diff --git a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp
index cecea6c795..7d4e9270c9 100644
--- a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp
+++ b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp
@@ -1,989 +1,991 @@
/*============================================================================
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 <mitkSurfaceInterpolationController.h>
#include <mitkCreateDistanceImageFromSurfaceFilter.h>
#include <mitkComputeContourSetNormalsFilter.h>
#include <mitkImageAccessByItk.h>
#include <mitkImagePixelReadAccessor.h>
#include <mitkImageTimeSelector.h>
#include <mitkImageToSurfaceFilter.h>
#include <mitkLabelSetImage.h>
#include <mitkMemoryUtilities.h>
#include <mitkNodePredicateDataUID.h>
#include <mitkNodePredicateProperty.h>
#include <mitkPlanarCircle.h>
#include <mitkPlaneGeometry.h>
#include <mitkReduceContourSetFilter.h>
#include <vtkFieldData.h>
#include <vtkMath.h>
#include <vtkPolygon.h>
// Check whether the given contours are coplanar
bool ContoursCoplanar(mitk::SurfaceInterpolationController::ContourPositionInformation leftHandSide,
mitk::SurfaceInterpolationController::ContourPositionInformation rightHandSide)
{
// Here we check two things:
// 1. Whether the normals of both contours are at least parallel
// 2. Whether both contours lie in the same plane
// Check for coplanarity:
// a. Span a vector between two points one from each contour
// b. Calculate dot product for the vector and one of the normals
// c. If the dot is zero the two vectors are orthogonal and the contours are coplanar
double vec[3];
vec[0] = leftHandSide.ContourPoint[0] - rightHandSide.ContourPoint[0];
vec[1] = leftHandSide.ContourPoint[1] - rightHandSide.ContourPoint[1];
vec[2] = leftHandSide.ContourPoint[2] - rightHandSide.ContourPoint[2];
double n[3];
n[0] = rightHandSide.ContourNormal[0];
n[1] = rightHandSide.ContourNormal[1];
n[2] = rightHandSide.ContourNormal[2];
double dot = vtkMath::Dot(n, vec);
double n2[3];
n2[0] = leftHandSide.ContourNormal[0];
n2[1] = leftHandSide.ContourNormal[1];
n2[2] = leftHandSide.ContourNormal[2];
// The normals of both contours have to be parallel but not of the same orientation
double lengthLHS = leftHandSide.ContourNormal.GetNorm();
double lengthRHS = rightHandSide.ContourNormal.GetNorm();
double dot2 = vtkMath::Dot(n, n2);
bool contoursParallel = mitk::Equal(fabs(lengthLHS * lengthRHS), fabs(dot2), 0.001);
if (mitk::Equal(dot, 0.0, 0.001) && contoursParallel)
return true;
else
return false;
}
mitk::SurfaceInterpolationController::ContourPositionInformation CreateContourPositionInformation(
const mitk::Surface* contour, const mitk::PlaneGeometry* planeGeometry)
{
mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
contourInfo.Contour = contour;
mitk::ScalarType n[3];
vtkPolygon::ComputeNormal(contour->GetVtkPolyData()->GetPoints(), n);
contourInfo.ContourNormal = n;
contourInfo.Pos = -1;
contourInfo.TimeStep = std::numeric_limits<long unsigned int>::max();
contourInfo.Plane = planeGeometry;
auto contourIntArray = vtkIntArray::SafeDownCast( contour->GetVtkPolyData()->GetFieldData()->GetAbstractArray(0) );
if (contourIntArray->GetSize() < 2)
{
MITK_ERROR << "In CreateContourPositionInformation. The contourIntArray is empty.";
}
contourInfo.LabelValue = contourIntArray->GetValue(0);
if (contourIntArray->GetSize() >= 3)
{
contourInfo.TimeStep = contourIntArray->GetValue(2);
}
return contourInfo;
};
mitk::SurfaceInterpolationController::SurfaceInterpolationController()
: m_SelectedSegmentation(nullptr),
- m_CurrentTimePoint(0.),
- m_ContourPosIndex(0)
+ m_CurrentTimePoint(0.)
{
m_DistanceImageSpacing = 0.0;
m_ReduceFilter = ReduceContourSetFilter::New();
m_NormalsFilter = ComputeContourSetNormalsFilter::New();
m_InterpolateSurfaceFilter = CreateDistanceImageFromSurfaceFilter::New();
m_ReduceFilter->SetUseProgressBar(false);
// m_ReduceFilter->SetProgressStepSize(1);
m_NormalsFilter->SetUseProgressBar(true);
m_NormalsFilter->SetProgressStepSize(1);
m_InterpolateSurfaceFilter->SetUseProgressBar(true);
m_InterpolateSurfaceFilter->SetProgressStepSize(7);
m_Contours = Surface::New();
- m_PolyData = vtkSmartPointer<vtkPolyData>::New();
- vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
- m_PolyData->SetPoints(points);
-
m_InterpolationResult = nullptr;
m_CurrentNumberOfReducedContours = 0;
}
mitk::SurfaceInterpolationController::~SurfaceInterpolationController()
{
this->RemoveObservers();
}
void mitk::SurfaceInterpolationController::RemoveObservers()
{
// Removing all observers
auto dataIter = m_SegmentationObserverTags.begin();
for (; dataIter != m_SegmentationObserverTags.end(); ++dataIter)
{
(*dataIter).first->RemoveObserver((*dataIter).second);
}
m_SegmentationObserverTags.clear();
- if (m_SelectedSegmentation.IsNotNull())
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNotNull())
{
- m_SelectedSegmentation->RemoveLabelRemovedListener(mitk::MessageDelegate1<SurfaceInterpolationController, mitk::LabelSetImage::LabelValueType>(
+ selectedSegmentation->RemoveLabelRemovedListener(mitk::MessageDelegate1<SurfaceInterpolationController, mitk::LabelSetImage::LabelValueType>(
this, &SurfaceInterpolationController::OnRemoveLabel));
}
}
mitk::SurfaceInterpolationController *mitk::SurfaceInterpolationController::GetInstance()
{
static mitk::SurfaceInterpolationController::Pointer m_Instance;
if (m_Instance.IsNull())
{
m_Instance = SurfaceInterpolationController::New();
}
return m_Instance;
}
void mitk::SurfaceInterpolationController::AddNewContour(mitk::Surface::Pointer newContour)
{
if (newContour->GetVtkPolyData()->GetNumberOfPoints() > 0)
{
ContourPositionInformation contourInfo = CreateContourPositionInformation(newContour, nullptr);
this->AddToInterpolationPipeline(contourInfo);
this->Modified();
}
}
void mitk::SurfaceInterpolationController::AddNewContours(const std::vector<mitk::Surface::Pointer>& newContours,
std::vector<const mitk::PlaneGeometry*>& contourPlanes,
bool reinitializationAction)
{
- if (nullptr == m_SelectedSegmentation) return;
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull()) return;
if (newContours.size() != contourPlanes.size())
{
MITK_ERROR << "SurfaceInterpolationController::AddNewContours. contourPlanes and newContours are not of the same size.";
}
for (size_t i = 0; i < newContours.size(); ++i)
{
const auto &newContour = newContours[i];
const mitk::PlaneGeometry * planeGeometry = contourPlanes[i];
if (newContour->GetVtkPolyData()->GetNumberOfPoints() > 0)
{
auto contourInfo = CreateContourPositionInformation(newContour, planeGeometry);
if (!reinitializationAction)
{
- contourInfo.ContourPoint = this->ComputeInteriorPointOfContour(contourInfo, m_SelectedSegmentation);
+ contourInfo.ContourPoint = this->ComputeInteriorPointOfContour(contourInfo, selectedSegmentation);
}
else
{
auto vtkPolyData = contourInfo.Contour->GetVtkPolyData();
auto pointVtkArray = vtkDoubleArray::SafeDownCast(vtkPolyData->GetFieldData()->GetAbstractArray(1));
mitk::ScalarType *ptArr = new mitk::ScalarType[3];
for (int i = 0; i < pointVtkArray->GetSize(); ++i)
ptArr[i] = pointVtkArray->GetValue(i);
mitk::Point3D pt3D;
pt3D.FillPoint(ptArr);
contourInfo.ContourPoint = pt3D;
}
this->AddToInterpolationPipeline(contourInfo, reinitializationAction);
}
}
this->Modified();
}
mitk::DataNode* mitk::SurfaceInterpolationController::GetSegmentationImageNode()
{
if (m_DataStorage.IsNull()) return nullptr;
- if (m_SelectedSegmentation.IsNull()) return nullptr;
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull()) return nullptr;
DataNode* segmentationNode = nullptr;
- mitk::NodePredicateDataUID::Pointer dataUIDPredicate = mitk::NodePredicateDataUID::New(m_SelectedSegmentation->GetUID());
+ mitk::NodePredicateDataUID::Pointer dataUIDPredicate = mitk::NodePredicateDataUID::New(selectedSegmentation->GetUID());
auto dataNodeObjects = m_DataStorage->GetSubset(dataUIDPredicate);
if (dataNodeObjects->Size() != 0)
{
for (auto it = dataNodeObjects->Begin(); it != dataNodeObjects->End(); ++it)
{
segmentationNode = it->Value();
}
}
else
{
MITK_ERROR << "Unable to find the labelSetImage with the desired UID.";
}
return segmentationNode;
}
void mitk::SurfaceInterpolationController::AddPlaneGeometryNodeToDataStorage(const ContourPositionInformation& contourInfo)
{
- if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull())
+ {
+ mitkThrow()<< "Cannot add plane geometries. No valid segmentation selected.";
+ }
+
+ if (!selectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
{
MITK_ERROR << "Invalid time point requested in AddPlaneGeometryNodeToDataStorage.";
return;
}
auto planeGeometry = contourInfo.Plane;
if (planeGeometry)
{
auto planeGeometryData = mitk::PlanarCircle::New();
planeGeometryData->SetPlaneGeometry(planeGeometry->Clone());
mitk::Point2D p1;
planeGeometry->Map(planeGeometry->GetCenter(), p1);
planeGeometryData->PlaceFigure(p1);
planeGeometryData->SetCurrentControlPoint(p1);
planeGeometryData->SetProperty("initiallyplaced", mitk::BoolProperty::New(true));
auto segmentationNode = this->GetSegmentationImageNode();
auto isContourPlaneGeometry = mitk::NodePredicateProperty::New("isContourPlaneGeometry", mitk::BoolProperty::New(true));
mitk::DataStorage::SetOfObjects::ConstPointer contourNodes =
m_DataStorage->GetDerivations(segmentationNode, isContourPlaneGeometry);
mitk::DataNode::Pointer contourPlaneGeometryDataNode;
// Go through the pre-existing contours and check if the contour position matches them.
for (auto it = contourNodes->Begin(); it != contourNodes->End(); ++it)
{
auto labelID = dynamic_cast<mitk::UShortProperty *>(it->Value()->GetProperty("labelID"))->GetValue();
auto posID = dynamic_cast<mitk::IntProperty *>(it->Value()->GetProperty("position"))->GetValue();
bool sameLabel = (labelID == contourInfo.LabelValue);
bool samePos = (posID == contourInfo.Pos);
if (samePos && sameLabel)
{
contourPlaneGeometryDataNode = it->Value();
break;
}
}
// Go through the contourPlaneGeometry Data and add the segmentationNode to it.
if (contourPlaneGeometryDataNode.IsNull())
{
- const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
+ const auto currentTimeStep = selectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
std::string contourName = "contourPlane T " + std::to_string(currentTimeStep) + " L " + std::to_string(contourInfo.LabelValue) + "P " + std::to_string(contourInfo.Pos);
contourPlaneGeometryDataNode = mitk::DataNode::New();
contourPlaneGeometryDataNode->SetData(planeGeometryData);
// No need to change properties
contourPlaneGeometryDataNode->SetProperty("helper object", mitk::BoolProperty::New(false));
contourPlaneGeometryDataNode->SetProperty("hidden object", mitk::BoolProperty::New(true));
contourPlaneGeometryDataNode->SetProperty("isContourPlaneGeometry", mitk::BoolProperty::New(true));
contourPlaneGeometryDataNode->SetVisibility(false);
// Need to change properties
contourPlaneGeometryDataNode->SetProperty("name", mitk::StringProperty::New(contourName) );
contourPlaneGeometryDataNode->SetProperty("labelID", mitk::UShortProperty::New(contourInfo.LabelValue));
contourPlaneGeometryDataNode->SetProperty("position", mitk::IntProperty::New(contourInfo.Pos));
contourPlaneGeometryDataNode->SetProperty("timeStep", mitk::IntProperty::New(currentTimeStep));
contourPlaneGeometryDataNode->SetProperty("px", mitk::DoubleProperty::New(contourInfo.ContourPoint[0]));
contourPlaneGeometryDataNode->SetProperty("py", mitk::DoubleProperty::New(contourInfo.ContourPoint[1]));
contourPlaneGeometryDataNode->SetProperty("pz", mitk::DoubleProperty::New(contourInfo.ContourPoint[2]));
m_DataStorage->Add(contourPlaneGeometryDataNode, segmentationNode);
}
contourPlaneGeometryDataNode->SetData(planeGeometryData);
}
}
void mitk::SurfaceInterpolationController::AddToInterpolationPipeline(ContourPositionInformation& contourInfo, bool reinitializationAction)
{
- if (m_SelectedSegmentation.IsNull())
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull())
return;
- if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
+ if (!selectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
{
MITK_ERROR << "Invalid time point requested for interpolation pipeline.";
return;
}
if (contourInfo.Plane == nullptr)
{
MITK_ERROR << "contourInfo plane is null.";
return;
}
if (contourInfo.Contour->GetVtkPolyData()->GetNumberOfPoints() == 0)
{
this->RemoveContour(contourInfo);
MITK_DEBUG << "contourInfo contour is empty.";
return;
}
- const auto currentTimeStep = reinitializationAction ? contourInfo.TimeStep : m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
+ const auto currentTimeStep = reinitializationAction ? contourInfo.TimeStep : selectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
- const auto currentLabelValue = reinitializationAction ? contourInfo.LabelValue : m_SelectedSegmentation->GetActiveLabel()->GetValue();
+ const auto currentLabelValue = reinitializationAction ? contourInfo.LabelValue : selectedSegmentation->GetActiveLabel()->GetValue();
- auto& currentImageContours = m_CPIMap[m_SelectedSegmentation];
+ auto& currentImageContours = m_CPIMap[selectedSegmentation];
auto& currentLabelContours = currentImageContours[currentLabelValue];
auto& currentContourList = currentLabelContours[currentTimeStep];
auto finding = std::find_if(currentContourList.begin(), currentContourList.end(), [contourInfo](const ContourPositionInformation& element) {return ContoursCoplanar(contourInfo, element); });
if (finding != currentContourList.end())
{
contourInfo.Pos = finding->Pos;
*finding = contourInfo;
}
else
{
contourInfo.Pos = currentContourList.size();
currentContourList.push_back(contourInfo);
}
if (!reinitializationAction)
{
this->AddPlaneGeometryNodeToDataStorage(contourInfo);
}
}
bool mitk::SurfaceInterpolationController::RemoveContour(ContourPositionInformation contourInfo)
{
- if (!m_SelectedSegmentation)
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull())
{
return false;
}
- if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
+ if (!selectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
{
return false;
}
- const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
- const auto currentLabel = m_SelectedSegmentation->GetActiveLabel()->GetValue();
- auto it = m_CPIMap.at(m_SelectedSegmentation).at(currentLabel).at(currentTimeStep).begin();
+ const auto currentTimeStep = selectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
+ const auto currentLabel = selectedSegmentation->GetActiveLabel()->GetValue();
+ auto it = m_CPIMap.at(selectedSegmentation).at(currentLabel).at(currentTimeStep).begin();
- while (it != m_CPIMap.at(m_SelectedSegmentation).at(currentLabel).at(currentTimeStep).end())
+ while (it != m_CPIMap.at(selectedSegmentation).at(currentLabel).at(currentTimeStep).end())
{
const ContourPositionInformation ¤tContour = (*it);
if (ContoursCoplanar(currentContour, contourInfo))
{
- m_CPIMap.at(m_SelectedSegmentation).at(currentLabel).at(currentTimeStep).erase(it);
+ m_CPIMap.at(selectedSegmentation).at(currentLabel).at(currentTimeStep).erase(it);
this->ReinitializeInterpolation();
return true;
}
++it;
}
return false;
}
-const mitk::Surface *mitk::SurfaceInterpolationController::GetContour(const ContourPositionInformation &contourInfo)
+void mitk::SurfaceInterpolationController::AddActiveLabelContoursForInterpolation(mitk::Label::PixelType activeLabel)
{
- if (!m_SelectedSegmentation)
- {
- return nullptr;
- }
+ this->ReinitializeInterpolation();
- if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull())
{
- return nullptr;
+ mitkThrow() << "Cannot add active label contours. No valid segmentation selected.";
}
- const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
- const auto currentLabel = m_SelectedSegmentation->GetActiveLabel()->GetValue();
- const auto &contourList = m_CPIMap.at(m_SelectedSegmentation).at(currentLabel).at(currentTimeStep);
- for (auto ¤tContour : contourList)
+ if (!selectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
{
- if (ContoursCoplanar(contourInfo, currentContour))
- {
- return currentContour.Contour;
- }
+ MITK_ERROR << "Invalid time point requested for interpolation pipeline.";
+ return;
}
- return nullptr;
-}
-
-//unsigned int mitk::SurfaceInterpolationController::GetNumberOfContours()
-//{
-// if (!m_SelectedSegmentation)
-// {
-// return -1;
-// }
-//
-// if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
-// {
-// return -1;
-// }
-// const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
-// auto contourDoubleList = m_CPIMap.at(m_SelectedSegmentation).at(currentTimeStep);
-//
-// unsigned int numContours = 0;
-// for (auto& contourList : contourDoubleList)
-// {
-//
-// numContours += contourList.size();
-// }
-//
-// return numContours;
-//}
-void mitk::SurfaceInterpolationController::AddActiveLabelContoursForInterpolation(mitk::Label::PixelType activeLabel)
-{
- this->ReinitializeInterpolation();
-
- if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
+ if (!selectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
{
MITK_ERROR << "Invalid time point requested for interpolation pipeline.";
return;
}
- const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
+ const auto currentTimeStep = selectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
- auto& currentImageContours = m_CPIMap.at(m_SelectedSegmentation);
+ auto& currentImageContours = m_CPIMap.at(selectedSegmentation);
auto finding = currentImageContours.find(activeLabel);
if (finding == currentImageContours.end())
{
MITK_INFO << "Contours for label don't exist. Label value: " << activeLabel;
return;
}
auto currentLabelContoursMap = finding->second;
auto tsfinding = currentLabelContoursMap.find(currentTimeStep);
if (tsfinding == currentLabelContoursMap.end())
{
MITK_INFO << "Contours for current time step don't exist.";
return;
}
CPIVector& currentContours = tsfinding->second;
unsigned int index = 0;
m_ReduceFilter->Reset();
for (const auto& cpi : currentContours)
{
m_ReduceFilter->SetInput(index, cpi.Contour);
++index;
}
}
void mitk::SurfaceInterpolationController::Interpolate()
{
- if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull())
+ {
+ mitkThrow() << "Cannot interpolate. No valid segmentation selected.";
+ }
+
+ if (!selectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
{
MITK_WARN << "No interpolation possible, currently selected timepoint is not in the time bounds of currently selected segmentation. Time point: " << m_CurrentTimePoint;
m_InterpolationResult = nullptr;
return;
}
- const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
+ const auto currentTimeStep = selectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
m_ReduceFilter->Update();
m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs();
if (m_CurrentNumberOfReducedContours == 1)
{
vtkPolyData *tmp = m_ReduceFilter->GetOutput(0)->GetVtkPolyData();
if (tmp == nullptr)
{
m_CurrentNumberOfReducedContours = 0;
}
}
// We use the timeSelector to get the segmentation image for the current segmentation.
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
- timeSelector->SetInput(m_SelectedSegmentation);
+ timeSelector->SetInput(selectedSegmentation);
timeSelector->SetTimeNr(currentTimeStep);
timeSelector->SetChannelNr(0);
timeSelector->Update();
mitk::Image::Pointer refSegImage = timeSelector->GetOutput();
itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New();
AccessFixedDimensionByItk_1(refSegImage, GetImageBase, 3, itkImage);
m_NormalsFilter->SetSegmentationBinaryImage(refSegImage);
for (size_t i = 0; i < m_CurrentNumberOfReducedContours; ++i)
{
mitk::Surface::Pointer reducedContour = m_ReduceFilter->GetOutput(i);
reducedContour->DisconnectPipeline();
m_NormalsFilter->SetInput(i, reducedContour);
m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i));
}
if (m_CurrentNumberOfReducedContours < 2)
{
// If no interpolation is possible reset the interpolation result
MITK_INFO << "Interpolation impossible: not enough contours.";
m_InterpolationResult = nullptr;
return;
}
// Setting up progress bar
mitk::ProgressBar::GetInstance()->AddStepsToDo(10);
// create a surface from the distance-image
mitk::ImageToSurfaceFilter::Pointer imageToSurfaceFilter = mitk::ImageToSurfaceFilter::New();
imageToSurfaceFilter->SetInput(m_InterpolateSurfaceFilter->GetOutput());
imageToSurfaceFilter->SetThreshold(0);
imageToSurfaceFilter->SetSmooth(true);
imageToSurfaceFilter->SetSmoothIteration(1);
imageToSurfaceFilter->Update();
mitk::Surface::Pointer interpolationResult = mitk::Surface::New();
- interpolationResult->Expand(m_SelectedSegmentation->GetTimeSteps());
+ interpolationResult->Expand(selectedSegmentation->GetTimeSteps());
- auto geometry = m_SelectedSegmentation->GetTimeGeometry()->Clone();
+ auto geometry = selectedSegmentation->GetTimeGeometry()->Clone();
geometry->ReplaceTimeStepGeometries(mitk::Geometry3D::New());
interpolationResult->SetTimeGeometry(geometry);
interpolationResult->SetVtkPolyData(imageToSurfaceFilter->GetOutput()->GetVtkPolyData(), currentTimeStep);
m_InterpolationResult = interpolationResult;
m_DistanceImageSpacing = m_InterpolateSurfaceFilter->GetDistanceImageSpacing();
auto* contoursGeometry = static_cast<mitk::ProportionalTimeGeometry*>(m_Contours->GetTimeGeometry());
auto timeBounds = geometry->GetTimeBounds(currentTimeStep);
contoursGeometry->SetFirstTimePoint(timeBounds[0]);
contoursGeometry->SetStepDuration(timeBounds[1] - timeBounds[0]);
// Last progress step
mitk::ProgressBar::GetInstance()->Progress(20);
m_InterpolationResult->DisconnectPipeline();
}
mitk::Surface::Pointer mitk::SurfaceInterpolationController::GetInterpolationResult()
{
return m_InterpolationResult;
}
mitk::Surface *mitk::SurfaceInterpolationController::GetContoursAsSurface()
{
return m_Contours;
}
void mitk::SurfaceInterpolationController::SetDataStorage(DataStorage::Pointer ds)
{
m_DataStorage = ds;
}
void mitk::SurfaceInterpolationController::SetMinSpacing(double minSpacing)
{
m_ReduceFilter->SetMinSpacing(minSpacing);
}
void mitk::SurfaceInterpolationController::SetMaxSpacing(double maxSpacing)
{
m_ReduceFilter->SetMaxSpacing(maxSpacing);
m_NormalsFilter->SetMaxSpacing(maxSpacing);
}
void mitk::SurfaceInterpolationController::SetDistanceImageVolume(unsigned int distImgVolume)
{
m_InterpolateSurfaceFilter->SetDistanceImageVolume(distImgVolume);
}
mitk::LabelSetImage* mitk::SurfaceInterpolationController::GetCurrentSegmentation()
{
- return m_SelectedSegmentation;
+ return m_SelectedSegmentation.Lock();
}
mitk::Image *mitk::SurfaceInterpolationController::GetInterpolationImage()
{
return m_InterpolateSurfaceFilter->GetOutput();
}
double mitk::SurfaceInterpolationController::EstimatePortionOfNeededMemory()
{
double numberOfPointsAfterReduction = m_ReduceFilter->GetNumberOfPointsAfterReduction() * 3;
double sizeOfPoints = pow(numberOfPointsAfterReduction, 2) * sizeof(double);
double totalMem = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam();
double percentage = sizeOfPoints / totalMem;
return percentage;
}
unsigned int mitk::SurfaceInterpolationController::GetNumberOfInterpolationSessions()
{
return m_CPIMap.size();
}
template <typename TPixel, unsigned int VImageDimension>
void mitk::SurfaceInterpolationController::GetImageBase(itk::Image<TPixel, VImageDimension> *input,
itk::ImageBase<3>::Pointer &result)
{
result->Graft(input);
}
void mitk::SurfaceInterpolationController::SetCurrentInterpolationSession(mitk::LabelSetImage* currentSegmentationImage)
{
- if (currentSegmentationImage == m_SelectedSegmentation)
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+
+ if (currentSegmentationImage == selectedSegmentation)
{
return;
}
- if (m_SelectedSegmentation.IsNotNull())
+ if (selectedSegmentation.IsNotNull())
{
- m_SelectedSegmentation->RemoveLabelRemovedListener(mitk::MessageDelegate1<SurfaceInterpolationController, mitk::LabelSetImage::LabelValueType>(
+ selectedSegmentation->RemoveLabelRemovedListener(mitk::MessageDelegate1<SurfaceInterpolationController, mitk::LabelSetImage::LabelValueType>(
this, &SurfaceInterpolationController::OnRemoveLabel));
}
m_SelectedSegmentation = currentSegmentationImage;
+ selectedSegmentation = m_SelectedSegmentation.Lock();
- if (m_SelectedSegmentation.IsNotNull())
+ if (selectedSegmentation.IsNotNull())
{
- auto it = m_CPIMap.find(currentSegmentationImage);
+ auto it = m_CPIMap.find(selectedSegmentation);
if (it == m_CPIMap.end())
{
- m_CPIMap[m_SelectedSegmentation] = CPITimeStepLabelMap();
+ m_CPIMap[selectedSegmentation] = CPITimeStepLabelMap();
auto command = itk::MemberCommand<SurfaceInterpolationController>::New();
command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted);
- m_SegmentationObserverTags[m_SelectedSegmentation] = m_SelectedSegmentation->AddObserver(itk::DeleteEvent(), command);
+ m_SegmentationObserverTags[selectedSegmentation] = selectedSegmentation->AddObserver(itk::DeleteEvent(), command);
}
- m_SelectedSegmentation->AddLabelRemovedListener(mitk::MessageDelegate1<SurfaceInterpolationController, mitk::LabelSetImage::LabelValueType>(
+ selectedSegmentation->AddLabelRemovedListener(mitk::MessageDelegate1<SurfaceInterpolationController, mitk::LabelSetImage::LabelValueType>(
this, &SurfaceInterpolationController::OnRemoveLabel));
}
m_InterpolationResult = nullptr;
m_CurrentNumberOfReducedContours = 0;
m_NormalsFilter->SetSegmentationBinaryImage(nullptr);
this->ReinitializeInterpolation();
}
void mitk::SurfaceInterpolationController::RemoveInterpolationSession(mitk::LabelSetImage* segmentationImage)
{
- if (nullptr == segmentationImage)
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+
+ if (nullptr != segmentationImage)
{
- if (m_SelectedSegmentation == segmentationImage)
+ if (selectedSegmentation == segmentationImage)
{
- m_SelectedSegmentation->RemoveLabelRemovedListener(mitk::MessageDelegate1<SurfaceInterpolationController, mitk::LabelSetImage::LabelValueType>(
+ selectedSegmentation->RemoveLabelRemovedListener(mitk::MessageDelegate1<SurfaceInterpolationController, mitk::LabelSetImage::LabelValueType>(
this, &SurfaceInterpolationController::OnRemoveLabel));
m_NormalsFilter->SetSegmentationBinaryImage(nullptr);
m_SelectedSegmentation = nullptr;
}
m_CPIMap.erase(segmentationImage);
// Remove observer
auto pos = m_SegmentationObserverTags.find(segmentationImage);
if (pos != m_SegmentationObserverTags.end())
{
segmentationImage->RemoveObserver((*pos).second);
m_SegmentationObserverTags.erase(pos);
}
}
}
void mitk::SurfaceInterpolationController::RemoveAllInterpolationSessions()
{
this->RemoveObservers();
m_NormalsFilter->SetSegmentationBinaryImage(nullptr);
m_SelectedSegmentation = nullptr;
m_CPIMap.clear();
}
void mitk::SurfaceInterpolationController::RemoveContours(mitk::Label::PixelType label,
TimeStepType timeStep)
{
- auto cpiLabelMap = m_CPIMap[m_SelectedSegmentation];
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull())
+ {
+ mitkThrow() << "Cannot remove contours. No valid segmentation selected.";
+ }
+
+ auto cpiLabelMap = m_CPIMap[selectedSegmentation];
auto finding = cpiLabelMap.find(label);
if (finding != cpiLabelMap.end())
{
finding->second.erase(timeStep);
}
}
void mitk::SurfaceInterpolationController::RemoveContours(mitk::Label::PixelType label)
{
- m_CPIMap[m_SelectedSegmentation].erase(label);
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+ if (selectedSegmentation.IsNull())
+ {
+ mitkThrow() << "Cannot remove contours. No valid segmentation selected.";
+ }
+
+ m_CPIMap[selectedSegmentation].erase(label);
}
void mitk::SurfaceInterpolationController::OnSegmentationDeleted(const itk::Object *caller,
const itk::EventObject & /*event*/)
{
auto *tempImage = dynamic_cast<mitk::LabelSetImage *>(const_cast<itk::Object *>(caller));
if (tempImage)
{
- if (m_SelectedSegmentation == tempImage)
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+
+ if (selectedSegmentation == tempImage)
{
this->SetCurrentInterpolationSession(nullptr);
}
m_SegmentationObserverTags.erase(tempImage);
m_CPIMap.erase(tempImage);
}
}
void mitk::SurfaceInterpolationController::ReinitializeInterpolation()
{
// If session has changed reset the pipeline
m_ReduceFilter->Reset();
m_NormalsFilter->Reset();
m_InterpolateSurfaceFilter->Reset();
itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New();
- if (m_SelectedSegmentation.IsNotNull())
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+
+ if (selectedSegmentation.IsNotNull())
{
- if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
+ if (!selectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint))
{
MITK_WARN << "Interpolation cannot be reinitialized. Currently selected timepoint is not in the time bounds of the currently selected segmentation. Time point: " << m_CurrentTimePoint;
return;
}
- const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
+ const auto currentTimeStep = selectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint);
// Set reference image for interpolation surface filter
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
- timeSelector->SetInput(m_SelectedSegmentation);
+ timeSelector->SetInput(selectedSegmentation);
timeSelector->SetTimeNr(currentTimeStep);
timeSelector->SetChannelNr(0);
timeSelector->Update();
mitk::Image::Pointer refSegImage = timeSelector->GetOutput();
AccessFixedDimensionByItk_1(refSegImage, GetImageBase, 3, itkImage);
m_InterpolateSurfaceFilter->SetReferenceImage(itkImage.GetPointer());
}
}
void mitk::SurfaceInterpolationController::OnRemoveLabel(mitk::Label::PixelType removedLabelValue)
{
- if (m_SelectedSegmentation.IsNotNull())
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+
+ if (selectedSegmentation.IsNotNull())
{
this->RemoveContours(removedLabelValue);
}
}
mitk::SurfaceInterpolationController::CPIVector* mitk::SurfaceInterpolationController::GetContours(TimeStepType timeStep, LabelSetImage::LabelValueType labelValue)
{
- if (m_SelectedSegmentation == nullptr)
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+
+ if (selectedSegmentation == nullptr)
return nullptr;
- auto labelFinding = m_CPIMap[m_SelectedSegmentation].find(labelValue);
+ auto labelFinding = m_CPIMap[selectedSegmentation].find(labelValue);
- if (labelFinding != m_CPIMap[m_SelectedSegmentation].end())
+ if (labelFinding != m_CPIMap[selectedSegmentation].end())
{
- auto tsFinding = labelFinding->second.find(labelValue);
+ auto tsFinding = labelFinding->second.find(timeStep);
if (tsFinding != labelFinding->second.end())
{
return &(tsFinding->second);
}
}
return nullptr;
}
void mitk::SurfaceInterpolationController::CompleteReinitialization(const std::vector<mitk::Surface::Pointer>& contourList,
std::vector<const mitk::PlaneGeometry *>& contourPlanes)
{
this->ClearInterpolationSession();
// Now the layers should be empty and the new layers can be added.
this->AddNewContours(contourList, contourPlanes, true);
}
void mitk::SurfaceInterpolationController::ClearInterpolationSession()
{
- if (m_SelectedSegmentation != nullptr)
+ auto selectedSegmentation = m_SelectedSegmentation.Lock();
+
+ if (selectedSegmentation != nullptr)
{
- m_CPIMap[m_SelectedSegmentation].clear();
+ m_CPIMap[selectedSegmentation].clear();
}
}
std::vector< mitk::Point3D > mitk::ContourExt::GetBoundingBoxGridPoints(
size_t planeDimension,
double startDim1,
size_t numPointsToSampleDim1,
double deltaDim1,
double startDim2,
size_t numPointsToSampleDim2,
double deltaDim2,
double valuePlaneDim)
{
std::vector< mitk::Point3D > gridPoints;
for (size_t i = 0; i < numPointsToSampleDim1; ++i)
{
for (size_t j = 0; j < numPointsToSampleDim2; ++j)
{
mitk::ScalarType *ptVec = new mitk::ScalarType[3];
if (planeDimension == 0)
{
ptVec[0] = valuePlaneDim;
ptVec[1] = startDim1 + deltaDim1 * i;
ptVec[2] = startDim2 + deltaDim2 * j;
}
else if (planeDimension == 1)
{
ptVec[0] = startDim1 + deltaDim1 * i;
ptVec[1] = valuePlaneDim;
ptVec[2] = startDim2 + deltaDim2 * j;
}
else if (planeDimension == 2)
{
ptVec[0] = startDim1 + deltaDim1 * i;
ptVec[1] = startDim2 + deltaDim2 * j;
ptVec[2] = valuePlaneDim;
}
mitk::Point3D pt3D;
pt3D.FillPoint(ptVec);
gridPoints.push_back(pt3D);
}
}
return gridPoints;
}
mitk::Point3D mitk::SurfaceInterpolationController::ComputeInteriorPointOfContour(
const mitk::SurfaceInterpolationController::ContourPositionInformation& contour,
mitk::LabelSetImage * labelSetImage)
{
if (labelSetImage->GetDimension() == 4)
{
return mitk::ContourExt::ComputeInteriorPointOfContour<4>(contour, labelSetImage, m_CurrentTimePoint);
}
else
{
return mitk::ContourExt::ComputeInteriorPointOfContour<3>(contour, labelSetImage, m_CurrentTimePoint);
}
}
template<unsigned int VImageDimension>
mitk::Point3D mitk::ContourExt::ComputeInteriorPointOfContour(
const mitk::SurfaceInterpolationController::ContourPositionInformation& contour,
mitk::LabelSetImage * labelSetImage,
mitk::TimePointType currentTimePoint)
{
mitk::ImagePixelReadAccessor<mitk::Label::PixelType, VImageDimension> readAccessor(labelSetImage);
if (!labelSetImage->GetTimeGeometry()->IsValidTimePoint(currentTimePoint))
{
MITK_ERROR << "Invalid time point requested for interpolation pipeline.";
mitk::Point3D pt;
return pt;
}
std::vector<mitk::Label::PixelType> pixelsPresent;
const auto currentTimeStep = labelSetImage->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint);
auto polyData = contour.Contour->GetVtkPolyData();
polyData->ComputeCellsBounds();
mitk::ScalarType cellBounds[6];
polyData->GetCellsBounds(cellBounds);
size_t numPointsToSample = 10;
mitk::ScalarType StartX = cellBounds[0];
mitk::ScalarType StartY = cellBounds[2];
mitk::ScalarType StartZ = cellBounds[4];
size_t deltaX = (cellBounds[1] - cellBounds[0]) / numPointsToSample;
size_t deltaY = (cellBounds[3] - cellBounds[2]) / numPointsToSample;
size_t deltaZ = (cellBounds[5] - cellBounds[4]) / numPointsToSample;
auto planeOrientation = mitk::ContourExt::GetContourOrientation(contour.ContourNormal);
std::vector<mitk::Point3D> points;
if (planeOrientation == 0)
{
points = mitk::ContourExt::GetBoundingBoxGridPoints(planeOrientation,
StartY, numPointsToSample, deltaY,
StartZ, numPointsToSample, deltaZ,
StartX);
}
else if (planeOrientation == 1)
{
points = mitk::ContourExt::GetBoundingBoxGridPoints(planeOrientation,
StartX, numPointsToSample, deltaX,
StartZ, numPointsToSample, deltaZ,
StartY);
}
else if (planeOrientation == 2)
{
points = mitk::ContourExt::GetBoundingBoxGridPoints(planeOrientation,
StartX, numPointsToSample, deltaX,
StartY, numPointsToSample, deltaY,
StartZ);
}
mitk::Label::PixelType pixelVal;
mitk::Point3D pt3D;
std::vector<mitk::Label::PixelType> pixelVals;
for (size_t i = 0; i < points.size(); ++i)
{
pt3D = points[i];
itk::Index<3> itkIndex;
labelSetImage->GetGeometry()->WorldToIndex(pt3D, itkIndex);
if (VImageDimension == 4)
{
itk::Index<VImageDimension> time3DIndex;
for (size_t i = 0; i < itkIndex.size(); ++i)
time3DIndex[i] = itkIndex[i];
time3DIndex[3] = currentTimeStep;
pixelVal = readAccessor.GetPixelByIndexSafe(time3DIndex);
}
else if (VImageDimension == 3)
{
itk::Index<VImageDimension> geomIndex;
for (size_t i=0;i<itkIndex.size();++i)
geomIndex[i] = itkIndex[i];
pixelVal = readAccessor.GetPixelByIndexSafe(geomIndex);
}
if (pixelVal == contour.LabelValue)
break;
}
return pt3D;
}
size_t mitk::ContourExt::GetContourOrientation(const mitk::Vector3D& ContourNormal)
{
double n[3];
n[0] = ContourNormal[0];
n[1] = ContourNormal[1];
n[2] = ContourNormal[2];
double XVec[3];
XVec[0] = 1.0; XVec[1] = 0.0; XVec[2] = 0.0;
double dotX = vtkMath::Dot(n, XVec);
double YVec[3];
YVec[0] = 0.0; YVec[1] = 1.0; YVec[2] = 0.0;
double dotY = vtkMath::Dot(n, YVec);
double ZVec[3];
ZVec[0] = 0.0; ZVec[1] = 0.0; ZVec[2] = 1.0;
double dotZ = vtkMath::Dot(n, ZVec);
size_t planeOrientation = 0;
if (fabs(dotZ) > mitk::eps)
{
planeOrientation = 2;
}
else if (fabs(dotY) > mitk::eps)
{
planeOrientation = 1;
}
else if(fabs(dotX) > mitk::eps)
{
planeOrientation = 0;
}
return planeOrientation;
}
diff --git a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.h b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.h
index 202dfc3abe..95b96e8585 100644
--- a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.h
+++ b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.h
@@ -1,371 +1,360 @@
/*============================================================================
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 mitkSurfaceInterpolationController_h
#define mitkSurfaceInterpolationController_h
#include <mitkDataStorage.h>
#include <mitkLabelSetImage.h>
#include <mitkLabel.h>
#include <mitkSurface.h>
#include <MitkSurfaceInterpolationExports.h>
namespace mitk
{
class ComputeContourSetNormalsFilter;
class CreateDistanceImageFromSurfaceFilter;
class LabelSetImage;
class ReduceContourSetFilter;
class MITKSURFACEINTERPOLATION_EXPORT SurfaceInterpolationController : public itk::Object
{
public:
mitkClassMacroItkParent(SurfaceInterpolationController, itk::Object);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
itkGetMacro(DistanceImageSpacing, double);
struct MITKSURFACEINTERPOLATION_EXPORT ContourPositionInformation
{
int Pos;
Surface::ConstPointer Contour;
Vector3D ContourNormal;
Point3D ContourPoint;
PlaneGeometry::ConstPointer Plane;
Label::PixelType LabelValue;
TimeStepType TimeStep;
ContourPositionInformation()
: Pos(-1),
Plane(nullptr),
LabelValue(std::numeric_limits<Label::PixelType>::max()),
TimeStep(std::numeric_limits<TimeStepType>::max())
{
}
};
typedef std::vector<ContourPositionInformation> CPIVector;
typedef std::map<TimeStepType, CPIVector> CPITimeStepMap;
typedef std::map<LabelSetImage::LabelValueType, CPITimeStepMap> CPITimeStepLabelMap;
typedef std::map<LabelSetImage*, CPITimeStepLabelMap> CPITimeStepLabelSegMap;
static SurfaceInterpolationController *GetInstance();
void SetCurrentTimePoint(TimePointType tp)
{
if (m_CurrentTimePoint != tp)
{
m_CurrentTimePoint = tp;
if (m_SelectedSegmentation)
{
this->ReinitializeInterpolation();
}
}
};
TimePointType GetCurrentTimePoint() const { return m_CurrentTimePoint; };
/**
* @brief Adds a new extracted contour to the list
* @param newContour the contour to be added. If a contour at that position
* already exists the related contour will be updated
*/
void AddNewContour(Surface::Pointer newContour);
/**
* @brief Adds new extracted contours to the list. If one or more contours at a given position
* already exist they will be updated respectively
*/
void AddNewContours(const std::vector<Surface::Pointer>& newContours, std::vector<const mitk::PlaneGeometry*>& contourPlanes, bool reinitializeAction = false);
/**
- * @brief Returns the contour for a given plane for the current selected segmenation
- * @param contourInfo the contour which should be returned
- * @return the contour as an mitk::Surface. If no contour is available at the give position nullptr is returned
- */
- const mitk::Surface *GetContour(const ContourPositionInformation& contourInfo);
+ * @brief Removes the contour for a given plane for the current selected segmenation
+ * @param contourInfo the contour which should be removed
+ * @return true if a contour was found and removed, false if no contour was found
+ */
+ bool RemoveContour(ContourPositionInformation contourInfo);
/**
* @brief Computes an interior point of the input contour. It's used to detect merge and erase operations.
*
* @param contour Contour for which to compute the contour
* @param labelSetImage LabelSetImage used input to check contour Label.
* @return mitk::Point3D 3D Interior point of the contour returned.
*/
mitk::Point3D ComputeInteriorPointOfContour(const ContourPositionInformation& contour,
mitk::LabelSetImage * labelSetImage);
/**
* @brief Resets the pipeline for interpolation. The various filters used are reset.
*
*/
void ReinitializeInterpolation();
void RemoveObservers();
/**
* @brief Performs the interpolation.
*
*/
void Interpolate();
/**
* @brief Get the Result of the interpolation operation.
*
* @return mitk::Surface::Pointer
*/
mitk::Surface::Pointer GetInterpolationResult();
/**
* @brief Sets the minimum spacing of the current selected segmentation
* This is needed since the contour points we reduced before they are used to interpolate the surface.
*
* @param minSpacing Paramter to set
*/
void SetMinSpacing(double minSpacing);
/**
* @brief Sets the minimum spacing of the current selected segmentation
* This is needed since the contour points we reduced before they are used to interpolate the surface
* @param maxSpacing Set the max Spacing for interpolation
*/
void SetMaxSpacing(double maxSpacing);
/**
* Sets the volume i.e. the number of pixels that the distance image should have
* By evaluation we found out that 50.000 pixel delivers a good result
*/
void SetDistanceImageVolume(unsigned int distImageVolume);
/**
* @brief Get the current selected segmentation for which the interpolation is performed
* @return the current segmentation image
*/
mitk::LabelSetImage* GetCurrentSegmentation();
Surface *GetContoursAsSurface();
void SetDataStorage(DataStorage::Pointer ds);
/**
* Sets the current list of contourpoints which is used for the surface interpolation
* @param currentSegmentationImage The current selected segmentation
*/
void SetCurrentInterpolationSession(LabelSetImage* currentSegmentationImage);
/**
* @brief Remove interpolation session
* @param segmentationImage the session to be removed
*/
void RemoveInterpolationSession(LabelSetImage* segmentationImage);
/**
* @brief Removes all sessions
*/
void RemoveAllInterpolationSessions();
mitk::Image *GetInterpolationImage();
/**
* @brief Get the Contours at a certain timeStep and layerID.
*
* @param timeStep Time Step from which to get the contours.
* @param layerID Layer from which to get the contours.
* @return std::vector<ContourPositionInformation> Returns contours.
*/
CPIVector* GetContours(TimeStepType timeStep, LabelSetImage::LabelValueType labelValue);
/**
* @brief Trigerred with the "Reinit Interpolation" action. The contours are used to repopulate the
* surfaceInterpolator data structures so that interpolation can be performed after reloading data.
*
* @param contourList List of contours extracted
* @param contourPlanes List of planes at which the contours were extracted
*/
void CompleteReinitialization(const std::vector<mitk::Surface::Pointer>& contourList,
std::vector<const mitk::PlaneGeometry *>& contourPlanes);
/**
* @brief Removes contours of a particular label and at a given time step for the current session/segmentation.
*
* @param label Label of contour to remove.
* @param timeStep Time step in which to remove the contours.
* @remark if the label or time step does not exist, nothing happens.
*/
void RemoveContours(mitk::Label::PixelType label, TimeStepType timeStep);
/**
* @brief Removes contours of a particular label and at a given time step for the current session/segmentation.
*
* @param label Label of contour to remove.
* @param timeStep Time step in which to remove the contours.
* @remark if the label or time step does not exist, nothing happens.
*/
void RemoveContours(mitk::Label::PixelType label);
/**
* Estimates the memory which is needed to build up the equationsystem for the interpolation.
* \returns The percentage of the real memory which will be used by the interpolation
*/
double EstimatePortionOfNeededMemory();
/**
* Adds Contours from the active Label to the interpolation pipeline
*/
void AddActiveLabelContoursForInterpolation(mitk::Label::PixelType activeLabel);
unsigned int GetNumberOfInterpolationSessions();
- /**
- * @brief Removes the contour for a given plane for the current selected segmenation
- * @param contourInfo the contour which should be removed
- * @return true if a contour was found and removed, false if no contour was found
- */
- bool RemoveContour(ContourPositionInformation contourInfo);
-
/**
* @brief Get the Segmentation Image Node object
*
* @return DataNode* returns the DataNode containing the segmentation image.
*/
mitk::DataNode* GetSegmentationImageNode();
protected:
SurfaceInterpolationController();
~SurfaceInterpolationController() override;
template <typename TPixel, unsigned int VImageDimension>
void GetImageBase(itk::Image<TPixel, VImageDimension> *input, itk::ImageBase<3>::Pointer &result);
private:
/**
* @brief
*
* @param caller
* @param event
*/
void OnSegmentationDeleted(const itk::Object *caller, const itk::EventObject &event);
/**
* @brief Function that removes contours of a particular label when the "Remove Label" event is trigerred in the labelSetImage.
*
*/
void OnRemoveLabel(mitk::Label::PixelType removedLabelValue);
/**
* @brief When a new contour is added to the pipeline or an existing contour is replaced,
* the plane geometry information of that contour is added as a child node to the
* current node of the segmentation image. This is useful in the retrieval of contour information
* when data is reloaded after saving.
*
* @param contourInfo contourInfo struct to add to data storage.
*/
void AddPlaneGeometryNodeToDataStorage(const ContourPositionInformation& contourInfo);
/**
* @brief Clears the interpolation data structures. Called from CompleteReinitialization().
*
*/
void ClearInterpolationSession();
/**
* @brief Add contour to the interpolation pipeline
*
* @param contourInfo Contour information to be added
* @param reinitializationAction If the contour is coming from a reinitialization process or not
*/
void AddToInterpolationPipeline(ContourPositionInformation& contourInfo, bool reinitializationAction = false);
itk::SmartPointer<ReduceContourSetFilter> m_ReduceFilter;
itk::SmartPointer<ComputeContourSetNormalsFilter> m_NormalsFilter;
itk::SmartPointer<CreateDistanceImageFromSurfaceFilter> m_InterpolateSurfaceFilter;
mitk::Surface::Pointer m_Contours;
double m_DistanceImageSpacing;
- vtkSmartPointer<vtkPolyData> m_PolyData;
-
mitk::DataStorage::Pointer m_DataStorage;
CPITimeStepLabelSegMap m_CPIMap;
mitk::Surface::Pointer m_InterpolationResult;
unsigned int m_CurrentNumberOfReducedContours;
- mitk::LabelSetImage::Pointer m_SelectedSegmentation;
+ WeakPointer<LabelSetImage> m_SelectedSegmentation;
std::map<mitk::Image *, unsigned long> m_SegmentationObserverTags;
mitk::TimePointType m_CurrentTimePoint;
-
- unsigned int m_ContourPosIndex;
};
namespace ContourExt
{
/**
* @brief Returns the plane the contour belongs to.
*
* @param ContourNormal
* @return size_t
*/
size_t GetContourOrientation(const mitk::Vector3D& ContourNormal);
/**
* @brief Function used to compute an interior point of the contour.
* Used to react to the merge label and erase label actions.
*
*
* @tparam VImageDimension Dimension of the image
* @param contour Contour for which to compute the interior point
* @param labelSetImage Label Set Image For which to find the contour
* @param currentTimePoint Current Time Point of the Image
* @return mitk::Point3D The returned point in the interior of the contour.s
*/
template<unsigned int VImageDimension>
mitk::Point3D ComputeInteriorPointOfContour(const mitk::SurfaceInterpolationController::ContourPositionInformation& contour,
mitk::LabelSetImage * labelSetImage,
mitk::TimePointType currentTimePoint);
/**
* @brief Get a Grid points within the bounding box of the contour at a certain spacing.
*
* @param planeDimension Plane orientation (Sagittal, Coronal, Axial)
* @param startDim1 Starting coordinate along dimension 1 to start the grid point sampling from
* @param numPointsToSampleDim1 Number of points to sample along dimension 1
* @param deltaDim1 Spacing for dimension 1 at which points should be sampled
* @param startDim2 Starting coordinate along dimension 2 to start the grid point sampling from
* @param numPointsToSampleDim2 Number of points to sample along dimension 2
* @param deltaDim2 Spacing for dimension 1 at which points should be sampled
* @param valuePlaneDim Slice index of the plane in the volume
* @return std::vector< mitk::Point3D > The computed grid points are returned by the function.
*/
std::vector< mitk::Point3D > GetBoundingBoxGridPoints(size_t planeDimension,
double startDim1,
size_t numPointsToSampleDim1,
double deltaDim1,
double startDim2,
size_t numPointsToSampleDim2,
double deltaDim2,
double valuePlaneDim);
};
}
#endif