diff --git a/Modules/Segmentation/Algorithms/mitkImageLiveWireContourModelFilter.cpp b/Modules/Segmentation/Algorithms/mitkImageLiveWireContourModelFilter.cpp
index 33c9d9100f..57e4636d0a 100644
--- a/Modules/Segmentation/Algorithms/mitkImageLiveWireContourModelFilter.cpp
+++ b/Modules/Segmentation/Algorithms/mitkImageLiveWireContourModelFilter.cpp
@@ -1,444 +1,444 @@
/*============================================================================
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 "mitkImageLiveWireContourModelFilter.h"
#include <itkCastImageFilter.h>
#include <itkGradientMagnitudeImageFilter.h>
#include <itkImageRegionIterator.h>
#include "mitkIOUtil.h"
mitk::ImageLiveWireContourModelFilter::ImageLiveWireContourModelFilter()
{
OutputType::Pointer output = dynamic_cast<OutputType *>(this->MakeOutput(0).GetPointer());
this->SetNumberOfRequiredInputs(1);
this->SetNumberOfIndexedOutputs(1);
this->SetNthOutput(0, output.GetPointer());
m_CostFunction = CostFunctionType::New();
m_ShortestPathFilter = ShortestPathImageFilterType::New();
m_ShortestPathFilter->SetCostFunction(m_CostFunction);
m_UseDynamicCostMap = false;
m_TimeStep = 0;
}
mitk::ImageLiveWireContourModelFilter::~ImageLiveWireContourModelFilter()
{
}
mitk::ImageLiveWireContourModelFilter::OutputType *mitk::ImageLiveWireContourModelFilter::GetOutput()
{
return Superclass::GetOutput();
}
void mitk::ImageLiveWireContourModelFilter::SetInput(const mitk::ImageLiveWireContourModelFilter::InputType *input)
{
this->SetInput(0, input);
}
void mitk::ImageLiveWireContourModelFilter::SetInput(unsigned int idx,
const mitk::ImageLiveWireContourModelFilter::InputType *input)
{
if (idx + 1 > this->GetNumberOfInputs())
{
this->SetNumberOfRequiredInputs(idx + 1);
}
if (input != static_cast<InputType *>(this->ProcessObject::GetInput(idx)))
{
this->ProcessObject::SetNthInput(idx, const_cast<InputType *>(input));
this->Modified();
AccessFixedDimensionByItk(input, ItkPreProcessImage, 2);
}
}
const mitk::ImageLiveWireContourModelFilter::InputType *mitk::ImageLiveWireContourModelFilter::GetInput(void)
{
if (this->GetNumberOfInputs() < 1)
return nullptr;
return static_cast<const mitk::ImageLiveWireContourModelFilter::InputType *>(this->ProcessObject::GetInput(0));
}
const mitk::ImageLiveWireContourModelFilter::InputType *mitk::ImageLiveWireContourModelFilter::GetInput(
unsigned int idx)
{
if (this->GetNumberOfInputs() < 1)
return nullptr;
return static_cast<const mitk::ImageLiveWireContourModelFilter::InputType *>(this->ProcessObject::GetInput(idx));
}
void mitk::ImageLiveWireContourModelFilter::GenerateData()
{
mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(this->GetInput());
if (!input)
{
MITK_ERROR << "No input available.";
- itkExceptionMacro("mitk::ImageToLiveWireContourFilter: No input available. Please set the input!");
+ itkExceptionMacro("mitk::ImageToLiveWireContourModelFilter: No input available. Please set the input!");
return;
}
if (input->GetDimension() != 2)
{
MITK_ERROR << "Filter is only working on 2D images.";
- itkExceptionMacro("mitk::ImageToLiveWireContourFilter: Filter is only working on 2D images.. Please make sure that "
+ itkExceptionMacro("mitk::ImageToLiveWireContourModelFilter: Filter is only working on 2D images.. Please make sure that "
"the input is 2D!");
return;
}
input->GetGeometry()->WorldToIndex(m_StartPoint, m_StartPointInIndex);
input->GetGeometry()->WorldToIndex(m_EndPoint, m_EndPointInIndex);
m_StartPointInIndex[0] = std::round(m_StartPointInIndex[0]);
m_StartPointInIndex[1] = std::round(m_StartPointInIndex[1]);
m_StartPointInIndex[2] = std::round(m_StartPointInIndex[2]);
m_EndPointInIndex[0] = std::round(m_EndPointInIndex[0]);
m_EndPointInIndex[1] = std::round(m_EndPointInIndex[1]);
m_EndPointInIndex[2] = std::round(m_EndPointInIndex[2]);
// only start calculating if both indices are inside image geometry
if (input->GetGeometry()->IsIndexInside(this->m_StartPointInIndex) &&
input->GetGeometry()->IsIndexInside(this->m_EndPointInIndex))
{
try
{
this->UpdateLiveWire();
}
catch (itk::ExceptionObject &e)
{
MITK_INFO << "Exception caught during live wiring calculation: " << e;
return;
}
}
}
template <typename TPixel, unsigned int VImageDimension>
void mitk::ImageLiveWireContourModelFilter::ItkPreProcessImage(const itk::Image<TPixel, VImageDimension> *inputImage)
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef itk::CastImageFilter<InputImageType, InternalImageType> CastFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput(inputImage);
castFilter->Update();
m_InternalImage = castFilter->GetOutput();
m_CostFunction->SetImage(m_InternalImage);
m_ShortestPathFilter->SetInput(m_InternalImage);
}
void mitk::ImageLiveWireContourModelFilter::ClearRepulsivePoints()
{
m_CostFunction->ClearRepulsivePoints();
}
void mitk::ImageLiveWireContourModelFilter::AddRepulsivePoint(const itk::Index<2> &idx)
{
m_CostFunction->AddRepulsivePoint(idx);
}
void mitk::ImageLiveWireContourModelFilter::DumpMaskImage()
{
mitk::Image::Pointer mask = mitk::Image::New();
mask->InitializeByItk(this->m_CostFunction->GetMaskImage());
mask->SetVolume(this->m_CostFunction->GetMaskImage()->GetBufferPointer());
mitk::IOUtil::Save(mask, "G:\\Data\\mask.nrrd");
}
void mitk::ImageLiveWireContourModelFilter::RemoveRepulsivePoint(const itk::Index<2> &idx)
{
m_CostFunction->RemoveRepulsivePoint(idx);
}
void mitk::ImageLiveWireContourModelFilter::SetRepulsivePoints(const ShortestPathType &points)
{
m_CostFunction->ClearRepulsivePoints();
auto iter = points.begin();
for (; iter != points.end(); iter++)
{
m_CostFunction->AddRepulsivePoint((*iter));
}
}
void mitk::ImageLiveWireContourModelFilter::UpdateLiveWire()
{
// compute the requested region for itk filters
InternalImageType::IndexType startPoint, endPoint;
startPoint[0] = m_StartPointInIndex[0];
startPoint[1] = m_StartPointInIndex[1];
endPoint[0] = m_EndPointInIndex[0];
endPoint[1] = m_EndPointInIndex[1];
// minimum value in each direction for startRegion
InternalImageType::IndexType startRegion;
startRegion[0] = startPoint[0] < endPoint[0] ? startPoint[0] : endPoint[0];
startRegion[1] = startPoint[1] < endPoint[1] ? startPoint[1] : endPoint[1];
// maximum value in each direction for size
InternalImageType::SizeType size;
size[0] = std::abs(startPoint[0] - endPoint[0]) + 1;
size[1] = std::abs(startPoint[1] - endPoint[1]) + 1;
CostFunctionType::RegionType region;
region.SetSize(size);
region.SetIndex(startRegion);
// inputImage->SetRequestedRegion(region);
// extracts features from image and calculates costs
// m_CostFunction->SetImage(m_InternalImage);
m_CostFunction->SetStartIndex(startPoint);
m_CostFunction->SetEndIndex(endPoint);
m_CostFunction->SetRequestedRegion(region);
m_CostFunction->SetUseCostMap(m_UseDynamicCostMap);
// calculate shortest path between start and end point
m_ShortestPathFilter->SetFullNeighborsMode(true);
// m_ShortestPathFilter->SetInput( m_CostFunction->SetImage(m_InternalImage) );
m_ShortestPathFilter->SetMakeOutputImage(false);
// m_ShortestPathFilter->SetCalcAllDistances(true);
m_ShortestPathFilter->SetStartIndex(startPoint);
m_ShortestPathFilter->SetEndIndex(endPoint);
m_ShortestPathFilter->Update();
// construct contour from path image
// get the shortest path as vector
ShortestPathType shortestPath = m_ShortestPathFilter->GetVectorPath();
// fill the output contour with control points from the path
OutputType::Pointer output = dynamic_cast<OutputType *>(this->MakeOutput(0).GetPointer());
this->SetNthOutput(0, output.GetPointer());
// OutputType::Pointer output = dynamic_cast<OutputType*> ( this->GetOutput() );
output->Expand(m_TimeStep + 1);
// output->Clear();
mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(this->GetInput());
ShortestPathType::const_iterator pathIterator = shortestPath.begin();
while (pathIterator != shortestPath.end())
{
mitk::Point3D currentPoint;
currentPoint[0] = static_cast<mitk::ScalarType>((*pathIterator)[0]);
currentPoint[1] = static_cast<mitk::ScalarType>((*pathIterator)[1]);
currentPoint[2] = 0.0;
input->GetGeometry()->IndexToWorld(currentPoint, currentPoint);
output->AddVertex(currentPoint, false, m_TimeStep);
pathIterator++;
}
}
bool mitk::ImageLiveWireContourModelFilter::CreateDynamicCostMap(mitk::ContourModel *path)
{
mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(this->GetInput());
if (!input)
return false;
try
{
AccessFixedDimensionByItk_1(input, CreateDynamicCostMapByITK, 2, path);
}
catch (itk::ExceptionObject &e)
{
MITK_INFO << "Exception caught during dynamic cost map alculation: " << e;
return false;
}
return true;
}
template <typename TPixel, unsigned int VImageDimension>
void mitk::ImageLiveWireContourModelFilter::CreateDynamicCostMapByITK(
const itk::Image<TPixel, VImageDimension> *inputImage, mitk::ContourModel *path)
{
/*++++++++++ create dynamic cost transfer map ++++++++++*/
/* Compute the costs of the gradient magnitude dynamically.
* using a map of the histogram of gradient magnitude image.
* Use the histogram gradient map to interpolate the costs
* with gaussing function including next two bins right and left
* to current position x. With the histogram gradient costs are interpolated
* with a gaussing function summation of next two bins right and left
* to current position x.
*/
std::vector<itk::Index<VImageDimension>> shortestPath;
mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(this->GetInput());
if (path == nullptr)
{
OutputType::Pointer output = this->GetOutput();
auto it = output->IteratorBegin();
while (it != output->IteratorEnd())
{
itk::Index<VImageDimension> cur;
mitk::Point3D c = (*it)->Coordinates;
input->GetGeometry()->WorldToIndex(c, c);
cur[0] = c[0];
cur[1] = c[1];
shortestPath.push_back(cur);
it++;
}
}
else
{
auto it = path->IteratorBegin();
while (it != path->IteratorEnd())
{
itk::Index<VImageDimension> cur;
mitk::Point3D c = (*it)->Coordinates;
input->GetGeometry()->WorldToIndex(c, c);
cur[0] = c[0];
cur[1] = c[1];
shortestPath.push_back(cur);
it++;
}
}
// filter image gradient magnitude
typedef itk::GradientMagnitudeImageFilter<itk::Image<TPixel, VImageDimension>, itk::Image<TPixel, VImageDimension>>
GradientMagnitudeFilterType;
typename GradientMagnitudeFilterType::Pointer gradientFilter = GradientMagnitudeFilterType::New();
gradientFilter->SetInput(inputImage);
gradientFilter->Update();
typename itk::Image<TPixel, VImageDimension>::Pointer gradientMagnImage = gradientFilter->GetOutput();
// get the path
// iterator of path
auto pathIterator = shortestPath.begin();
std::map<int, int> histogram;
// create histogram within path
while (pathIterator != shortestPath.end())
{
// count pixel values
// use scale factor to avoid mapping gradients between 0.0 and 1.0 to same bin
histogram[static_cast<int>(gradientMagnImage->GetPixel((*pathIterator)) *
ImageLiveWireContourModelFilter::CostFunctionType::MAPSCALEFACTOR)] += 1;
pathIterator++;
}
double max = 1.0;
if (!histogram.empty())
{
std::map<int, int>::iterator itMAX;
// get max of histogramm
int currentMaxValue = 0;
auto it = histogram.begin();
while (it != histogram.end())
{
if ((*it).second > currentMaxValue)
{
itMAX = it;
currentMaxValue = (*it).second;
}
it++;
}
std::map<int, int>::key_type keyOfMax = itMAX->first;
// compute the to max of gaussian summation
auto end = histogram.end();
auto last = --(histogram.end());
std::map<int, int>::iterator left2;
std::map<int, int>::iterator left1;
std::map<int, int>::iterator right1;
std::map<int, int>::iterator right2;
right1 = itMAX;
if (right1 == end || right1 == last)
{
right2 = end;
}
else //( right1 <= last )
{
auto temp = right1;
right2 = ++right1; // rght1 + 1
right1 = temp;
}
if (right1 == histogram.begin())
{
left1 = end;
left2 = end;
}
else if (right1 == (++(histogram.begin())))
{
auto temp = right1;
left1 = --right1; // rght1 - 1
right1 = temp;
left2 = end;
}
else
{
auto temp = right1;
left1 = --right1; // rght1 - 1
left2 = --right1; // rght1 - 2
right1 = temp;
}
double partRight1, partRight2, partLeft1, partLeft2;
partRight1 = partRight2 = partLeft1 = partLeft2 = 0.0;
/*
f(x) = v(bin) * e^ ( -1/2 * (|x-k(bin)| / sigma)^2 )
gaussian approximation
where
v(bin) is the value in the map
k(bin) is the key
*/
if (left2 != end)
{
partLeft2 = ImageLiveWireContourModelFilter::CostFunctionType::Gaussian(keyOfMax, left2->first, left2->second);
}
if (left1 != end)
{
partLeft1 = ImageLiveWireContourModelFilter::CostFunctionType::Gaussian(keyOfMax, left1->first, left1->second);
}
if (right1 != end)
{
partRight1 = ImageLiveWireContourModelFilter::CostFunctionType::Gaussian(keyOfMax, right1->first, right1->second);
}
if (right2 != end)
{
partRight2 = ImageLiveWireContourModelFilter::CostFunctionType::Gaussian(keyOfMax, right2->first, right2->second);
}
max = (partRight1 + partRight2 + partLeft1 + partLeft2);
}
this->m_CostFunction->SetDynamicCostMap(histogram);
this->m_CostFunction->SetCostMapMaximum(max);
}
diff --git a/Modules/Segmentation/Algorithms/mitkImageToLiveWireContourFilter.cpp b/Modules/Segmentation/Algorithms/mitkImageToLiveWireContourFilter.cpp
deleted file mode 100644
index f62050ebc7..0000000000
--- a/Modules/Segmentation/Algorithms/mitkImageToLiveWireContourFilter.cpp
+++ /dev/null
@@ -1,169 +0,0 @@
-/*============================================================================
-
-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 "mitkImageToLiveWireContourFilter.h"
-
-#include <itkImageRegionIterator.h>
-#include <itkShortestPathCostFunctionLiveWire.h>
-#include <itkShortestPathImageFilter.h>
-
-mitk::ImageToLiveWireContourFilter::ImageToLiveWireContourFilter()
-{
- OutputType::Pointer output = dynamic_cast<OutputType *>(this->MakeOutput(0).GetPointer());
- this->SetNumberOfRequiredInputs(1);
- this->SetNumberOfIndexedOutputs(1);
- this->SetNthOutput(0, output.GetPointer());
-}
-
-mitk::ImageToLiveWireContourFilter::~ImageToLiveWireContourFilter()
-{
-}
-
-void mitk::ImageToLiveWireContourFilter::SetInput(const mitk::ImageToLiveWireContourFilter::InputType *input)
-{
- this->SetInput(0, input);
-}
-
-void mitk::ImageToLiveWireContourFilter::SetInput(unsigned int idx,
- const mitk::ImageToLiveWireContourFilter::InputType *input)
-{
- if (idx + 1 > this->GetNumberOfInputs())
- {
- this->SetNumberOfRequiredInputs(idx + 1);
- }
- if (input != static_cast<InputType *>(this->ProcessObject::GetInput(idx)))
- {
- this->ProcessObject::SetNthInput(idx, const_cast<InputType *>(input));
- this->Modified();
- }
-}
-
-const mitk::ImageToLiveWireContourFilter::InputType *mitk::ImageToLiveWireContourFilter::GetInput(void)
-{
- if (this->GetNumberOfInputs() < 1)
- return nullptr;
- return static_cast<const mitk::ImageToLiveWireContourFilter::InputType *>(this->ProcessObject::GetInput(0));
-}
-
-const mitk::ImageToLiveWireContourFilter::InputType *mitk::ImageToLiveWireContourFilter::GetInput(unsigned int idx)
-{
- if (this->GetNumberOfInputs() < 1)
- return nullptr;
- return static_cast<const mitk::ImageToLiveWireContourFilter::InputType *>(this->ProcessObject::GetInput(idx));
-}
-
-void mitk::ImageToLiveWireContourFilter::GenerateData()
-{
- mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(this->GetInput());
-
- if (!input)
- {
- MITK_ERROR << "No input available.";
- itkExceptionMacro("mitk::ImageToLiveWireContourFilter: No input available. Please set the input!");
- return;
- }
-
- if (input->GetDimension() != 2)
- {
- MITK_ERROR << "Filter is only working on 2D images.";
- itkExceptionMacro("mitk::ImageToLiveWireContourFilter: Filter is only working on 2D images.. Please make sure that "
- "the input is 2D!");
- return;
- }
-
- input->GetGeometry()->WorldToIndex(m_StartPoint, m_StartPointInIndex);
- input->GetGeometry()->WorldToIndex(m_EndPoint, m_EndPointInIndex);
-
- AccessFixedDimensionByItk(input, ItkProcessImage, 2);
-}
-
-template <typename TPixel, unsigned int VImageDimension>
-void mitk::ImageToLiveWireContourFilter::ItkProcessImage(const itk::Image<TPixel, VImageDimension> *)
-{
- // typedef itk::Image< TPixel, VImageDimension > InputImageType;
- // typedef itk::Image< float, 2 > FloatImageType;
-
- // typedef typename itk::ShortestPathImageFilter< InputImageType, InputImageType > ShortestPathImageFilterType;
- // typedef typename itk::ShortestPathCostFunctionLiveWire< InputImageType > CostFunctionType;
-
- // typedef InputImageType::IndexType IndexType;
-
- ///* compute the requested region for itk filters */
-
- // typename IndexType startPoint, endPoint;
- //
- // startPoint[0] = m_StartPointInIndex[0];
- // startPoint[1] = m_StartPointInIndex[1];
-
- // endPoint[0] = m_EndPointInIndex[0];
- // endPoint[1] = m_EndPointInIndex[1];
-
- ////minimum value in each direction for startRegion
- // typename IndexType startRegion;
- // startRegion[0] = startPoint[0] < endPoint[0] ? startPoint[0] : endPoint[0];
- // startRegion[1] = startPoint[1] < endPoint[1] ? startPoint[1] : endPoint[1];
-
- ////maximum value in each direction for size
- // typename InputImageType::SizeType size;
- // size[0] = startPoint[0] > endPoint[0] ? startPoint[0] : endPoint[0];
- // size[1] = startPoint[1] > endPoint[1] ? startPoint[1] : endPoint[1];
-
- // typename InputImageType::RegionType region;
- // region.SetSize( size );
- // region.SetIndex( startRegion );
- ///*---------------------------------------------*/
-
- ///* extracts features from image and calculates costs */
- // typename CostFunctionType::Pointer costFunction = CostFunctionType::New();
- // costFunction->SetImage(inputImage);
- // costFunction->SetStartIndex(startPoint);
- // costFunction->SetEndIndex(endPoint);
- // costFunction->SetRequestedRegion(region);
- ///*---------------------------------------------*/
-
- ///* calculate shortest path between start and end point */
- // ShortestPathImageFilterType::Pointer shortestPathFilter = ShortestPathImageFilterType::New();
- // shortestPathFilter->SetFullNeighborsMode(true);
- // shortestPathFilter->SetInput(inputImage);
- // shortestPathFilter->SetMakeOutputImage(true);
- // shortestPathFilter->SetStoreVectorOrder(false);
- ////shortestPathFilter->SetActivateTimeOut(true);
- // shortestPathFilter->SetStartIndex(startPoint);
- // shortestPathFilter->SetEndIndex(endPoint);
-
- // shortestPathFilter->Update();
-
- ///*---------------------------------------------*/
-
- ///* construct contour from path image */
- ////get the shortest path as vector
- // std::vector< itk::Index<3> > shortestPath = shortestPathFilter->GetVectorPath();
-
- ////fill the output contour with controll points from the path
- // OutputType::Pointer outputContour = this->GetOutput();
- // mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image*>(this->GetInput());
-
- // std::vector< itk::Index<3> >::iterator pathIterator = shortestPath.begin();
-
- // while(pathIterator != shortestPath.end())
- //{
- // mitk::Point3D currentPoint;
- // currentPoint[0] = (*pathIterator)[0];
- // currentPoint[1] = (*pathIterator)[1];
-
- // input->GetGeometry(0)->IndexToWorld(currentPoint, currentPoint);
- // outputContour->AddVertex(currentPoint);
- //
- // pathIterator++;
- //}
- /*---------------------------------------------*/
-}
diff --git a/Modules/Segmentation/Algorithms/mitkImageToLiveWireContourFilter.h b/Modules/Segmentation/Algorithms/mitkImageToLiveWireContourFilter.h
deleted file mode 100644
index b8e4f2c779..0000000000
--- a/Modules/Segmentation/Algorithms/mitkImageToLiveWireContourFilter.h
+++ /dev/null
@@ -1,80 +0,0 @@
-/*============================================================================
-
-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 mitkImageToLiveWireContourFilter_h
-#define mitkImageToLiveWireContourFilter_h
-
-#include "mitkCommon.h"
-#include "mitkContourModel.h"
-#include "mitkContourModelSource.h"
-#include <MitkSegmentationExports.h>
-
-#include <mitkImage.h>
-#include <mitkImageAccessByItk.h>
-#include <mitkImageCast.h>
-
-namespace mitk
-{
- /**
- *
- * \brief
- *
- * \ingroup ContourModelFilters
- * \ingroup Process
- */
- class MITKSEGMENTATION_EXPORT ImageToLiveWireContourFilter : public ContourModelSource
- {
- public:
- mitkClassMacro(ImageToLiveWireContourFilter, ContourModelSource);
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- typedef ContourModel OutputType;
- typedef OutputType::Pointer OutputTypePointer;
- typedef mitk::Image InputType;
-
- itkSetMacro(StartPoint, mitk::Point3D);
- itkGetMacro(StartPoint, mitk::Point3D);
-
- itkSetMacro(EndPoint, mitk::Point3D);
- itkGetMacro(EndPoint, mitk::Point3D);
-
- virtual void SetInput(const InputType *input);
-
- using Superclass::SetInput;
- virtual void SetInput(unsigned int idx, const InputType *input);
-
- const InputType *GetInput(void);
-
- const InputType *GetInput(unsigned int idx);
-
- protected:
- ImageToLiveWireContourFilter();
-
- ~ImageToLiveWireContourFilter() override;
-
- void GenerateData() override;
-
- void GenerateOutputInformation() override{};
-
- mitk::Point3D m_StartPoint;
- mitk::Point3D m_EndPoint;
-
- mitk::Point3D m_StartPointInIndex;
- mitk::Point3D m_EndPointInIndex;
-
- private:
- template <typename TPixel, unsigned int VImageDimension>
- void ItkProcessImage(const itk::Image<TPixel, VImageDimension> *inputImage);
- };
-}
-#endif
diff --git a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp
index 7754a8e450..8c2903ef39 100644
--- a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp
+++ b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp
@@ -1,262 +1,262 @@
/*============================================================================
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 <mitkContourModelUtils.h>
#include <mitkLiveWireTool2D.h>
#include <mitkLiveWireTool2D.xpm>
#include <mitkToolManager.h>
#include <mitkTimeNavigationController.h>
#include <usGetModuleContext.h>
#include <usModuleResource.h>
#include <type_traits>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, LiveWireTool2D, "LiveWire tool");
}
mitk::LiveWireTool2D::LiveWireTool2D()
: EditableContourTool(), m_CreateAndUseDynamicCosts(false)
{
}
mitk::LiveWireTool2D::~LiveWireTool2D()
{
}
void mitk::LiveWireTool2D::ConnectActionsAndFunctions()
{
mitk::EditableContourTool::ConnectActionsAndFunctions();
CONNECT_FUNCTION("MovePoint", OnMouseMoveNoDynamicCosts);
}
const char **mitk::LiveWireTool2D::GetXPM() const
{
return mitkLiveWireTool2D_xpm;
}
us::ModuleResource mitk::LiveWireTool2D::GetIconResource() const
{
return us::GetModuleContext()->GetModule()->GetResource("LiveWire.svg");
}
us::ModuleResource mitk::LiveWireTool2D::GetCursorIconResource() const
{
return us::GetModuleContext()->GetModule()->GetResource("LiveWire_Cursor.svg");
}
const char *mitk::LiveWireTool2D::GetName() const
{
return "Live Wire";
}
void mitk::LiveWireTool2D::UpdateLiveWireContour()
{
auto contour = this->GetContour();
if (nullptr != contour)
{
auto timeGeometry = contour->GetTimeGeometry()->Clone();
m_PreviewContour = this->m_LiveWireFilter->GetOutput();
// needed because the results of the filter are always from 0 ms
// to 1 ms and the filter also resets its outputs.
// generate a time geometry that is always visible as the working contour should always be.
auto contourTimeGeometry = ProportionalTimeGeometry::New();
contourTimeGeometry->SetStepDuration(std::numeric_limits<TimePointType>::max());
contourTimeGeometry->SetTimeStepGeometry(contour->GetTimeGeometry()->GetGeometryForTimeStep(0)->Clone(), 0);
m_PreviewContour->SetTimeGeometry(contourTimeGeometry);
m_PreviewContourNode->SetData(this->m_PreviewContour);
}
}
void mitk::LiveWireTool2D::OnTimePointChanged()
{
auto reference = this->GetReferenceData();
if (nullptr == reference || m_PlaneGeometry.IsNull() || m_LiveWireFilter.IsNull() || m_PreviewContourNode.IsNull())
return;
auto timeStep = reference->GetTimeGeometry()->TimePointToTimeStep(this->GetLastTimePointTriggered());
m_ReferenceDataSlice = GetAffectedImageSliceAs2DImageByTimePoint(m_PlaneGeometry, reference, timeStep);
m_LiveWireFilter->SetInput(m_ReferenceDataSlice);
m_LiveWireFilter->Update();
this->UpdateLiveWireContour();
RenderingManager::GetInstance()->RequestUpdateAll();
};
mitk::Point3D mitk::LiveWireTool2D::PrepareInitContour(const mitk::Point3D& clickedPoint)
{
- // Set current slice as input for ImageToLiveWireContourFilter
+ // Set current slice as input for ImageToLiveWireContourModelFilter
m_LiveWireFilter = ImageLiveWireContourModelFilter::New();
m_LiveWireFilter->SetUseCostFunction(true);
m_LiveWireFilter->SetInput(m_ReferenceDataSlice);
itk::Index<3> idx;
m_ReferenceDataSlice->GetGeometry()->WorldToIndex(clickedPoint, idx);
// Get the pixel with the highest gradient in a 7x7 region
itk::Index<3> indexWithHighestGradient;
AccessFixedDimensionByItk_2(m_ReferenceDataSlice, FindHighestGradientMagnitudeByITK, 2, idx, indexWithHighestGradient);
Point3D adaptedClick;
m_ReferenceDataSlice->GetGeometry()->IndexToWorld(indexWithHighestGradient, adaptedClick);
m_CreateAndUseDynamicCosts = true;
return adaptedClick;
}
void mitk::LiveWireTool2D::FinalizePreviewContour(const Point3D& clickedPoint)
{
// Add repulsive points to avoid getting the same path again
std::for_each(m_PreviewContour->IteratorBegin(), m_PreviewContour->IteratorEnd(), [this](ContourElement::VertexType* vertex) {
ImageLiveWireContourModelFilter::InternalImageType::IndexType idx;
this->m_ReferenceDataSlice->GetGeometry()->WorldToIndex(vertex->Coordinates, idx);
this->m_LiveWireFilter->AddRepulsivePoint(idx);
});
EditableContourTool::FinalizePreviewContour(clickedPoint);
}
void mitk::LiveWireTool2D::InitializePreviewContour(const Point3D& clickedPoint)
{
m_PreviewContour->Clear();
// Set new start point
m_LiveWireFilter->SetStartPoint(clickedPoint);
if (m_CreateAndUseDynamicCosts)
{
auto contour = this->GetContour();
// Use dynamic cost map for next update
m_LiveWireFilter->CreateDynamicCostMap(contour);
m_LiveWireFilter->SetUseDynamicCostMap(true);
}
}
void mitk::LiveWireTool2D::UpdatePreviewContour(const Point3D& clickedPoint)
{ // Compute LiveWire segment from last control point to current mouse position
m_LiveWireFilter->SetEndPoint(clickedPoint);
m_LiveWireFilter->Update();
this->UpdateLiveWireContour();
}
void mitk::LiveWireTool2D::OnMouseMoveNoDynamicCosts(StateMachineAction *, InteractionEvent *interactionEvent)
{
m_LiveWireFilter->SetUseDynamicCostMap(false);
this->OnMouseMoved(nullptr, interactionEvent);
m_LiveWireFilter->SetUseDynamicCostMap(true);
}
void mitk::LiveWireTool2D::FinishTool()
{
m_LiveWireFilter->SetUseDynamicCostMap(false);
m_ContourInteractor = mitk::ContourModelLiveWireInteractor::New();
m_ContourInteractor->SetDataNode(m_ContourNode);
m_ContourInteractor->LoadStateMachine("ContourModelModificationInteractor.xml", us::GetModuleContext()->GetModule());
m_ContourInteractor->SetEventConfig("ContourModelModificationConfig.xml", us::GetModuleContext()->GetModule());
m_ContourInteractor->SetWorkingImage(this->m_ReferenceDataSlice);
m_ContourInteractor->SetRestrictedArea(this->m_CurrentRestrictedArea);
m_ContourNode->SetDataInteractor(m_ContourInteractor.GetPointer());
}
template <typename TPixel, unsigned int VImageDimension>
void mitk::LiveWireTool2D::FindHighestGradientMagnitudeByITK(itk::Image<TPixel, VImageDimension> *inputImage,
itk::Index<3> &index,
itk::Index<3> &returnIndex)
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef typename InputImageType::IndexType IndexType;
const auto MAX_X = inputImage->GetLargestPossibleRegion().GetSize()[0];
const auto MAX_Y = inputImage->GetLargestPossibleRegion().GetSize()[1];
returnIndex[0] = index[0];
returnIndex[1] = index[1];
returnIndex[2] = 0.0;
double gradientMagnitude = 0.0;
double maxGradientMagnitude = 0.0;
// The size and thus the region of 7x7 is only used to calculate the gradient magnitude in that region,
// not for searching the maximum value.
// Maximum value in each direction for size
typename InputImageType::SizeType size;
size[0] = 7;
size[1] = 7;
// Minimum value in each direction for startRegion
IndexType startRegion;
startRegion[0] = index[0] - 3;
startRegion[1] = index[1] - 3;
if (startRegion[0] < 0)
startRegion[0] = 0;
if (startRegion[1] < 0)
startRegion[1] = 0;
if (MAX_X - index[0] < 7)
startRegion[0] = MAX_X - 7;
if (MAX_Y - index[1] < 7)
startRegion[1] = MAX_Y - 7;
index[0] = startRegion[0] + 3;
index[1] = startRegion[1] + 3;
typename InputImageType::RegionType region;
region.SetSize(size);
region.SetIndex(startRegion);
typedef typename itk::GradientMagnitudeImageFilter<InputImageType, InputImageType> GradientMagnitudeFilterType;
typename GradientMagnitudeFilterType::Pointer gradientFilter = GradientMagnitudeFilterType::New();
gradientFilter->SetInput(inputImage);
gradientFilter->GetOutput()->SetRequestedRegion(region);
gradientFilter->Update();
typename InputImageType::Pointer gradientMagnitudeImage;
gradientMagnitudeImage = gradientFilter->GetOutput();
IndexType currentIndex;
currentIndex[0] = 0;
currentIndex[1] = 0;
// Search max (approximate) gradient magnitude
for (int x = -1; x <= 1; ++x)
{
currentIndex[0] = index[0] + x;
for (int y = -1; y <= 1; ++y)
{
currentIndex[1] = index[1] + y;
gradientMagnitude = gradientMagnitudeImage->GetPixel(currentIndex);
// Check for new max
if (maxGradientMagnitude < gradientMagnitude)
{
maxGradientMagnitude = gradientMagnitude;
returnIndex[0] = currentIndex[0];
returnIndex[1] = currentIndex[1];
returnIndex[2] = 0.0;
}
}
currentIndex[1] = index[1];
}
}
diff --git a/Modules/Segmentation/files.cmake b/Modules/Segmentation/files.cmake
index 26317aa6b3..31b461d399 100644
--- a/Modules/Segmentation/files.cmake
+++ b/Modules/Segmentation/files.cmake
@@ -1,118 +1,117 @@
set(CPP_FILES
Algorithms/mitkCalculateSegmentationVolume.cpp
Algorithms/mitkContourModelSetToImageFilter.cpp
Algorithms/mitkContourSetToPointSetFilter.cpp
Algorithms/mitkContourUtils.cpp
Algorithms/mitkCorrectorAlgorithm.cpp
Algorithms/mitkDiffImageApplier.cpp
Algorithms/mitkDiffSliceOperation.cpp
Algorithms/mitkDiffSliceOperationApplier.cpp
Algorithms/mitkGrowCutSegmentationFilter.cpp
Algorithms/mitkImageLiveWireContourModelFilter.cpp
Algorithms/mitkImageToContourFilter.cpp
- Algorithms/mitkImageToLiveWireContourFilter.cpp
Algorithms/mitkManualSegmentationToSurfaceFilter.cpp
Algorithms/mitkOtsuSegmentationFilter.cpp
Algorithms/mitkSegmentationHelper.cpp
Algorithms/mitkSegmentationObjectFactory.cpp
Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp
Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp
Algorithms/mitkShowSegmentationAsSurface.cpp
Algorithms/mitkVtkImageOverwrite.cpp
Controllers/mitkSegmentationInterpolationController.cpp
Controllers/mitkToolManager.cpp
Controllers/mitkSegmentationModuleActivator.cpp
Controllers/mitkToolManagerProvider.cpp
DataManagement/mitkContour.cpp
DataManagement/mitkContourSet.cpp
DataManagement/mitkExtrudedContour.cpp
Interactions/mitkAddContourTool.cpp
Interactions/mitkAutoCropTool.cpp
Interactions/mitkSegWithPreviewTool.cpp
Interactions/mitkBinaryThresholdBaseTool.cpp
Interactions/mitkBinaryThresholdTool.cpp
Interactions/mitkBinaryThresholdULTool.cpp
Interactions/mitkCloseRegionTool.cpp
Interactions/mitkContourModelInteractor.cpp
Interactions/mitkContourModelLiveWireInteractor.cpp
Interactions/mitkEditableContourTool.cpp
Interactions/mitkLiveWireTool2D.cpp
Interactions/mitkLassoTool.cpp
Interactions/mitkContourTool.cpp
Interactions/mitkDrawPaintbrushTool.cpp
Interactions/mitkErasePaintbrushTool.cpp
Interactions/mitkEraseRegionTool.cpp
Interactions/mitkFeedbackContourTool.cpp
Interactions/mitkFillRegionBaseTool.cpp
Interactions/mitkFillRegionTool.cpp
Interactions/mitkGrowCutTool.cpp
Interactions/mitkOtsuTool3D.cpp
Interactions/mitkPaintbrushTool.cpp
Interactions/mitkRegionGrowingTool.cpp
Interactions/mitkSegmentationsProcessingTool.cpp
Interactions/mitkSegTool2D.cpp
Interactions/mitkSubtractContourTool.cpp
Interactions/mitkTool.cpp
Interactions/mitkToolCommand.cpp
Interactions/mitkPickingTool.cpp
Interactions/mitknnUnetTool.cpp
Interactions/mitkProcessExecutor.cpp
Interactions/mitkSegmentAnythingProcessExecutor.cpp
Interactions/mitkTotalSegmentatorTool.cpp
Interactions/mitkSegmentAnythingTool.cpp
Interactions/mitkMedSAMTool.cpp
Interactions/mitkSegmentAnythingPythonService.cpp
Rendering/mitkContourMapper2D.cpp
Rendering/mitkContourSetMapper2D.cpp
Rendering/mitkContourSetVtkMapper3D.cpp
Rendering/mitkContourVtkMapper3D.cpp
SegmentationUtilities/BooleanOperations/mitkBooleanOperation.cpp
SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp
#Added from ML
Algorithms/mitkSurfaceStampImageFilter.cpp
)
set(RESOURCE_FILES
Add.svg
Add_Cursor.svg
AI.svg
AI_Cursor.svg
Close.svg
Close_Cursor.svg
Erase.svg
Erase_Cursor.svg
Fill.svg
Fill_Cursor.svg
LiveWire.svg
LiveWire_Cursor.svg
Lasso.svg
GrowCut.svg
Lasso_Cursor.svg
Otsu.svg
Paint.svg
Paint_Cursor.svg
Picking.svg
RegionGrowing.svg
RegionGrowing_Cursor.svg
Subtract.svg
Subtract_Cursor.svg
Threshold.svg
ULThreshold.svg
Wipe.svg
Wipe_Cursor.svg
Interactions/dummy.xml
Interactions/EditableContourTool.xml
Interactions/PickingTool.xml
Interactions/MouseReleaseOnly.xml
Interactions/PressMoveRelease.xml
Interactions/PressMoveReleaseAndPointSetting.xml
Interactions/PressMoveReleaseWithCTRLInversion.xml
Interactions/PressMoveReleaseWithCTRLInversionAllMouseMoves.xml
Interactions/SegmentationConfig.xml
Interactions/SegmentationInteraction.xml
Interactions/SegmentationToolsConfig.xml
Interactions/ContourModelModificationConfig.xml
Interactions/ContourModelModificationInteractor.xml
)