diff --git a/Modules/Segmentation/Interactions/mitkSegTool2D.cpp b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp
index 9d6b91f3a1..c41f3027ef 100644
--- a/Modules/Segmentation/Interactions/mitkSegTool2D.cpp
+++ b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp
@@ -1,821 +1,795 @@
/*============================================================================
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 "mitkSegTool2D.h"
#include "mitkToolManager.h"
#include "mitkBaseRenderer.h"
#include "mitkDataStorage.h"
#include "mitkPlaneGeometry.h"
#include <mitkTimeNavigationController.h>
#include "mitkImageAccessByItk.h"
// Include of the new ImageExtractor
#include "mitkMorphologicalOperations.h"
#include "mitkPlanarCircle.h"
#include "usGetModuleContext.h"
// Includes for 3DSurfaceInterpolation
#include "mitkImageTimeSelector.h"
#include "mitkImageToContourFilter.h"
#include "mitkSurfaceInterpolationController.h"
// includes for resling and overwriting
#include <mitkExtractSliceFilter.h>
#include <mitkVtkImageOverwrite.h>
#include <vtkImageData.h>
#include <vtkSmartPointer.h>
#include "mitkOperationEvent.h"
#include "mitkUndoController.h"
#include <mitkDiffSliceOperationApplier.h>
#include "mitkAbstractTransformGeometry.h"
#include "mitkLabelSetImage.h"
#include "mitkContourModelUtils.h"
// #include <itkImageRegionIterator.h>
#include <vtkAbstractArray.h>
#include <vtkFieldData.h>
#define ROUND(a) ((a) > 0 ? (int)((a) + 0.5) : -(int)(0.5 - (a)))
bool mitk::SegTool2D::m_SurfaceInterpolationEnabled = true;
mitk::SegTool2D::SliceInformation::SliceInformation(const mitk::Image* aSlice, const mitk::PlaneGeometry* aPlane, mitk::TimeStepType aTimestep) :
slice(aSlice), plane(aPlane), timestep(aTimestep)
{
}
mitk::SegTool2D::SegTool2D(const char *type, const us::Module *interactorModule)
: Tool(type, interactorModule), m_Contourmarkername("Position")
{
Tool::m_EventConfig = "DisplayConfigBlockLMB.xml";
}
mitk::SegTool2D::~SegTool2D()
{
}
bool mitk::SegTool2D::FilterEvents(InteractionEvent *interactionEvent, DataNode *)
{
const auto *positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
bool isValidEvent =
(positionEvent && // Only events of type mitk::InteractionPositionEvent
interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D // Only events from the 2D renderwindows
);
return isValidEvent;
}
bool mitk::SegTool2D::DetermineAffectedImageSlice(const Image *image,
const PlaneGeometry *plane,
int &affectedDimension,
int &affectedSlice)
{
assert(image);
assert(plane);
// compare normal of plane to the three axis vectors of the image
Vector3D normal = plane->GetNormal();
Vector3D imageNormal0 = image->GetSlicedGeometry()->GetAxisVector(0);
Vector3D imageNormal1 = image->GetSlicedGeometry()->GetAxisVector(1);
Vector3D imageNormal2 = image->GetSlicedGeometry()->GetAxisVector(2);
normal.Normalize();
imageNormal0.Normalize();
imageNormal1.Normalize();
imageNormal2.Normalize();
imageNormal0.SetVnlVector(vnl_cross_3d<ScalarType>(normal.GetVnlVector(), imageNormal0.GetVnlVector()));
imageNormal1.SetVnlVector(vnl_cross_3d<ScalarType>(normal.GetVnlVector(), imageNormal1.GetVnlVector()));
imageNormal2.SetVnlVector(vnl_cross_3d<ScalarType>(normal.GetVnlVector(), imageNormal2.GetVnlVector()));
double eps(0.00001);
// axial
if (imageNormal2.GetNorm() <= eps)
{
affectedDimension = 2;
}
// sagittal
else if (imageNormal1.GetNorm() <= eps)
{
affectedDimension = 1;
}
// coronal
else if (imageNormal0.GetNorm() <= eps)
{
affectedDimension = 0;
}
else
{
affectedDimension = -1; // no idea
return false;
}
// determine slice number in image
BaseGeometry *imageGeometry = image->GetGeometry(0);
Point3D testPoint = imageGeometry->GetCenter();
Point3D projectedPoint;
plane->Project(testPoint, projectedPoint);
Point3D indexPoint;
imageGeometry->WorldToIndex(projectedPoint, indexPoint);
affectedSlice = ROUND(indexPoint[affectedDimension]);
MITK_DEBUG << "indexPoint " << indexPoint << " affectedDimension " << affectedDimension << " affectedSlice "
<< affectedSlice;
// check if this index is still within the image
if (affectedSlice < 0 || affectedSlice >= static_cast<int>(image->GetDimension(affectedDimension)))
return false;
return true;
}
void mitk::SegTool2D::UpdateAllSurfaceInterpolations(const LabelSetImage *workingImage,
TimeStepType timeStep,
const PlaneGeometry *plane,
bool detectIntersection)
{
if (nullptr == workingImage) mitkThrow() << "Cannot update surface interpolation. Invalid working image passed.";
if (nullptr == plane) mitkThrow() << "Cannot update surface interpolation. Invalid plane passed.";
auto affectedLabels = mitk::SurfaceInterpolationController::GetInstance()->GetAffectedLabels(workingImage, timeStep, plane);
for (auto affectedLabel : affectedLabels)
{
auto groupID = workingImage->GetGroupIndexOfLabel(affectedLabel);
auto slice = GetAffectedImageSliceAs2DImage(plane, workingImage->GetGroupImage(groupID), timeStep);
std::vector<SliceInformation> slices = { SliceInformation(slice, plane, timeStep) };
Self::UpdateSurfaceInterpolation(slices, workingImage, detectIntersection, affectedLabel);
}
}
void mitk::SegTool2D::RemoveContourFromInterpolator(const SliceInformation& sliceInfo, LabelSetImage::LabelValueType labelValue)
{
mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
contourInfo.LabelValue = labelValue;
contourInfo.TimeStep = sliceInfo.timestep;
contourInfo.Plane = sliceInfo.plane;
mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo, true);
}
template <typename ImageType>
void ClearBufferProcessing(ImageType* itkImage)
{
itkImage->FillBuffer(0);
}
void mitk::SegTool2D::UpdateSurfaceInterpolation(const std::vector<SliceInformation>& sliceInfos,
const Image* workingImage,
bool detectIntersection,
mitk::Label::PixelType activeLabelValue)
{
if (!m_SurfaceInterpolationEnabled)
return;
//Remark: the ImageTimeSelector is just needed to extract a timestep/channel of
//the image in order to get the image dimension (time dimension and channel dimension
//stripped away). Therfore it is OK to always use time step 0 and channel 0
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(workingImage);
timeSelector->SetTimeNr(0);
timeSelector->SetChannelNr(0);
timeSelector->Update();
const auto dimRefImg = timeSelector->GetOutput()->GetDimension();
if (dimRefImg != 3)
return;
std::vector<mitk::Surface::Pointer> contourList;
contourList.reserve(sliceInfos.size());
ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();
std::vector<SliceInformation> relevantSlices = sliceInfos;
if (detectIntersection)
{
relevantSlices.clear();
for (const auto& sliceInfo : sliceInfos)
{
// Test whether there is something to extract or whether the slice just contains intersections of others
//Remark we cannot just errode the clone of sliceInfo.slice, because Erode currently only
//works on pixel value 1. But we need to erode active label. Therefore we use TransferLabelContent
//as workarround.
//If MorphologicalOperations::Erode is supports user defined pixel values, the workarround
//can be removed.
//Workarround starts
mitk::Image::Pointer slice2 = Image::New();
slice2->Initialize(sliceInfo.slice);
AccessByItk(slice2, ClearBufferProcessing);
LabelSetImage::LabelValueType erodeValue = 1;
auto label = Label::New(erodeValue, "");
TransferLabelContent(sliceInfo.slice, slice2, { label }, LabelSetImage::UnlabeledValue, LabelSetImage::UnlabeledValue, false, { {activeLabelValue, erodeValue} });
//Workarround ends
mitk::MorphologicalOperations::Erode(slice2, 2, mitk::MorphologicalOperations::Ball);
contourExtractor->SetInput(slice2);
contourExtractor->SetContourValue(erodeValue);
contourExtractor->Update();
mitk::Surface::Pointer contour = contourExtractor->GetOutput();
if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0)
{
Self::RemoveContourFromInterpolator(sliceInfo, activeLabelValue);
}
else
{
relevantSlices.push_back(sliceInfo);
}
}
}
if (relevantSlices.empty())
return;
SurfaceInterpolationController::CPIVector cpis;
for (const auto& sliceInfo : relevantSlices)
{
contourExtractor->SetInput(sliceInfo.slice);
contourExtractor->SetContourValue(activeLabelValue);
contourExtractor->Update();
mitk::Surface::Pointer contour = contourExtractor->GetOutput();
if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0)
{
Self::RemoveContourFromInterpolator(sliceInfo, activeLabelValue);
}
else
{
cpis.emplace_back(contour, sliceInfo.plane->Clone(), activeLabelValue, sliceInfo.timestep);
}
}
mitk::SurfaceInterpolationController::GetInstance()->AddNewContours(cpis);
}
mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const InteractionPositionEvent *positionEvent, const Image *image, unsigned int component /*= 0*/)
{
if (!positionEvent)
{
return nullptr;
}
assert(positionEvent->GetSender()); // sure, right?
const auto timeStep = positionEvent->GetSender()->GetTimeStep(image); // get the timestep of the visible part (time-wise) of the image
return GetAffectedImageSliceAs2DImage(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry(), image, timeStep, component);
}
mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint(const PlaneGeometry* planeGeometry, const Image* image, TimePointType timePoint, unsigned int component /*= 0*/)
{
if (!image || !planeGeometry)
{
return nullptr;
}
if (!image->GetTimeGeometry()->IsValidTimePoint(timePoint))
return nullptr;
return SegTool2D::GetAffectedImageSliceAs2DImage(planeGeometry, image, image->GetTimeGeometry()->TimePointToTimeStep(timePoint), component);
}
mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const PlaneGeometry *planeGeometry, const Image *image, TimeStepType timeStep, unsigned int component /*= 0*/)
{
if (!image || !planeGeometry)
{
return nullptr;
}
// Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk reslicer
vtkSmartPointer<mitkVtkImageOverwrite> reslice = vtkSmartPointer<mitkVtkImageOverwrite>::New();
// set to false to extract a slice
reslice->SetOverwriteMode(false);
reslice->Modified();
// use ExtractSliceFilter with our specific vtkImageReslice for overwriting and extracting
mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice);
extractor->SetInput(image);
extractor->SetTimeStep(timeStep);
extractor->SetWorldGeometry(planeGeometry);
extractor->SetVtkOutputRequest(false);
extractor->SetResliceTransformByGeometry(image->GetTimeGeometry()->GetGeometryForTimeStep(timeStep));
// additionally extract the given component
// default is 0; the extractor checks for multi-component images
extractor->SetComponent(component);
extractor->Modified();
extractor->Update();
Image::Pointer slice = extractor->GetOutput();
return slice;
}
mitk::Image::Pointer mitk::SegTool2D::GetAffectedWorkingSlice(const InteractionPositionEvent *positionEvent) const
{
const auto workingNode = this->GetWorkingDataNode();
if (!workingNode)
{
return nullptr;
}
const auto *workingImage = dynamic_cast<Image *>(workingNode->GetData());
if (!workingImage)
{
return nullptr;
}
return GetAffectedImageSliceAs2DImage(positionEvent, workingImage);
}
mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice(const InteractionPositionEvent *positionEvent) const
{
DataNode* referenceNode = this->GetReferenceDataNode();
if (!referenceNode)
{
return nullptr;
}
auto *referenceImage = dynamic_cast<Image *>(referenceNode->GetData());
if (!referenceImage)
{
return nullptr;
}
int displayedComponent = 0;
if (referenceNode->GetIntProperty("Image.Displayed Component", displayedComponent))
{
// found the displayed component
return GetAffectedImageSliceAs2DImage(positionEvent, referenceImage, displayedComponent);
}
else
{
return GetAffectedImageSliceAs2DImage(positionEvent, referenceImage);
}
}
mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice(const PlaneGeometry* planeGeometry, TimeStepType timeStep) const
{
DataNode* referenceNode = this->GetReferenceDataNode();
if (!referenceNode)
{
return nullptr;
}
auto* referenceImage = dynamic_cast<Image*>(referenceNode->GetData());
if (!referenceImage)
{
return nullptr;
}
int displayedComponent = 0;
if (referenceNode->GetIntProperty("Image.Displayed Component", displayedComponent))
{
// found the displayed component
return GetAffectedImageSliceAs2DImage(planeGeometry, referenceImage, timeStep, displayedComponent);
}
else
{
return GetAffectedImageSliceAs2DImage(planeGeometry, referenceImage, timeStep);
}
}
void mitk::SegTool2D::Activated()
{
Superclass::Activated();
this->GetToolManager()->SelectedTimePointChanged +=
mitk::MessageDelegate<mitk::SegTool2D>(this, &mitk::SegTool2D::OnTimePointChangedInternal);
m_LastTimePointTriggered = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
}
void mitk::SegTool2D::Deactivated()
{
this->GetToolManager()->SelectedTimePointChanged -=
mitk::MessageDelegate<mitk::SegTool2D>(this, &mitk::SegTool2D::OnTimePointChangedInternal);
Superclass::Deactivated();
}
void mitk::SegTool2D::OnTimePointChangedInternal()
{
if (m_IsTimePointChangeAware && nullptr != this->GetWorkingDataNode())
{
const TimePointType timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
if (timePoint != m_LastTimePointTriggered)
{
m_LastTimePointTriggered = timePoint;
this->OnTimePointChanged();
}
}
}
void mitk::SegTool2D::OnTimePointChanged()
{
//default implementation does nothing
}
mitk::DataNode* mitk::SegTool2D::GetWorkingDataNode() const
{
if (nullptr != this->GetToolManager())
{
return this->GetToolManager()->GetWorkingData(0);
}
return nullptr;
}
mitk::Image* mitk::SegTool2D::GetWorkingData() const
{
auto node = this->GetWorkingDataNode();
if (nullptr != node)
{
return dynamic_cast<Image*>(node->GetData());
}
return nullptr;
}
mitk::DataNode* mitk::SegTool2D::GetReferenceDataNode() const
{
if (nullptr != this->GetToolManager())
{
return this->GetToolManager()->GetReferenceData(0);
}
return nullptr;
}
mitk::Image* mitk::SegTool2D::GetReferenceData() const
{
auto node = this->GetReferenceDataNode();
if (nullptr != node)
{
return dynamic_cast<Image*>(node->GetData());
}
return nullptr;
}
void mitk::SegTool2D::WriteBackSegmentationResult(const InteractionPositionEvent *positionEvent, const Image * segmentationResult)
{
if (!positionEvent)
return;
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
const auto *abstractTransformGeometry(
dynamic_cast<const AbstractTransformGeometry *>(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
if (planeGeometry && segmentationResult && !abstractTransformGeometry)
{
const auto workingNode = this->GetWorkingDataNode();
auto *image = dynamic_cast<Image *>(workingNode->GetData());
const auto timeStep = positionEvent->GetSender()->GetTimeStep(image);
this->WriteBackSegmentationResult(planeGeometry, segmentationResult, timeStep);
}
}
void mitk::SegTool2D::WriteBackSegmentationResult(const DataNode* workingNode, const PlaneGeometry* planeGeometry, const Image* segmentationResult, TimeStepType timeStep)
{
if (!planeGeometry || !segmentationResult)
return;
SliceInformation sliceInfo(segmentationResult, const_cast<mitk::PlaneGeometry*>(planeGeometry), timeStep);
Self::WriteBackSegmentationResults(workingNode, { sliceInfo }, true);
}
void mitk::SegTool2D::WriteBackSegmentationResult(const PlaneGeometry *planeGeometry,
const Image * segmentationResult,
TimeStepType timeStep)
{
if (!planeGeometry || !segmentationResult)
return;
if(m_LastEventSender == nullptr)
{
return;
}
unsigned int currentSlicePosition = m_LastEventSender->GetSliceNavigationController()->GetStepper()->GetPos();
SliceInformation sliceInfo(segmentationResult, const_cast<mitk::PlaneGeometry *>(planeGeometry), timeStep);
sliceInfo.slicePosition = currentSlicePosition;
WriteBackSegmentationResults({ sliceInfo }, true);
}
void mitk::SegTool2D::WriteBackSegmentationResults(const std::vector<SegTool2D::SliceInformation> &sliceList,
bool writeSliceToVolume)
{
if (sliceList.empty())
{
return;
}
if (nullptr == m_LastEventSender)
{
MITK_WARN << "Cannot write tool results. Tool seems to be in an invalid state, as no interaction event was recieved but is expected.";
return;
}
const auto workingNode = this->GetWorkingDataNode();
// the first geometry is needed otherwise restoring the position is not working
const auto* plane3 =
dynamic_cast<const PlaneGeometry*>(dynamic_cast<const mitk::SlicedGeometry3D*>(
m_LastEventSender->GetSliceNavigationController()->GetCurrentGeometry3D())
->GetPlaneGeometry(0));
const unsigned int slicePosition = m_LastEventSender->GetSliceNavigationController()->GetStepper()->GetPos();
mitk::SegTool2D::WriteBackSegmentationResults(workingNode, sliceList, writeSliceToVolume);
/* A cleaner solution would be to add a contour marker for each slice info. It currently
does not work as the contour markers expect that the plane is always the plane of slice 0.
Had not the time to do it properly no. Should be solved by T28146*/
this->AddContourmarker(plane3, slicePosition);
}
void mitk::SegTool2D::WriteBackSegmentationResults(const DataNode* workingNode, const std::vector<SliceInformation>& sliceList, bool writeSliceToVolume)
{
if (sliceList.empty())
{
return;
}
if (nullptr == workingNode)
{
mitkThrow() << "Cannot write slice to working node. Working node is invalid.";
}
auto image = dynamic_cast<Image*>(workingNode->GetData());
mitk::Label::PixelType activeLabelValue = 0;
try{
auto labelSetImage = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData());
activeLabelValue = labelSetImage->GetActiveLabel()->GetValue();
}
catch(...)
{
mitkThrow() << "Working node does not contain labelSetImage.";
}
if (nullptr == image)
{
mitkThrow() << "Cannot write slice to working node. Working node does not contain an image.";
}
for (const auto& sliceInfo : sliceList)
{
if (writeSliceToVolume && nullptr != sliceInfo.plane && sliceInfo.slice.IsNotNull())
{
SegTool2D::WriteSliceToVolume(image, sliceInfo, true);
}
}
SegTool2D::UpdateSurfaceInterpolation(sliceList, image, false, activeLabelValue);
// also mark its node as modified (T27308). Can be removed if T27307
// is properly solved
if (workingNode != nullptr) workingNode->Modified();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::SegTool2D::WriteSliceToVolume(Image* workingImage, const PlaneGeometry* planeGeometry, const Image* slice, TimeStepType timeStep, bool allowUndo)
{
SliceInformation sliceInfo(slice, planeGeometry, timeStep);
WriteSliceToVolume(workingImage, sliceInfo, allowUndo);
}
void mitk::SegTool2D::WriteSliceToVolume(Image* workingImage, const SliceInformation &sliceInfo, bool allowUndo)
{
if (nullptr == workingImage)
{
mitkThrow() << "Cannot write slice to working node. Working node does not contain an image.";
}
DiffSliceOperation* undoOperation = nullptr;
if (allowUndo)
{
/*============= BEGIN undo/redo feature block ========================*/
// Create undo operation by caching the not yet modified slices
mitk::Image::Pointer originalSlice = GetAffectedImageSliceAs2DImage(sliceInfo.plane, workingImage, sliceInfo.timestep);
undoOperation =
new DiffSliceOperation(workingImage,
originalSlice,
dynamic_cast<SlicedGeometry3D*>(originalSlice->GetGeometry()),
sliceInfo.timestep,
sliceInfo.plane);
/*============= END undo/redo feature block ========================*/
}
// Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk
// reslicer
vtkSmartPointer<mitkVtkImageOverwrite> reslice = vtkSmartPointer<mitkVtkImageOverwrite>::New();
// Set the slice as 'input'
// casting const away is needed and OK as long the OverwriteMode of
// mitkVTKImageOverwrite is true.
// Reason: because then the input slice is not touched but
// used to overwrite the input of the ExtractSliceFilter.
auto noneConstSlice = const_cast<Image*>(sliceInfo.slice.GetPointer());
reslice->SetInputSlice(noneConstSlice->GetVtkImageData());
// set overwrite mode to true to write back to the image volume
reslice->SetOverwriteMode(true);
reslice->Modified();
mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice);
extractor->SetInput(workingImage);
extractor->SetTimeStep(sliceInfo.timestep);
extractor->SetWorldGeometry(sliceInfo.plane);
extractor->SetVtkOutputRequest(false);
extractor->SetResliceTransformByGeometry(workingImage->GetGeometry(sliceInfo.timestep));
extractor->Modified();
extractor->Update();
// the image was modified within the pipeline, but not marked so
workingImage->Modified();
workingImage->GetVtkImageData()->Modified();
if (allowUndo)
{
/*============= BEGIN undo/redo feature block ========================*/
// specify the redo operation with the edited slice
auto* doOperation =
new DiffSliceOperation(workingImage,
extractor->GetOutput(),
dynamic_cast<SlicedGeometry3D*>(sliceInfo.slice->GetGeometry()),
sliceInfo.timestep,
sliceInfo.plane);
// create an operation event for the undo stack
OperationEvent* undoStackItem =
new OperationEvent(DiffSliceOperationApplier::GetInstance(), doOperation, undoOperation, "Segmentation");
// add it to the undo controller
UndoStackItem::IncCurrObjectEventId();
UndoStackItem::IncCurrGroupEventId();
UndoController::GetCurrentUndoModel()->SetOperationEvent(undoStackItem);
/*============= END undo/redo feature block ========================*/
}
}
void mitk::SegTool2D::SetShowMarkerNodes(bool status)
{
m_ShowMarkerNodes = status;
}
void mitk::SegTool2D::SetEnable3DInterpolation(bool enabled)
{
m_SurfaceInterpolationEnabled = enabled;
}
int mitk::SegTool2D::AddContourmarker(const PlaneGeometry* planeGeometry, unsigned int sliceIndex)
{
if (planeGeometry == nullptr)
return -1;
us::ServiceReference<PlanePositionManagerService> serviceRef =
us::GetModuleContext()->GetServiceReference<PlanePositionManagerService>();
PlanePositionManagerService *service = us::GetModuleContext()->GetService(serviceRef);
unsigned int size = service->GetNumberOfPlanePositions();
unsigned int id = service->AddNewPlanePosition(planeGeometry, sliceIndex);
mitk::PlanarCircle::Pointer contourMarker = mitk::PlanarCircle::New();
mitk::Point2D p1;
planeGeometry->Map(planeGeometry->GetCenter(), p1);
contourMarker->SetPlaneGeometry(planeGeometry->Clone());
contourMarker->PlaceFigure(p1);
contourMarker->SetCurrentControlPoint(p1);
contourMarker->SetProperty("initiallyplaced", mitk::BoolProperty::New(true));
std::stringstream markerStream;
auto workingNode = this->GetWorkingDataNode();
markerStream << m_Contourmarkername;
markerStream << " ";
markerStream << id + 1;
DataNode::Pointer rotatedContourNode = DataNode::New();
rotatedContourNode->SetData(contourMarker);
rotatedContourNode->SetProperty("name", StringProperty::New(markerStream.str()));
rotatedContourNode->SetProperty("isContourMarker", BoolProperty::New(true));
rotatedContourNode->SetBoolProperty("PlanarFigureInitializedWindow", true, m_LastEventSender);
rotatedContourNode->SetProperty("includeInBoundingBox", BoolProperty::New(false));
rotatedContourNode->SetProperty("helper object", mitk::BoolProperty::New(!m_ShowMarkerNodes));
rotatedContourNode->SetProperty("planarfigure.drawcontrolpoints", BoolProperty::New(false));
rotatedContourNode->SetProperty("planarfigure.drawname", BoolProperty::New(false));
rotatedContourNode->SetProperty("planarfigure.drawoutline", BoolProperty::New(false));
rotatedContourNode->SetProperty("planarfigure.drawshadow", BoolProperty::New(false));
if (planeGeometry)
{
if (id == size)
{
this->GetToolManager()->GetDataStorage()->Add(rotatedContourNode, workingNode);
}
else
{
mitk::NodePredicateProperty::Pointer isMarker =
mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true));
mitk::DataStorage::SetOfObjects::ConstPointer markers =
this->GetToolManager()->GetDataStorage()->GetDerivations(workingNode, isMarker);
for (auto iter = markers->begin(); iter != markers->end(); ++iter)
{
std::string nodeName = (*iter)->GetName();
unsigned int t = nodeName.find_last_of(" ");
unsigned int markerId = atof(nodeName.substr(t + 1).c_str()) - 1;
if (id == markerId)
{
return id;
}
}
this->GetToolManager()->GetDataStorage()->Add(rotatedContourNode, workingNode);
}
}
return id;
}
void mitk::SegTool2D::InteractiveSegmentationBugMessage(const std::string &message) const
{
MITK_ERROR << "********************************************************************************" << std::endl
<< " " << message << std::endl
<< "********************************************************************************" << std::endl
<< " " << std::endl
<< " If your image is rotated or the 2D views don't really contain the patient image, try to press the "
"button next to the image selection. "
<< std::endl
<< " " << std::endl
<< " Please file a BUG REPORT: " << std::endl
<< " https://phabricator.mitk.org/" << std::endl
<< " Contain the following information:" << std::endl
<< " - What image were you working on?" << std::endl
<< " - Which region of the image?" << std::endl
<< " - Which tool did you use?" << std::endl
<< " - What did you do?" << std::endl
<< " - What happened (not)? What did you expect?" << std::endl;
}
-void mitk::SegTool2D::WritePreviewOnWorkingImage(
- Image *targetSlice, const Image *sourceSlice, const Image *workingImage, int paintingPixelValue)
-{
- if (nullptr == targetSlice)
- {
- mitkThrow() << "Cannot write preview on working image. Target slice does not point to a valid instance.";
- }
-
- if (nullptr == sourceSlice)
- {
- mitkThrow() << "Cannot write preview on working image. Source slice does not point to a valid instance.";
- }
-
- if (nullptr == workingImage)
- {
- mitkThrow() << "Cannot write preview on working image. Working image does not point to a valid instance.";
- }
-
- auto constVtkSource = sourceSlice->GetVtkImageData();
- /*Need to const cast because Vtk interface does not support const correctly.
- (or I am not experienced enough to use it correctly)*/
- auto nonConstVtkSource = const_cast<vtkImageData*>(constVtkSource);
-
- ContourModelUtils::FillSliceInSlice(nonConstVtkSource, targetSlice->GetVtkImageData(), workingImage, paintingPixelValue, 1.0);
-}
-
bool mitk::SegTool2D::IsPositionEventInsideImageRegion(mitk::InteractionPositionEvent* positionEvent,
const mitk::BaseData* data)
{
bool isPositionEventInsideImageRegion =
nullptr != data && data->GetGeometry()->IsInside(positionEvent->GetPositionInWorld());
if (!isPositionEventInsideImageRegion)
MITK_WARN("EditableContourTool") << "PositionEvent is outside ImageRegion!";
return isPositionEventInsideImageRegion;
}
diff --git a/Modules/Segmentation/Interactions/mitkSegTool2D.h b/Modules/Segmentation/Interactions/mitkSegTool2D.h
index 2a7ac4b830..6be2ad9459 100644
--- a/Modules/Segmentation/Interactions/mitkSegTool2D.h
+++ b/Modules/Segmentation/Interactions/mitkSegTool2D.h
@@ -1,303 +1,289 @@
/*============================================================================
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 mitkSegTool2D_h
#define mitkSegTool2D_h
#include <mitkCommon.h>
#include <mitkImage.h>
#include <mitkTool.h>
#include <MitkSegmentationExports.h>
#include <mitkInteractionPositionEvent.h>
#include <mitkInteractionConst.h>
#include <mitkPlanePositionManager.h>
#include <mitkRestorePlanePositionOperation.h>
#include <mitkDiffSliceOperation.h>
namespace mitk
{
class BaseRenderer;
/**
\brief Abstract base class for segmentation tools.
\sa Tool
\ingroup Interaction
\ingroup ToolManagerEtAl
Implements 2D segmentation specific helper methods, that might be of use to
all kind of 2D segmentation tools. At the moment these are:
- Determination of the slice where the user paints upon (DetermineAffectedImageSlice)
- Projection of a 3D contour onto a 2D plane/slice
SegTool2D tries to structure the interaction a bit. If you pass "PressMoveRelease" as the interaction type
of your derived tool, you might implement the methods OnMousePressed, OnMouseMoved, and OnMouseReleased.
Yes, your guess about when they are called is correct.
\warning Only to be instantiated by mitk::ToolManager.
$Author$
*/
class MITKSEGMENTATION_EXPORT SegTool2D : public Tool
{
public:
mitkClassMacro(SegTool2D, Tool);
/**
\brief Calculates for a given Image and PlaneGeometry, which slice of the image (in index corrdinates) is meant by
the plane.
\return false, if no slice direction seems right (e.g. rotated planes)
\param image
\param plane
\param affectedDimension The image dimension, which is constant for all points in the plane, e.g. Axial --> 2
\param affectedSlice The index of the image slice
*/
static bool DetermineAffectedImageSlice(const Image *image,
const PlaneGeometry *plane,
int &affectedDimension,
int &affectedSlice);
/**
* @brief Updates the surface interpolations by extracting the contour form the given slice for all labels
* that have a surface contour information stored for the given plane at the given timestep.
* @param slice the slice from which the contour should be extracted
* @param workingImage the segmentation image
* @param timeStep the time step for wich the surface interpolation information should be updated.
* @param plane the plane in which the slice lies
* @param detectIntersection if true the slice is eroded before contour extraction. If the slice is empty after the
* erosion it is most
* likely an intersecting contour an will not be added to the SurfaceInterpolationController
*/
static void UpdateAllSurfaceInterpolations(const LabelSetImage* workingImage,
TimeStepType timeStep,
const PlaneGeometry *plane,
bool detectIntersection);
/**
* \brief Extract the slice of an image that the user just scribbles on. The given component denotes the vector component of an vector image.
*
* \param positionEvent Event that specifies the plane that should be used to slice
* \param image Image that should be sliced
* \param component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component.
*
* \return 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem
* getting the image data at that position.
*/
static Image::Pointer GetAffectedImageSliceAs2DImage(const InteractionPositionEvent* positionEvent, const Image* image, unsigned int component = 0);
/**
* \brief Extract the slice of an image cut by given plane. The given component denotes the vector component of a vector image.
*
* \param planeGeometry Geometry defining the slice that should be cut out.
* \param image Image that should be sliced
* \param timeStep TimeStep of the image that shold be sliced
* \param component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component.
*
* \return 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem
* getting the image data at that position.
*/
static Image::Pointer GetAffectedImageSliceAs2DImage(const PlaneGeometry* planeGeometry,
const Image* image,
TimeStepType timeStep,
unsigned int component = 0);
static Image::Pointer GetAffectedImageSliceAs2DImageByTimePoint(const PlaneGeometry* planeGeometry,
const Image* image,
TimePointType timePoint,
unsigned int component = 0);
/** Convenience overloaded version that can be called for a given planeGeometry, slice image and time step.
* Calls static WriteBackSegmentationResults*/
static void WriteBackSegmentationResult(const DataNode* workingNode, const PlaneGeometry* planeGeometry, const Image* segmentationResult, TimeStepType timeStep);
/** Convenience overloaded version that can be called for a given planeGeometry, slice image and time step.
* For more details see protected WriteSliceToVolume version.*/
static void WriteSliceToVolume(Image* workingImage, const PlaneGeometry* planeGeometry, const Image* slice, TimeStepType timeStep, bool allowUndo);
void SetShowMarkerNodes(bool);
/**
* \brief Enables or disables the 3D interpolation after writing back the 2D segmentation result, and defaults to
* true.
*/
void SetEnable3DInterpolation(bool);
void Activated() override;
void Deactivated() override;
itkSetMacro(IsTimePointChangeAware, bool);
itkGetMacro(IsTimePointChangeAware, bool);
itkBooleanMacro(IsTimePointChangeAware);
protected:
SegTool2D(); // purposely hidden
SegTool2D(const char *, const us::Module *interactorModule = nullptr); // purposely hidden
~SegTool2D() override;
/**
* @brief returns the segmentation node that should be modified by the tool.
*/
DataNode* GetWorkingDataNode() const;
Image* GetWorkingData() const;
DataNode* GetReferenceDataNode() const;
Image* GetReferenceData() const;
/**
* This function can be reimplemented by derived classes to react on changes of the current
* time point. Default implementation does nothing.*/
virtual void OnTimePointChanged();
struct SliceInformation
{
mitk::Image::ConstPointer slice;
const mitk::PlaneGeometry *plane = nullptr;
mitk::TimeStepType timestep = 0;
unsigned int slicePosition;
SliceInformation() = default;
SliceInformation(const mitk::Image* aSlice, const mitk::PlaneGeometry* aPlane, mitk::TimeStepType aTimestep);
};
/**
* @brief Updates the surface interpolation by extracting the contour form the given slice.
* @param sliceInfos vector of slice information instances from which the contours should be extracted
* @param workingImage the segmentation image
* @param detectIntersection if true the slice is eroded before contour extraction. If the slice is empty after the
* @param activeLabelValue The label value of the active label.
* erosion it is most
* likely an intersecting contour an will not be added to the SurfaceInterpolationController
*/
static void UpdateSurfaceInterpolation(const std::vector<SliceInformation>& sliceInfos,
const Image* workingImage,
bool detectIntersection,
mitk::Label::PixelType activeLabelValue);
/**
* \brief Filters events that cannot be handled by 2D segmentation tools
*
* Currently an event is discarded if it was not sent by a 2D renderwindow and if it is
* not of type InteractionPositionEvent
*/
bool FilterEvents(InteractionEvent *interactionEvent, DataNode *dataNode) override;
/**
\brief Extract the slice of the currently selected working image that the user just scribbles on.
\return nullptr if SegTool2D is either unable to determine which slice was affected, or if there was some problem
getting the image data at that position,
or just no working image is selected.
*/
Image::Pointer GetAffectedWorkingSlice(const InteractionPositionEvent *) const;
/**
\brief Extract the slice of the currently selected reference image that the user just scribbles on.
\return nullptr if SegTool2D is either unable to determine which slice was affected, or if there was some problem
getting the image data at that position,
or just no reference image is selected.
*/
Image::Pointer GetAffectedReferenceSlice(const InteractionPositionEvent *) const;
/** Overload version that gets the reference slice passed on the passed plane geometry and timestep.*/
Image::Pointer GetAffectedReferenceSlice(const PlaneGeometry* planeGeometry, TimeStepType timeStep) const;
/** Convenience version that can be called for a given event (which is used to deduce timepoint and plane) and a slice image.
* Calls non static WriteBackSegmentationResults*/
void WriteBackSegmentationResult(const InteractionPositionEvent *, const Image* segmentationResult);
/** Convenience version that can be called for a given planeGeometry, slice image and time step.
* Calls non static WriteBackSegmentationResults*/
void WriteBackSegmentationResult(const PlaneGeometry *planeGeometry, const Image* segmentationResult, TimeStepType timeStep);
/** Overloaded version that calls the static version and also adds the contour markers.
* @remark If the sliceList is empty, this function does nothing.*/
void WriteBackSegmentationResults(const std::vector<SliceInformation> &sliceList, bool writeSliceToVolume = true);
/** \brief Writes all provided source slices into the data of the passed workingNode.
* The function does the following: 1) for every passed slice write it to workingNode (and generate and undo/redo step);
* 2) update the surface interpolation and 3) mark the node as modified.
* @param workingNode Pointer to the node that contains the working image.
* @param sliceList Vector of all slices that should be written into the workingNode. If the list is
* empty, the function call does nothing.
* @param writeSliceToVolume If set to false the write operation (WriteSliceToVolume will be skipped)
* and only the surface interpolation will be updated.
* @pre workingNode must point to a valid instance and contain an image instance as data.*/
static void WriteBackSegmentationResults(const DataNode* workingNode, const std::vector<SliceInformation>& sliceList, bool writeSliceToVolume = true);
- /** Writes the provided source slice into the target slice with the given pixel value.
- * If passed workingImage is a LabelSetImage the label set rules will be applied when
- * writing all non zero source pixels into the target slice (e.g. locked lables will not be touched)
- * with the given paintingPixelValue.
- * @param targetSlice Pointer to the slice that should be filled with the content of the sourceSlice.
- * @param sourceSlice Pointer to the slice that is the source/preview every pixel will be (tried to be) transfered .
- * @param workingImage Will be used to check if LabeSetImageRules have to be applied and the label set state.
- * @param paintingPixelValue Value that will be used to paint onto target slice.
- * @pre targetSlice must point to a valid instance.
- * @pre sourceSlice must point to a valid instance.
- * @pre workingImage must point to a valid instance.*/
- static void WritePreviewOnWorkingImage(
- Image *targetSlice, const Image *sourceSlice, const Image *workingImage, int paintingPixelValue);
-
/** Writes a provided slice into the passed working image. The content of working image that is covered
* by the slice will be completly overwritten. If asked for it also generates the needed
* undo/redo steps.
* @param workingImage Pointer to the image that is the target of the write operation.
* @param sliceInfo SliceInfo instance that containes the slice image, the defining plane geometry and time step.
* @param allowUndo Indicates if undo/redo operations should be registered for the write operation
* performed by this call. true: undo/redo will be generated; false: no undo/redo will be generated, so
* this operation cannot be revoked by the user.
* @pre workingImage must point to a valid instance.*/
static void WriteSliceToVolume(Image* workingImage, const SliceInformation &sliceInfo, bool allowUndo);
/**
\brief Adds a new node called Contourmarker to the datastorage which holds a mitk::PlanarFigure.
By selecting this node the slicestack will be reoriented according to the passed
PlanarFigure's Geometry
*/
int AddContourmarker(const PlaneGeometry* planeGeometry, unsigned int sliceIndex);
void InteractiveSegmentationBugMessage(const std::string &message) const;
/** Helper function to check if a position events points to a point inside the boundingbox of a passed
data instance.*/
static bool IsPositionEventInsideImageRegion(InteractionPositionEvent* positionEvent, const BaseData* data);
BaseRenderer *m_LastEventSender = nullptr;
unsigned int m_LastEventSlice = 0;
itkGetMacro(LastTimePointTriggered, TimePointType);
private:
/** Internal method that gets triggered as soon as the tool manager indicates a
* time point change. If the time point has changed since last time and tool
* is set to be time point change aware, OnTimePointChanged() will be called.*/
void OnTimePointChangedInternal();
static void RemoveContourFromInterpolator(const SliceInformation& sliceInfo, LabelSetImage::LabelValueType labelValue);
// The prefix of the contourmarkername. Suffix is a consecutive number
const std::string m_Contourmarkername;
bool m_ShowMarkerNodes = false;
static bool m_SurfaceInterpolationEnabled;
bool m_IsTimePointChangeAware = true;
TimePointType m_LastTimePointTriggered = 0.;
};
} // namespace
#endif