk::FiberBundle::Pointer MergedPrediction = mitk::FiberBundle::New(vNewPolyData);
+ MergedPrediction->SetFiberWeights(weights);
+
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData(MergedPrediction);
+ node->SetName("MergedPrediction");
+ this->GetDataStorage()->Add(node);
+
+
+}
+
+void QmitkInteractiveFiberDissectionView::CleanTestArray()
+{
+
+ mitk::FiberBundle::Pointer fib_pos = dynamic_cast<mitk::FiberBundle*>(m_positiveBundleNode->GetData());
+ mitk::FiberBundle::Pointer fib_neg = dynamic_cast<mitk::FiberBundle*>(m_negativeBundleNode->GetData());
+// mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
+ mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_testnode->GetData());
+ vtkCell* cur_cell;
+ vtkCell* cur_cell2;
+ MITK_INFO << fib_neg->GetFiberPolyData()->GetNumberOfCells();
+ MITK_INFO << fib_pos->GetFiberPolyData()->GetNumberOfCells();
+ MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells();
+
+
+ std::vector<float> array;
+ std::vector<float> array2;
+
+
+ // cv::parallel_for_(cv::Range(0, fib->GetFiberPolyData()->GetNumberOfCells()), [&](const cv::Range &range)
+ // {
+ // for (int i = range.start; i < range.end; i++)
+ for (int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
+ {
+ cur_cell = fib->GetFiberPolyData()->GetCell(i);
+ auto numPoints = cur_cell->GetNumberOfPoints();
+ vtkPoints* points = cur_cell->GetPoints();
+ for (unsigned int j=0; j<numPoints; j++)
+ {
+ double p[3];
+ points->GetPoint(j, p);
+ array.push_back(*p);
+ }
+ for (int ik=0; ik<fib_neg->GetFiberPolyData()->GetNumberOfCells(); ik++)
+ {
+ cur_cell2 = fib_neg->GetFiberPolyData()->GetCell(ik);
+ auto numPoints2 = cur_cell2->GetNumberOfPoints();
+ vtkPoints* points2 = cur_cell2->GetPoints();
+ for (unsigned int j2=0; j2<numPoints2; j2++)
+ {
+ double p2[3];
+ points2->GetPoint(j2, p2);
+ array2.push_back(*p2);
+
+ }
+ if (array==array2)
+ {
+ fib->GetFiberPolyData()->DeleteCell(i);
+ MITK_INFO << "Delete Cell";
+ }
+ array2.clear();
+ }
+ for (int ik=0; ik<fib_pos->GetFiberPolyData()->GetNumberOfCells(); ik++)
+ {
+
+ cur_cell2 = fib_pos->GetFiberPolyData()->GetCell(ik);
+ auto numPoints2 = cur_cell2->GetNumberOfPoints();
+ vtkPoints* points2 = cur_cell2->GetPoints();
+ for (unsigned int j2=0; j2<numPoints2; j2++)
+ {
+ double p2[3];
+ points2->GetPoint(j2, p2);
+ array2.push_back(*p2);
+ }
+ if (array==array2)
+ {
+ fib->GetFiberPolyData()->DeleteCell(i);
+ MITK_INFO << "Delete Cell";
+ }
+ array2.clear();
+ }
+ array.clear();
+ }
+ // });
+
+// fib->GetFiberPolyData()->RemoveDeletedCells();
+
+ MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells();
+
+
+
+}
+
+void QmitkInteractiveFiberDissectionView::ResetClassifier()
+{
+ m_IterationCounter = 0;
+ m_RandomExtractionCounter = 0;
+ m_activeCycleCounter = 0;
+ m_createdStreamlineCounter = 0;
+
+ classifier.reset();
+ this->GetDataStorage()->Remove(m_positiveBundleNode);
+ this->GetDataStorage()->Remove(m_negativeBundleNode);
+ this->GetDataStorage()->Remove(m_negativeBundleNode);
+
+ m_positiveBundleNode = NULL;
+ m_negativeBundleNode = NULL;
+ m_negativeBundleNode = NULL;
+ m_positiveBundle = NULL;
+ m_negativeBundle = NULL;
+ m_negativeBundle = NULL;
+ m_Controls->m_TrainClassifier->setEnabled(false);
+ m_Controls->m_CreatePrediction->setEnabled(false);
+ m_Controls->m_CreateUncertantyMap->setEnabled(false);
+
+
+
+}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h
new file mode 100644
index 0000000..acab0f6
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h
@@ -0,0 +1,191 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center.
+
+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 QmitkInteractiveFiberDissectionView_h
+#define QmitkInteractiveFiberDissectionView_h
+#include "ui_QmitkInteractiveFiberDissectionViewControls.h"
+
+#include <QInputDialog> //Pointset
+#include <QmitkPointListWidget.h>//Pointset
+
+#include <QmitkAbstractView.h>//Pointset
+#include <QmitkSingleNodeSelectionWidget.h>//Pointset
+
+
+#include <mitkFiberBundle.h>
+#include <mitkDataInteractor.h>
+#include <mitkIRenderWindowPartListener.h> //Pointset
+#include <mitkStreamlineInteractor.h>
+#include <mitkStreamlineInteractorBrush.h>
+#include <mitkStreamlineFeatureExtractor.h>
+
+#include <itkCastImageFilter.h>
+#include <itkVTKImageImport.h>
+#include <itkVTKImageExport.h>
+#include <itkRegionOfInterestImageFilter.h>
+
+#include <vtkLinearExtrusionFilter.h>
+#include <vtkPolyDataToImageStencil.h>
+#include <vtkSelectEnclosedPoints.h>
+#include <vtkImageImport.h>
+#include <vtkImageExport.h>
+#include <vtkImageStencil.h>
+#include <vtkSmartPointer.h>
+#include <vtkSelection.h>
+#include <vtkSelectionNode.h>
+#include <vtkExtractSelectedThresholds.h>
+#include <vtkFloatArray.h>
+#include <vtkCellPicker.h>
+
+/*!
+\brief View to process fiber bundles. Supplies methods to extract fibers from the bundle, fiber resampling, mirroring, join and subtract bundles and much more.
+*/
+class QmitkInteractiveFiberDissectionView : public QmitkAbstractView, public mitk::IRenderWindowPartListener
+{
+ // this is needed for all Qt objects that should have a Qt meta-object
+ // (everything that derives from QObject and wants to have signal/slots)
+ Q_OBJECT
+
+public:
+
+ typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
+ typedef itk::Image< float, 3 > ItkFloatImageType;
+
+ static const std::string VIEW_ID;
+
+ QmitkInteractiveFiberDissectionView();
+ virtual ~QmitkInteractiveFiberDissectionView();
+
+ virtual void CreateQtPartControl(QWidget *parent) override;
+
+ ///
+ /// Sets the focus to an internal widget.
+ ///
+ virtual void SetFocus() override;
+
+protected slots:
+
+ void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; //Pointset
+ void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; //Pointset
+ void OnAddPointSetClicked();//Pointset
+ void CreateStreamline();
+ void RemovefromBundle( bool checked );
+ void RemovefromBundleBrush( bool checked );
+ void ExtractRandomFibersFromTractogram();
+ void StartAlgorithm();
+ void CreatePredictionNode();
+ void CreateCertainNode();
+ void CreateUncertaintySampleNode();
+ void CreateDistanceSampleNode();
+ void RemovefromUncertainty( bool checked );
+ void RemovefromUncertaintyBrush( bool checked );
+ void RemovefromDistance( bool checked );
+ void RemovefromPrediction( bool checked );
+ void RemovefromPredictionBrush( bool checked );
+ void RemovefromSelection( bool checked );
+ void ResampleTractogram();
+ void RandomPrototypes();
+ void SFFPrototypes();
+ void StartValidation();
+ void AutomaticLabelling();
+ void RemoveCertainData();
+ void ResetClassifier();
+
+
+
+ void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection
+
+
+
+
+protected:
+ void OnCurrentSelectionChanged(QmitkSingleNodeSelectionWidget::NodeList nodes);//Pointset
+
+
+ virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
+
+ void OnEndInteraction();
+ void CreateStreamlineInteractor();
+ void CreateStreamlineInteractorBrush();
+ void CleanTestArray();
+
+ Ui::QmitkInteractiveFiberDissectionViewControls* m_Controls;
+
+
+
+ int m_IterationCounter; ///< used for data node naming
+ int m_RandomExtractionCounter; ///< used for random extracton of different Streamlines
+ int m_activeCycleCounter;
+ int m_newpos;
+ int m_newneg;
+ int m_startneg;
+ int m_createdStreamlineCounter;
+ int m_uncCounter;
+// int m_thresh2;
+
+
+ std::vector<mitk::DataNode::Pointer> m_SelectedFB; ///< selected fiber bundle nodes
+ mitk::DataNode::Pointer m_testnode;
+// mitk::DataNode::Pointer m_trainbundle;
+ mitk::Image::Pointer m_SelectedImage;
+ mitk::DataNode::Pointer m_SelectedPS;
+ mitk::DataNode::Pointer m_SelectedImageNode;
+ mitk::FiberBundle::Pointer m_positiveBundle;
+ mitk::FiberBundle::Pointer m_newfibersBundle;
+ mitk::FiberBundle::Pointer m_negativeBundle;
+ mitk::FiberBundle::Pointer m_Prediction;
+ mitk::FiberBundle::Pointer m_CertainPlus;
+ mitk::FiberBundle::Pointer m_CertainMinus;
+ mitk::FiberBundle::Pointer m_CertainBetweenPlus;
+ mitk::FiberBundle::Pointer m_CertainBetweenMinus;
+ mitk::FiberBundle::Pointer m_UncertaintyLabel;
+ mitk::FiberBundle::Pointer m_DistanceLabel;
+
+
+ mitk::DataNode::Pointer m_positiveBundleNode;
+ mitk::DataNode::Pointer m_newfibersBundleNode;
+ mitk::DataNode::Pointer m_negativeBundleNode;
+ mitk::DataNode::Pointer m_PredictionNode;
+ mitk::DataNode::Pointer m_CertainPlusNode;
+ mitk::DataNode::Pointer m_CertainMinusNode;
+ mitk::DataNode::Pointer m_CertainBetweenPlusNode;
+ mitk::DataNode::Pointer m_CertainBetweenMinusNode;
+ mitk::DataNode::Pointer m_UncertaintyLabelNode;
+ mitk::DataNode::Pointer m_DistanceLabelNode;
+
+ vtkSmartPointer<vtkPolyData> m_positiveFibersData;
+ vtkSmartPointer<vtkPolyData> m_newfibersFibersData;
+
+ vtkSmartPointer<vtkCellPicker> m_picker1;
+ mitk::StreamlineInteractor::Pointer m_StreamlineInteractor;
+ mitk::StreamlineInteractorBrush::Pointer m_StreamlineInteractorBrush;
+
+ std::shared_ptr< mitk::StreamlineFeatureExtractor > classifier;
+ std::shared_ptr< mitk::StreamlineFeatureExtractor > validater;
+
+
+ std::vector<vnl_vector<float>> m_metrics;
+
+ std::vector<std::vector<unsigned int>> m_index;
+
+};
+
+
+
+#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
+
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui
new file mode 100644
index 0000000..1747417
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui
@@ -0,0 +1,1125 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>QmitkInteractiveFiberDissectionViewControls</class>
+ <widget class="QWidget" name="QmitkInteractiveFiberDissectionViewControls">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>417</width>
+ <height>711</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>Form</string>
+ </property>
+ <property name="styleSheet">
+ <string>QCommandLinkButton:disabled {
+ border: none;
+}
+
+QGroupBox {
+ background-color: transparent;
+}</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_3">
+ <property name="leftMargin">
+ <number>9</number>
+ </property>
+ <property name="topMargin">
+ <number>9</number>
+ </property>
+ <property name="rightMargin">
+ <number>9</number>
+ </property>
+ <property name="bottomMargin">
+ <number>9</number>
+ </property>
+ <item row="2" column="0">
+ <widget class="QToolBox" name="toolBoxx">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="font">
+ <font>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="toolTip">
+ <string>Label Fibers</string>
+ </property>
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="currentIndex">
+ <number>3</number>
+ </property>
+ <property name="tabSpacing">
+ <number>6</number>
+ </property>
+ <widget class="QWidget" name="page">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>399</width>
+ <height>439</height>
+ </rect>
+ </property>
+ <attribute name="label">
+ <string>Generate Prototypes</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_5">
+ <item row="2" column="0" colspan="2">
+ <widget class="QToolBox" name="toolBox">
+ <property name="toolTipDuration">
+ <number>0</number>
+ </property>
+ <property name="currentIndex">
+ <number>0</number>
+ </property>
+ <widget class="QWidget" name="Defaults">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>381</width>
+ <height>359</height>
+ </rect>
+ </property>
+ <attribute name="label">
+ <string>Defaults</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_27">
+ <item row="0" column="0">
+ <widget class="QLabel" name="inputImageOneLabel">
+ <property name="text">
+ <string>Extract from</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QmitkDataStorageComboBox" name="m_BundleBox"/>
+ </item>
+ <item row="1" column="0">
+ <widget class="QPushButton" name="m_SFFPrototypesButton">
+ <property name="text">
+ <string>SFF Extraction</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <spacer name="verticalSpacer_23">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="page_17">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>273</width>
+ <height>171</height>
+ </rect>
+ </property>
+ <attribute name="label">
+ <string>Advanced Settings</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_29">
+ <item row="0" column="0" colspan="2">
+ <widget class="QLabel" name="inputImageOneLabel_3">
+ <property name="text">
+ <string>Number of Prototypes</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QSpinBox" name="m_NumPrototypes">
+ <property name="minimum">
+ <number>10</number>
+ </property>
+ <property name="maximum">
+ <number>200</number>
+ </property>
+ <property name="value">
+ <number>100</number>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0" colspan="2">
+ <widget class="QPushButton" name="m_RandomPrototypesButton">
+ <property name="text">
+ <string>Random Extraction</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0" colspan="2">
+ <widget class="QPushButton" name="m_ResampleButton">
+ <property name="text">
+ <string>Resample Bundle</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0" colspan="2">
+ <widget class="QRadioButton" name="m_useStandardP">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="text">
+ <string>Use Standard Prototypes</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <widget class="QLabel" name="inputImageOneLabel_2">
+ <property name="text">
+ <string>Choose own Prototypes</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="1" colspan="2">
+ <widget class="QmitkDataStorageComboBox" name="m_PrototypeBox"/>
+ </item>
+ <item row="5" column="0">
+ <spacer name="verticalSpacer_5">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>170</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="page_3">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>399</width>
+ <height>439</height>
+ </rect>
+ </property>
+ <attribute name="label">
+ <string>Fiber Creation</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_7">
+ <item row="0" column="0">
+ <widget class="QFrame" name="frame">
+ <property name="frameShape">
+ <enum>QFrame::StyledPanel</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_11">
+ <item row="0" column="0">
+ <widget class="QLabel" name="m_selectedPointSetLabel">
+ <property name="text">
+ <string>Selected Streamline Pointset</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="1">
+ <spacer name="horizontalSpacer_14">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="4" column="0" colspan="2">
+ <widget class="QGroupBox" name="groupBox">
+ <property name="title">
+ <string>Streamline Points</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_10">
+ <item row="0" column="0">
+ <widget class="QmitkPointListWidget" name="m_poinSetListWidget" native="true"/>
+ </item>
+ <item row="1" column="0">
+ <spacer name="verticalSpacer_7">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <spacer name="horizontalSpacer_13">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="0" column="1">
+ <spacer name="horizontalSpacer_12">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="0">
+ <widget class="QPushButton" name="m_addPointSetPushButton">
+ <property name="text">
+ <string>Add new Streamline Pointset</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QmitkSingleNodeSelectionWidget" name="m_selectedPointSetWidget" native="true">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Minimum">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>40</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="6" column="0">
+ <spacer name="verticalSpacer_3">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="7" column="0">
+ <widget class="QPushButton" name="m_StreamlineCreation">
+ <property name="text">
+ <string>Create Streamline</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="page_2">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>399</width>
+ <height>439</height>
+ </rect>
+ </property>
+ <property name="accessibleName">
+ <string/>
+ </property>
+ <attribute name="label">
+ <string>Fiber Labelling</string>
+ </attribute>
+ <attribute name="toolTip">
+ <string>Dissect/Eraze Fibers by Erasion and Highlighting</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_13">
+ <item row="1" column="0">
+ <widget class="QFrame" name="m_LabelFrame">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="cursor">
+ <cursorShape>ArrowCursor</cursorShape>
+ </property>
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_4">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label">
+ <property name="text">
+ <string>Label individual Streamlines</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <spacer name="verticalSpacer_4">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_3">
+ <property name="text">
+ <string>Streamlines to be labeled</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <widget class="QFrame" name="m_ExtractionToolsFrame">
+ <property name="frameShape">
+ <enum>QFrame::StyledPanel</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QGridLayout" name="gridLayout">
+ <item row="3" column="0">
+ <widget class="QLabel" name="label_4">
+ <property name="text">
+ <string>Label Streamlines</string>
+ </property>
+ </widget>
+ </item>
+ <item row="6" column="0">
+ <widget class="QLabel" name="label_10">
+ <property name="text">
+ <string>Unlabel: Leftclick + shift/alt</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <widget class="QLabel" name="label_6">
+ <property name="text">
+ <string>Reject: Rightclick + shift</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="1" colspan="2">
+ <widget class="QPushButton" name="m_ErazorButton">
+ <property name="maximumSize">
+ <size>
+ <width>30</width>
+ <height>30</height>
+ </size>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ <property name="icon">
+ <iconset>
+ <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png</iconset>
+ </property>
+ <property name="iconSize">
+ <size>
+ <width>32</width>
+ <height>32</height>
+ </size>
+ </property>
+ <property name="flat">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="4" rowspan="3">
+ <spacer name="horizontalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="5" column="0">
+ <widget class="QLabel" name="label_8">
+ <property name="text">
+ <string>Accept: Rightclick + alt</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1" rowspan="3" colspan="2">
+ <widget class="QSpinBox" name="m_NumRandomFibers">
+ <property name="minimum">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <number>2000</number>
+ </property>
+ <property name="value">
+ <number>20</number>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_7">
+ <property name="text">
+ <string>Random Streamlines</string>
+ </property>
+ </widget>
+ </item>
+ <item row="7" column="0">
+ <spacer name="verticalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="0" column="3" rowspan="3">
+ <widget class="QPushButton" name="m_AddRandomFibers">
+ <property name="text">
+ <string>Add</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="3">
+ <widget class="QPushButton" name="m_BrushButton">
+ <property name="maximumSize">
+ <size>
+ <width>30</width>
+ <height>30</height>
+ </size>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ <property name="icon">
+ <iconset>
+ <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png</iconset>
+ </property>
+ <property name="iconSize">
+ <size>
+ <width>32</width>
+ <height>32</height>
+ </size>
+ </property>
+ <property name="flat">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="page_4">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>399</width>
+ <height>439</height>
+ </rect>
+ </property>
+ <attribute name="label">
+ <string>Active Learning</string>
+ </attribute>
+ <widget class="QFrame" name="frame_2">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>381</width>
+ <height>391</height>
+ </rect>
+ </property>
+ <property name="frameShape">
+ <enum>QFrame::StyledPanel</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_6">
+ <item row="8" column="1">
+ <widget class="QToolBox" name="toolBox_2">
+ <property name="currentIndex">
+ <number>0</number>
+ </property>
+ <widget class="QWidget" name="page_16">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>361</width>
+ <height>309</height>
+ </rect>
+ </property>
+ <attribute name="label">
+ <string>Default</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_2">
+ <item row="1" column="4">
+ <spacer name="horizontalSpacer_29">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>57</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="4">
+ <spacer name="horizontalSpacer_4">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>57</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="2" colspan="2">
+ <widget class="QPushButton" name="m_AddUncertainFibers">
+ <property name="text">
+ <string>Add </string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="4">
+ <spacer name="horizontalSpacer_30">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>57</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="3" column="0" colspan="2">
+ <widget class="QLabel" name="label_35">
+ <property name="text">
+ <string>Label from Uncertainy Node</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0" colspan="2">
+ <widget class="QPushButton" name="m_TrainClassifier">
+ <property name="text">
+ <string>Train Classifier</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="2">
+ <widget class="QPushButton" name="m_predlabeling">
+ <property name="maximumSize">
+ <size>
+ <width>30</width>
+ <height>30</height>
+ </size>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ <property name="icon">
+ <iconset>
+ <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png</iconset>
+ </property>
+ <property name="iconSize">
+ <size>
+ <width>32</width>
+ <height>32</height>
+ </size>
+ </property>
+ <property name="flat">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_5">
+ <property name="text">
+ <string>Unc: to label</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="0" colspan="2">
+ <widget class="QLabel" name="label_36">
+ <property name="text">
+ <string>Label from Prediction Node</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="4">
+ <spacer name="horizontalSpacer_5">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>57</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="4" column="3">
+ <widget class="QPushButton" name="m_predlabelingBrush">
+ <property name="maximumSize">
+ <size>
+ <width>30</width>
+ <height>30</height>
+ </size>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ <property name="icon">
+ <iconset>
+ <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png</iconset>
+ </property>
+ <property name="iconSize">
+ <size>
+ <width>32</width>
+ <height>32</height>
+ </size>
+ </property>
+ <property name="flat">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0" colspan="2">
+ <widget class="QPushButton" name="m_CreatePrediction">
+ <property name="text">
+ <string>Create Prediction</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="2">
+ <widget class="QPushButton" name="m_unclabeling">
+ <property name="maximumSize">
+ <size>
+ <width>30</width>
+ <height>30</height>
+ </size>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ <property name="icon">
+ <iconset>
+ <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png</iconset>
+ </property>
+ <property name="iconSize">
+ <size>
+ <width>32</width>
+ <height>32</height>
+ </size>
+ </property>
+ <property name="flat">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="1">
+ <widget class="QSpinBox" name="m_Numtolabel">
+ <property name="minimum">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <number>2000</number>
+ </property>
+ <property name="singleStep">
+ <number>0</number>
+ </property>
+ <property name="value">
+ <number>20</number>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="3">
+ <widget class="QPushButton" name="m_unclabelingBrush">
+ <property name="maximumSize">
+ <size>
+ <width>30</width>
+ <height>30</height>
+ </size>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ <property name="icon">
+ <iconset>
+ <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png</iconset>
+ </property>
+ <property name="iconSize">
+ <size>
+ <width>32</width>
+ <height>32</height>
+ </size>
+ </property>
+ <property name="flat">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="4">
+ <spacer name="horizontalSpacer_6">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>57</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="5" column="0" colspan="2">
+ <widget class="QPushButton" name="m_resetClassifier">
+ <property name="text">
+ <string>Reset Classifier</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="page_18">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>337</width>
+ <height>173</height>
+ </rect>
+ </property>
+ <attribute name="label">
+ <string>Advanced</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_30">
+ <item row="6" column="0" colspan="4">
+ <widget class="QLabel" name="label_37">
+ <property name="text">
+ <string>Label from Current Selection</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0" colspan="3">
+ <widget class="QPushButton" name="m_CreateUncertantyMap">
+ <property name="text">
+ <string>Create Uncertanty Map</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="5">
+ <spacer name="horizontalSpacer">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="0" colspan="6">
+ <widget class="QPushButton" name="m_distlabeling">
+ <property name="text">
+ <string>Unc_dis_Label</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="4" colspan="2">
+ <widget class="QPushButton" name="m_AddDistanceFibers">
+ <property name="text">
+ <string>Add</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QSpinBox" name="m_subsetfft">
+ <property name="maximum">
+ <number>100</number>
+ </property>
+ <property name="value">
+ <number>95</number>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="0" colspan="3">
+ <widget class="QPushButton" name="m_certainData">
+ <property name="text">
+ <string>Certain Data</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="3" colspan="2">
+ <widget class="QSpinBox" name="spinBox_2">
+ <property name="maximum">
+ <number>100</number>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="2" colspan="2">
+ <widget class="QSpinBox" name="m_Numtolabel2">
+ <property name="minimum">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <number>500</number>
+ </property>
+ <property name="value">
+ <number>20</number>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_9">
+ <property name="text">
+ <string>Dist: to label</string>
+ </property>
+ </widget>
+ </item>
+ <item row="7" column="3">
+ <spacer name="verticalSpacer_6">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="6" column="4" colspan="2">
+ <widget class="QPushButton" name="m_sellabeling">
+ <property name="text">
+ <string>Label</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="5">
+ <widget class="QPushButton" name="m_RemoveCertainData">
+ <property name="text">
+ <string>Remove</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </widget>
+ <widget class="QWidget" name="page_5">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>399</width>
+ <height>439</height>
+ </rect>
+ </property>
+ <attribute name="label">
+ <string>Validation</string>
+ </attribute>
+ <widget class="QFrame" name="frame_3">
+ <property name="geometry">
+ <rect>
+ <x>10</x>
+ <y>20</y>
+ <width>351</width>
+ <height>371</height>
+ </rect>
+ </property>
+ <property name="frameShape">
+ <enum>QFrame::StyledPanel</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_8">
+ <item row="11" column="2">
+ <spacer name="verticalSpacer_8">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="0" column="1" colspan="2">
+ <widget class="QmitkDataStorageComboBox" name="m_PredictionBox"/>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_11">
+ <property name="text">
+ <string>Prediction</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1" colspan="2">
+ <widget class="QmitkDataStorageComboBox" name="m_GroundtruthBox"/>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_12">
+ <property name="text">
+ <string>Groundtrouth</string>
+ </property>
+ </widget>
+ </item>
+ <item row="9" column="0" colspan="3">
+ <widget class="QPushButton" name="m_validate">
+ <property name="text">
+ <string>Validate</string>
+ </property>
+ </widget>
+ </item>
+ <item row="10" column="0" colspan="3">
+ <widget class="QPushButton" name="m_automaticLabelling">
+ <property name="text">
+ <string>Merge Prediction with Labled Data</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </widget>
+ </widget>
+ </item>
+ <item row="0" column="0" rowspan="2">
+ <widget class="QGroupBox" name="m_InputData">
+ <property name="title">
+ <string>Please Select Input Data</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_9">
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_13">
+ <property name="text">
+ <string>Training Fiber Bundle:</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_2">
+ <property name="toolTip">
+ <string>Input DTI</string>
+ </property>
+ <property name="text">
+ <string>Selectd Fiber Bundle:</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QmitkDataStorageComboBox" name="m_TestBundleBox"/>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLabel" name="m_FibLabel">
+ <property name="text">
+ <string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
+ </property>
+ <property name="wordWrap">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <customwidgets>
+ <customwidget>
+ <class>QmitkDataStorageComboBox</class>
+ <extends>QComboBox</extends>
+ <header location="global">QmitkDataStorageComboBox.h</header>
+ </customwidget>
+ <customwidget>
+ <class>QmitkSingleNodeSelectionWidget</class>
+ <extends>QWidget</extends>
+ <header location="global">QmitkSingleNodeSelectionWidget.h</header>
+ <container>1</container>
+ </customwidget>
+ <customwidget>
+ <class>QmitkPointListWidget</class>
+ <extends>QWidget</extends>
+ <header location="global">QmitkPointListWidget.h</header>
+ </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.cpp
index 042b6c0..666fd1c 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.cpp
@@ -1,51 +1,53 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center.
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 "mitkPluginActivator.h"
#include "src/internal/Perspectives/QmitkFiberProcessingPerspective.h"
#include "src/internal/QmitkFiberProcessingView.h"
#include "src/internal/QmitkFiberQuantificationView.h"
+#include "src/internal/QmitkInteractiveFiberDissectionView.h"
#include "src/internal/QmitkFiberClusteringView.h"
#include "src/internal/QmitkFiberFitView.h"
#include "src/internal/QmitkTractometryView.h"
ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
ctkPluginContext* mitk::PluginActivator::GetContext()
{
return m_Context;
}
void mitk::PluginActivator::start(ctkPluginContext* context)
{
BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingPerspective, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberQuantificationView, context)
+ BERRY_REGISTER_EXTENSION_CLASS(QmitkInteractiveFiberDissectionView, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingView, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberClusteringView, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberFitView, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkTractometryView, context)
m_Context = context;
}
void mitk::PluginActivator::stop(ctkPluginContext* context)
{
Q_UNUSED(context)
m_Context = nullptr;
}