diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/Filter/mitkFloatingImageToUltrasoundRegistrationFilter.cpp b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/Filter/mitkFloatingImageToUltrasoundRegistrationFilter.cpp
index 2f199dec32..b51c613baf 100644
--- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/Filter/mitkFloatingImageToUltrasoundRegistrationFilter.cpp
+++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/Filter/mitkFloatingImageToUltrasoundRegistrationFilter.cpp
@@ -1,205 +1,205 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "mitkFloatingImageToUltrasoundRegistrationFilter.h"
#include <itkScalableAffineTransform.h>
#include <itkScalableAffineTransform.hxx>
mitk::FloatingImageToUltrasoundRegistrationFilter::FloatingImageToUltrasoundRegistrationFilter()
: mitk::NavigationDataPassThroughFilter(),
m_Segmentation(nullptr),
m_TransformMarkerCSToSensorCS(mitk::AffineTransform3D::New()),
m_TransformMarkerCSToFloatingImageCS(mitk::AffineTransform3D::New()),
m_TransformUSimageCSToTrackingCS(mitk::AffineTransform3D::New()),
m_TransformCTimageIndexToWorld(mitk::AffineTransform3D::New()),
m_TrackedUltrasoundActive(false)
{
m_SurfaceGeometry = mitk::Geometry3D::New();
m_PointSet = nullptr;
m_CTimage = mitk::Image::New();
}
mitk::FloatingImageToUltrasoundRegistrationFilter::~FloatingImageToUltrasoundRegistrationFilter()
{
}
void mitk::FloatingImageToUltrasoundRegistrationFilter::InitializeTransformationMarkerCSToSensorCS( bool useNdiTracker)
{
//The following calculations are related to the 3mm | 15mm fiducial configuration
m_TransformMarkerCSToSensorCS = mitk::AffineTransform3D::New();
if (useNdiTracker) // Use the NDI disc tracker for performing the CT-to-US registration:
{
MITK_INFO << "Use NDI disc tracker for performing the CT-to-US-registration";
mitk::Vector3D translationNDI;
translationNDI[0] = 15.000;
translationNDI[1] = 8.000;
translationNDI[2] = -2.500; // use -2.500 instead of 0.000 for the z translation if working with v2 of the
// sensor adapter.
m_TransformMarkerCSToSensorCS->SetOffset(translationNDI);
// Quaternion (x, y, z, r) --> n = (0,0,1) --> q(0,0,sin(90�),cos(90�))
mitk::Quaternion qNDI(0, 0, 1, 0); // corresponding to a rotation of 180� around the normal z-axis.
// .transpose() is needed for changing the rows and the columns of the returned rotation_matrix_transpose
vnl_matrix_fixed<double, 3, 3> vnl_rotation = qNDI.rotation_matrix_transpose().transpose(); // :-)
mitk::Matrix3D rotationMatrix;
for (int i = 0; i < 3; ++i) {
for (int j = 0; j < 3; ++j) {
rotationMatrix[i][j] = vnl_rotation[i][j];
}
}
m_TransformMarkerCSToSensorCS->SetMatrix(rotationMatrix);
}
else // Use the polhemus RX2 tracker for performing the CT-to-US registration:
{
MITK_INFO << "Use Polhemus RX2 tracker for performing the CT-to-US-registration";
mitk::Vector3D translationPolhemus;
translationPolhemus[0] = -18.175;
translationPolhemus[1] = 15.000;
translationPolhemus[2] = 10.501; // considering a distance from the base plate of 0.315 inch and not 0.313 inch
// use 10.501 instead of 8.001 for the z translation if working with v2 of the
// sensor adapter.
m_TransformMarkerCSToSensorCS->SetOffset(translationPolhemus);
// Quaternion (x, y, z, r) --> n = (1,0,0) --> q(sin(90�),0,0,cos(90�))
mitk::Quaternion q1(1, 0, 0, 0); // corresponding to a rotation of 180� around the normal x-axis.
// .transpose() is needed for changing the rows and the columns of the returned rotation_matrix_transpose
vnl_matrix_fixed<double, 3, 3> vnl_rotation = q1.rotation_matrix_transpose().transpose(); // :-)
mitk::Matrix3D rotationMatrix;
for (int i = 0; i < 3; ++i) {
for (int j = 0; j < 3; ++j) {
rotationMatrix[i][j] = vnl_rotation[i][j];
}
}
m_TransformMarkerCSToSensorCS->SetMatrix(rotationMatrix);
}
//The transformation from the sensor-CS to the marker-CS is calculated now.
}
void mitk::FloatingImageToUltrasoundRegistrationFilter::SetSegmentation(mitk::DataNode::Pointer segmentationNode, mitk::Image::Pointer ctimage)
{
m_Segmentation = segmentationNode;
m_TransformCTimageIndexToWorld = m_Segmentation->GetData()->GetGeometry()->GetIndexToWorldTransform();
m_CTimage = ctimage;
}
void mitk::FloatingImageToUltrasoundRegistrationFilter::SetSurface(mitk::DataNode::Pointer surfaceNode)
{
m_Surface = surfaceNode;
m_SurfaceGeometry = m_Surface->GetData()->GetGeometry();
}
void mitk::FloatingImageToUltrasoundRegistrationFilter::SetPointSet(mitk::DataNode::Pointer pointSetNode)
{
m_PointSet = pointSetNode;
}
void mitk::FloatingImageToUltrasoundRegistrationFilter::SetTransformMarkerCSToFloatingImageCS(mitk::AffineTransform3D::Pointer transform)
{
m_TransformMarkerCSToFloatingImageCS = transform;
}
void mitk::FloatingImageToUltrasoundRegistrationFilter::SetTransformUSimageCSToTrackingCS(mitk::AffineTransform3D::Pointer transform)
{
m_TransformUSimageCSToTrackingCS = transform;
}
void mitk::FloatingImageToUltrasoundRegistrationFilter::GenerateData()
{
Superclass::GenerateData();
if (m_TrackedUltrasoundActive)
{
MITK_WARN << "The CT-to-US-registration is not supported by tracked ultrasound, yet.";
return;
}
- //IMPORTANT --- Hard coded --- First device = EM-Sensor | eventually second device = needle
- mitk::NavigationData::Pointer transformSensorCSToTracking = this->GetOutput(0);
+ //IMPORTANT --- Hard coded --- second tool = ct marker / sensor | eventually first tool = needle
+ mitk::NavigationData::Pointer transformSensorCSToTracking = this->GetOutput(1);
// cancel, if the EM-sensor is currently not being tracked
if (!transformSensorCSToTracking->IsDataValid())
{
return;
}
//We start the transformation with a new transform:
mitk::AffineTransform3D::Pointer totalTransformation = mitk::AffineTransform3D::New();
totalTransformation->SetIdentity();
//Compose it with the inverse transform of marker-CS to floating image-CS:
MITK_INFO << "Marker-to-CT Transform:" << m_TransformMarkerCSToFloatingImageCS;
totalTransformation->Compose(this->GetInverseTransform(m_TransformMarkerCSToFloatingImageCS)); //CT->Marker
MITK_INFO << "CT-to-Marker Transform:" << totalTransformation;
MITK_INFO << "Marker-to-Sensor Transform:" << m_TransformMarkerCSToSensorCS;
//Compose this with the inverse transform of EM-sensor-CS to marker-CS:
totalTransformation->Compose(m_TransformMarkerCSToSensorCS); //CT->Marker(Marker->Sensor) => CT->Sensor
MITK_INFO << "CT-to-Sensor Transform:" << totalTransformation;
//Compose this with the transform of the sensor-CS to Tracking-CS:
totalTransformation->Compose(transformSensorCSToTracking->GetAffineTransform3D());
//Compose this with the inverse transform of USimage-CS to tracking-CS:
totalTransformation->Modified();
//Finally, set the total transformation (from floatingImage-CS to US-image-CS
// to the selected floatingImageSurface:
//m_Segmentation->GetData()->GetGeometry()->SetIndexToWorldTransform(totalTransformation);
//m_Segmentation->Modified();
//m_CTimage->GetGeometry()->SetIndexToWorldTransform(totalTransformation);
//m_CTimage->Modified();
m_Surface->GetData()->GetGeometry()->SetIndexToWorldTransform(totalTransformation);
m_Surface->Modified();
m_PointSet->GetData()->GetGeometry()->SetIndexToWorldTransform(totalTransformation);
m_PointSet->Modified();
for (mitk::DataNode::Pointer node : m_additionalSurfaces) {
node->GetData()->GetGeometry()->SetIndexToWorldTransform(totalTransformation);
node->Modified();
}
}
void mitk::FloatingImageToUltrasoundRegistrationFilter::AddAdditionalSurface(mitk::DataNode::Pointer newSurfaceNode) {
m_additionalSurfaces.push_back(newSurfaceNode);
}
mitk::AffineTransform3D::Pointer mitk::FloatingImageToUltrasoundRegistrationFilter::GetInverseTransform(mitk::AffineTransform3D::Pointer transform)
{
mitk::AffineTransform3D::Pointer inverseTransform = mitk::AffineTransform3D::New();
mitk::AffineTransform3D::Pointer inverse = dynamic_cast<mitk::AffineTransform3D*>(transform->GetInverseTransform().GetPointer());
//itk::SmartPointer<itk::ScalableAffineTransform<mitk::ScalarType, 3U>> inverse = dynamic_cast<itk::ScalableAffineTransform<mitk::ScalarType, 3U>*> (transform->GetInverseTransform().GetPointer()); //itkScalableAffineTransform_hxx
if (inverse.IsNull())
{
MITK_WARN << "Could not get inverse transform of mitk::AffineTransform3D. Returning nullptr";
return nullptr;
}
inverseTransform->SetOffset(inverse->GetOffset());
inverseTransform->SetMatrix(inverse->GetMatrix());
return inverseTransform;
}