#include <itkBinaryBallStructuringElement.h>
#include <itkBinaryDilateImageFilter.h>
#include <itkConstantPadImageFilter.h>
+#include <itkImageSliceIteratorWithIndex.h>
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void ComputeBBFromImageRegion(const ImageType * image,
+ typename ImageType::RegionType region,
+ typename itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension>::Pointer bb) {
+ typedef typename ImageType::IndexType IndexType;
+ IndexType firstIndex;
+ IndexType lastIndex;
+ for(unsigned int i=0; i<image->GetImageDimension(); i++) {
+ firstIndex[i] = region.GetIndex()[i];
+ lastIndex[i] = firstIndex[i]+region.GetSize()[i];
+ }
-//--------------------------------------------------------------------
-template<class ImageType>
-void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image,
- typename ImageType::RegionType region,
- typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb) {
- typedef typename ImageType::IndexType IndexType;
- IndexType firstIndex;
- IndexType lastIndex;
- for(unsigned int i=0; i<image->GetImageDimension(); i++) {
- firstIndex[i] = region.GetIndex()[i];
- lastIndex[i] = firstIndex[i]+region.GetSize()[i];
- }
-
- typedef itk::BoundingBox<unsigned long,
- ImageType::ImageDimension> BBType;
- typedef typename BBType::PointType PointType;
- PointType lastPoint;
- PointType firstPoint;
- image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
- image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
-
- bb->SetMaximum(lastPoint);
- bb->SetMinimum(firstPoint);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<int Dimension>
-void clitk::ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
- typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
- typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
-
- typedef itk::BoundingBox<unsigned long, Dimension> BBType;
- typedef typename BBType::PointType PointType;
- PointType lastPoint;
- PointType firstPoint;
-
- for(unsigned int i=0; i<Dimension; i++) {
- firstPoint[i] = std::max(bbi1->GetMinimum()[i],
- bbi2->GetMinimum()[i]);
- lastPoint[i] = std::min(bbi1->GetMaximum()[i],
- bbi2->GetMaximum()[i]);
- }
-
- bbo->SetMaximum(lastPoint);
- bbo->SetMinimum(firstPoint);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-void clitk::ComputeRegionFromBB(typename ImageType::Pointer image,
- const typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb,
- typename ImageType::RegionType & region) {
- // Types
- typedef typename ImageType::IndexType IndexType;
- typedef typename ImageType::PointType PointType;
- typedef typename ImageType::RegionType RegionType;
- typedef typename ImageType::SizeType SizeType;
-
- // Region starting point
- IndexType regionStart;
- PointType start = bb->GetMinimum();
- image->TransformPhysicalPointToIndex(start, regionStart);
-
- // Region size
- SizeType regionSize;
- PointType maxs = bb->GetMaximum();
- PointType mins = bb->GetMinimum();
- for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
- // DD(maxs[i]);
- // DD(mins[i]);
- // DD((maxs[i] - mins[i])/image->GetSpacing()[i]);
- regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
- // DD(regionSize[i]);
+ typedef itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension> BBType;
+ typedef typename BBType::PointType PointType;
+ PointType lastPoint;
+ PointType firstPoint;
+ image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
+ image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
+
+ bb->SetMaximum(lastPoint);
+ bb->SetMinimum(firstPoint);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<int Dimension>
+ void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
+ typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
+ typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
+
+ typedef itk::BoundingBox<unsigned long, Dimension> BBType;
+ typedef typename BBType::PointType PointType;
+ PointType lastPoint;
+ PointType firstPoint;
+
+ for(unsigned int i=0; i<Dimension; i++) {
+ firstPoint[i] = std::max(bbi1->GetMinimum()[i],
+ bbi2->GetMinimum()[i]);
+ lastPoint[i] = std::min(bbi1->GetMaximum()[i],
+ bbi2->GetMaximum()[i]);
+ }
+
+ bbo->SetMaximum(lastPoint);
+ bbo->SetMinimum(firstPoint);
}
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void ComputeRegionFromBB(const ImageType * image,
+ const typename itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension>::Pointer bb,
+ typename ImageType::RegionType & region) {
+ // Types
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::PointType PointType;
+ typedef typename ImageType::RegionType RegionType;
+ typedef typename ImageType::SizeType SizeType;
+
+ // Region starting point
+ IndexType regionStart;
+ PointType start = bb->GetMinimum();
+ image->TransformPhysicalPointToIndex(start, regionStart);
+
+ // Region size
+ SizeType regionSize;
+ PointType maxs = bb->GetMaximum();
+ PointType mins = bb->GetMinimum();
+ for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
+ regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
+ }
- // Create region
- region.SetIndex(regionStart);
- region.SetSize(regionSize);
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template<class ImageType, class TMaskImageType>
-typename ImageType::Pointer
-clitk::SetBackground(const ImageType * input,
- const TMaskImageType * mask,
- typename TMaskImageType::PixelType maskBG,
- typename ImageType::PixelType outValue,
- bool inPlace) {
- typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
- SetBackgroundImageFilterType;
- typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
- = SetBackgroundImageFilterType::New();
- // if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
- setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
- setBackgroundFilter->SetInput(input);
- setBackgroundFilter->SetInput2(mask);
- setBackgroundFilter->SetMaskValue(maskBG);
- setBackgroundFilter->SetOutsideValue(outValue);
- setBackgroundFilter->Update();
- return setBackgroundFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-int clitk::GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
- typename ImageType::PixelType BG,
- bool isFullyConnected) {
- // Connected Component label
- typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
- typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
- connectFilter->SetInput(input);
- connectFilter->SetBackgroundValue(BG);
- connectFilter->SetFullyConnected(isFullyConnected);
- connectFilter->Update();
+ // Create region
+ region.SetIndex(regionStart);
+ region.SetSize(regionSize);
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ImageType, class TMaskImageType>
+ typename ImageType::Pointer
+ SetBackground(const ImageType * input,
+ const TMaskImageType * mask,
+ typename TMaskImageType::PixelType maskBG,
+ typename ImageType::PixelType outValue,
+ bool inPlace) {
+ typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
+ SetBackgroundImageFilterType;
+ typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
+ = SetBackgroundImageFilterType::New();
+ // if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
+ setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
+ setBackgroundFilter->SetInput(input);
+ setBackgroundFilter->SetInput2(mask);
+ setBackgroundFilter->SetMaskValue(maskBG);
+ setBackgroundFilter->SetOutsideValue(outValue);
+ setBackgroundFilter->Update();
+ return setBackgroundFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ int GetNumberOfConnectedComponentLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ bool isFullyConnected) {
+ // Connected Component label
+ typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
+ typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+ connectFilter->SetInput(input);
+ connectFilter->SetBackgroundValue(BG);
+ connectFilter->SetFullyConnected(isFullyConnected);
+ connectFilter->Update();
- // Return result
- return connectFilter->GetObjectCount();
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-/*
- Warning : in this cas, we consider outputType like inputType, not
- InternalImageType. Be sure it fits.
- */
-template<class ImageType>
-typename ImageType::Pointer
-clitk::Labelize(const ImageType * input,
- typename ImageType::PixelType BG,
- bool isFullyConnected,
- int minimalComponentSize) {
- // InternalImageType for storing large number of component
- typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
+ // Return result
+ return connectFilter->GetObjectCount();
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ /*
+ Warning : in this cas, we consider outputType like inputType, not
+ InternalImageType. Be sure it fits.
+ */
+ template<class ImageType>
+ typename ImageType::Pointer
+ Labelize(const ImageType * input,
+ typename ImageType::PixelType BG,
+ bool isFullyConnected,
+ int minimalComponentSize) {
+ // InternalImageType for storing large number of component
+ typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
- // Connected Component label
- typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
- typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
- // connectFilter->ReleaseDataFlagOn();
- connectFilter->SetInput(input);
- connectFilter->SetBackgroundValue(BG);
- connectFilter->SetFullyConnected(isFullyConnected);
+ // Connected Component label
+ typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
+ typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+ // connectFilter->ReleaseDataFlagOn();
+ connectFilter->SetInput(input);
+ connectFilter->SetBackgroundValue(BG);
+ connectFilter->SetFullyConnected(isFullyConnected);
- // Sort by size and remove too small area.
- typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
- typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
- // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
- relabelFilter->SetInput(connectFilter->GetOutput());
- relabelFilter->SetMinimumObjectSize(minimalComponentSize);
- relabelFilter->Update();
-
- // Return result
- typename ImageType::Pointer output = relabelFilter->GetOutput();
- return output;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::RemoveLabels(typename ImageType::Pointer input,
- typename ImageType::PixelType BG,
- std::vector<typename ImageType::PixelType> & labelsToRemove) {
- typename ImageType::Pointer working_image = input;
- for (unsigned int i=0; i <labelsToRemove.size(); i++) {
- typedef clitk::SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
- typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
- setBackgroundFilter->SetInput(input);
- setBackgroundFilter->SetInput2(input);
- setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
- setBackgroundFilter->SetOutsideValue(BG);
- setBackgroundFilter->Update();
- working_image = setBackgroundFilter->GetOutput();
- }
- return working_image;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::KeepLabels(const ImageType * input,
- typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- typename ImageType::PixelType firstKeep,
- typename ImageType::PixelType lastKeep,
- bool useLastKeep) {
- typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
- typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
- binarizeFilter->SetInput(input);
- binarizeFilter->SetLowerThreshold(firstKeep);
- if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
- binarizeFilter->SetInsideValue(FG);
- binarizeFilter->SetOutsideValue(BG);
- binarizeFilter->Update();
- return binarizeFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
- typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- bool isFullyConnected,
- int minimalComponentSize,
- LabelizeParameters<typename ImageType::PixelType> * param)
-{
- typename ImageType::Pointer working_image;
- working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
- working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
- working_image = KeepLabels<ImageType>(working_image,
- BG, FG,
- param->GetFirstKeep(),
- param->GetLastKeep(),
- param->GetUseLastKeep());
- return working_image;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::ResizeImageLike(typename ImageType::Pointer input,
- typename ImageType::Pointer like,
- typename ImageType::PixelType backgroundValue)
-{
- typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
- typename CropFilterType::Pointer cropFilter = CropFilterType::New();
- cropFilter->SetInput(input);
- cropFilter->SetCropLikeImage(like);
- cropFilter->SetBackgroundValue(backgroundValue);
- cropFilter->Update();
- return cropFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class MaskImageType>
-typename MaskImageType::Pointer
-clitk::SliceBySliceRelativePosition(const MaskImageType * input,
- const MaskImageType * object,
- int direction,
- double threshold,
- std::string orientation,
- bool uniqueConnectedComponent,
- double spacing,
- bool inverseflag)
-{
- typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
- typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
- sliceRelPosFilter->VerboseStepFlagOff();
- sliceRelPosFilter->WriteStepFlagOff();
- sliceRelPosFilter->SetInput(input);
- sliceRelPosFilter->SetInputObject(object);
- sliceRelPosFilter->SetDirection(direction);
- sliceRelPosFilter->SetFuzzyThreshold(threshold);
- sliceRelPosFilter->AddOrientationTypeString(orientation);
- sliceRelPosFilter->SetResampleBeforeRelativePositionFilter((spacing != -1));
- sliceRelPosFilter->SetIntermediateSpacing(spacing);
- sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
- sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
- // sliceRelPosFilter->SetAutoCropFlag(true); ??
- sliceRelPosFilter->Update();
- return sliceRelPosFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template<class ImageType>
-bool
-clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
- typename ImageType::PixelType bg,
- int direction, bool opposite,
- typename ImageType::PointType & point)
-{
- typename ImageType::PointType dummy;
- return clitk::FindExtremaPointInAGivenDirection(input, bg, direction,
- opposite, dummy, 0, point);
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template<class ImageType>
-bool
-clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
- typename ImageType::PixelType bg,
- int direction, bool opposite,
- typename ImageType::PointType refpoint,
- double distanceMax,
- typename ImageType::PointType & point)
-{
+ // Sort by size and remove too small area.
+ typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
+ typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+ // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
+ relabelFilter->SetInput(connectFilter->GetOutput());
+ relabelFilter->SetMinimumObjectSize(minimalComponentSize);
+ relabelFilter->Update();
+
+ // Return result
+ typename ImageType::Pointer output = relabelFilter->GetOutput();
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
/*
- loop over input pixels, store the index in the fg that is max
- according to the given direction.
+ Warning : in this cas, we consider outputType like inputType, not
+ InternalImageType. Be sure it fits.
*/
- typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
- IteratorType iter(input, input->GetLargestPossibleRegion());
- iter.GoToBegin();
- typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
- if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
- bool found=false;
- while (!iter.IsAtEnd()) {
- if (iter.Get() != bg) {
- bool test = iter.GetIndex()[direction] > max[direction];
- if (opposite) test = !test;
- if (test) {
- typename ImageType::PointType p;
- input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
- if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
- max = iter.GetIndex();
- found = true;
+ template<class ImageType>
+ typename ImageType::Pointer
+ LabelizeAndCountNumberOfObjects(const ImageType * input,
+ typename ImageType::PixelType BG,
+ bool isFullyConnected,
+ int minimalComponentSize,
+ int & nb) {
+ // InternalImageType for storing large number of component
+ typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
+
+ // Connected Component label
+ typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
+ typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+ // connectFilter->ReleaseDataFlagOn();
+ connectFilter->SetInput(input);
+ connectFilter->SetBackgroundValue(BG);
+ connectFilter->SetFullyConnected(isFullyConnected);
+
+ // Sort by size and remove too small area.
+ typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
+ typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+ // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
+ relabelFilter->SetInput(connectFilter->GetOutput());
+ relabelFilter->SetMinimumObjectSize(minimalComponentSize);
+ relabelFilter->Update();
+
+ nb = relabelFilter->GetNumberOfObjects();
+ // DD(relabelFilter->GetOriginalNumberOfObjects());
+ // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
+
+ // Return result
+ typename ImageType::Pointer output = relabelFilter->GetOutput();
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ RemoveLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ std::vector<typename ImageType::PixelType> & labelsToRemove) {
+ assert(labelsToRemove.size() != 0);
+ typename ImageType::Pointer working_image;// = input;
+ for (unsigned int i=0; i <labelsToRemove.size(); i++) {
+ typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
+ typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+ setBackgroundFilter->SetInput(input);
+ setBackgroundFilter->SetInput2(input);
+ setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
+ setBackgroundFilter->SetOutsideValue(BG);
+ setBackgroundFilter->Update();
+ working_image = setBackgroundFilter->GetOutput();
+ }
+ return working_image;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ KeepLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ typename ImageType::PixelType firstKeep,
+ typename ImageType::PixelType lastKeep,
+ bool useLastKeep) {
+ typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
+ typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
+ binarizeFilter->SetInput(input);
+ binarizeFilter->SetLowerThreshold(firstKeep);
+ if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
+ binarizeFilter->SetInsideValue(FG);
+ binarizeFilter->SetOutsideValue(BG);
+ binarizeFilter->Update();
+ return binarizeFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ LabelizeAndSelectLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool isFullyConnected,
+ int minimalComponentSize,
+ LabelizeParameters<typename ImageType::PixelType> * param)
+ {
+ typename ImageType::Pointer working_image;
+ working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
+ if (param->GetLabelsToRemove().size() != 0)
+ working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
+ working_image = KeepLabels<ImageType>(working_image,
+ BG, FG,
+ param->GetFirstKeep(),
+ param->GetLastKeep(),
+ param->GetUseLastKeep());
+ return working_image;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ ResizeImageLike(const ImageType * input,
+ const itk::ImageBase<ImageType::ImageDimension> * like,
+ typename ImageType::PixelType backgroundValue)
+ {
+ typedef CropLikeImageFilter<ImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(input);
+ cropFilter->SetCropLikeImage(like);
+ cropFilter->SetBackgroundValue(backgroundValue);
+ cropFilter->Update();
+ return cropFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class MaskImageType>
+ typename MaskImageType::Pointer
+ SliceBySliceRelativePosition(const MaskImageType * input,
+ const MaskImageType * object,
+ int direction,
+ double threshold,
+ std::string orientation,
+ bool uniqueConnectedComponent,
+ double spacing,
+ bool autocropFlag,
+ bool singleObjectCCL)
+ {
+ typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
+ typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
+ sliceRelPosFilter->VerboseStepFlagOff();
+ sliceRelPosFilter->WriteStepFlagOff();
+ sliceRelPosFilter->SetInput(input);
+ sliceRelPosFilter->SetInputObject(object);
+ sliceRelPosFilter->SetDirection(direction);
+ sliceRelPosFilter->SetFuzzyThreshold(threshold);
+ sliceRelPosFilter->AddOrientationTypeString(orientation);
+ sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
+ sliceRelPosFilter->SetIntermediateSpacing(spacing);
+ sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
+ sliceRelPosFilter->SetUseASingleObjectConnectedComponentBySliceFlag(singleObjectCCL);
+ // sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
+ sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
+ sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
+ sliceRelPosFilter->Update();
+ return sliceRelPosFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ bool
+ FindExtremaPointInAGivenDirection(const ImageType * input,
+ typename ImageType::PixelType bg,
+ int direction, bool opposite,
+ typename ImageType::PointType & point)
+ {
+ typename ImageType::PointType dummy;
+ return FindExtremaPointInAGivenDirection(input, bg, direction,
+ opposite, dummy, 0, point);
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ bool
+ FindExtremaPointInAGivenDirection(const ImageType * input,
+ typename ImageType::PixelType bg,
+ int direction, bool opposite,
+ typename ImageType::PointType refpoint,
+ double distanceMax,
+ typename ImageType::PointType & point)
+ {
+ /*
+ loop over input pixels, store the index in the fg that is max
+ according to the given direction.
+ */
+ typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
+ IteratorType iter(input, input->GetLargestPossibleRegion());
+ iter.GoToBegin();
+ typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
+ if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
+ bool found=false;
+ while (!iter.IsAtEnd()) {
+ if (iter.Get() != bg) {
+ bool test = iter.GetIndex()[direction] > max[direction];
+ if (opposite) test = !test;
+ if (test) {
+ typename ImageType::PointType p;
+ input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
+ if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
+ max = iter.GetIndex();
+ found = true;
+ }
}
}
+ ++iter;
}
- ++iter;
- }
- if (!found) return false;
- input->TransformIndexToPhysicalPoint(max, point);
- return true;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::CropImageAbove(typename ImageType::Pointer image,
- int dim, double min,
- bool autoCrop,
- typename ImageType::PixelType BG)
-{
- return clitk::CropImageAlongOneAxis<ImageType>(image, dim,
- image->GetOrigin()[dim],
- min,
- autoCrop, BG);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::CropImageBelow(typename ImageType::Pointer image,
- int dim, double max,
- bool autoCrop,
- typename ImageType::PixelType BG)
-{
- typename ImageType::PointType p;
- image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
- image->GetLargestPossibleRegion().GetSize(), p);
- return clitk::CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::CropImageAlongOneAxis(typename ImageType::Pointer image,
- int dim, double min, double max,
- bool autoCrop,
- typename ImageType::PixelType BG)
-{
- // Compute region size
- typename ImageType::RegionType region;
- typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
- typename ImageType::PointType p = image->GetOrigin();
- p[dim] = min;
- typename ImageType::IndexType start;
- image->TransformPhysicalPointToIndex(p, start);
- p[dim] = max;
- typename ImageType::IndexType end;
- image->TransformPhysicalPointToIndex(p, end);
- size[dim] = fabs(end[dim]-start[dim]);
- region.SetIndex(start);
- region.SetSize(size);
+ if (!found) return false;
+ input->TransformIndexToPhysicalPoint(max, point);
+ return true;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageAbove(const ImageType * image,
+ int dim, double min, bool autoCrop,
+ typename ImageType::PixelType BG)
+ {
+ return CropImageAlongOneAxis<ImageType>(image, dim,
+ image->GetOrigin()[dim],
+ min,
+ autoCrop, BG);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageBelow(const ImageType * image,
+ int dim, double max, bool autoCrop,
+ typename ImageType::PixelType BG)
+ {
+ typename ImageType::PointType p;
+ image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
+ image->GetLargestPossibleRegion().GetSize(), p);
+ return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageAlongOneAxis(const ImageType * image,
+ int dim, double min, double max,
+ bool autoCrop, typename ImageType::PixelType BG)
+ {
+ // Compute region size
+ typename ImageType::RegionType region;
+ typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
+ typename ImageType::PointType p = image->GetOrigin();
+ p[dim] = min;
+ typename ImageType::IndexType start;
+ image->TransformPhysicalPointToIndex(p, start);
+ p[dim] = max;
+ typename ImageType::IndexType end;
+ image->TransformPhysicalPointToIndex(p, end);
+ size[dim] = fabs(end[dim]-start[dim]);
+ region.SetIndex(start);
+ region.SetSize(size);
- // Perform Crop
- typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
- typename CropFilterType::Pointer cropFilter = CropFilterType::New();
- cropFilter->SetInput(image);
- cropFilter->SetRegionOfInterest(region);
- cropFilter->Update();
- typename ImageType::Pointer result = cropFilter->GetOutput();
+ // Perform Crop
+ typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(image);
+ cropFilter->SetRegionOfInterest(region);
+ cropFilter->Update();
+ typename ImageType::Pointer result = cropFilter->GetOutput();
- // Auto Crop
- if (autoCrop) {
- result = clitk::AutoCrop<ImageType>(result, BG);
- }
- return result;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-void
-clitk::ComputeCentroids(typename ImageType::Pointer image,
- typename ImageType::PixelType BG,
- std::vector<typename ImageType::PointType> & centroids)
-{
- typedef long LabelType;
- static const unsigned int Dim = ImageType::ImageDimension;
- typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
- typedef itk::LabelMap< LabelObjectType > LabelMapType;
- typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
- typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
- typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
- typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
- imageToLabelFilter->SetBackgroundValue(BG);
- imageToLabelFilter->SetInput(image);
- statFilter->SetInput(imageToLabelFilter->GetOutput());
- statFilter->Update();
- typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
-
- centroids.clear();
- typename ImageType::PointType dummy;
- centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
- for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
- centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
- }
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-void
-clitk::ExtractSlices(typename ImageType::Pointer image,
- int direction,
- std::vector<typename itk::Image<typename ImageType::PixelType,
- ImageType::ImageDimension-1>::Pointer > & slices)
-{
- typedef clitk::ExtractSliceFilter<ImageType> ExtractSliceFilterType;
- typedef typename ExtractSliceFilterType::SliceType SliceType;
- typename ExtractSliceFilterType::Pointer
- extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(image);
- extractSliceFilter->SetDirection(direction);
- extractSliceFilter->Update();
- extractSliceFilter->GetOutputSlices(slices);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
- ImageType::ImageDimension-1>::Pointer > & slices,
- typename ImageType::Pointer input,
- int direction) {
- typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
- typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
- typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
- joinFilter->SetOrigin(input->GetOrigin()[direction]);
- joinFilter->SetSpacing(input->GetSpacing()[direction]);
- for(unsigned int i=0; i<slices.size(); i++) {
- joinFilter->PushBackInput(slices[i]);
- }
- joinFilter->Update();
- return joinFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-void
-clitk::PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p,
- ImagePointer image,
- const int slice,
- PointType3D & p3D)
-{
- p3D[0] = p[0];
- p3D[1] = p[1];
- p3D[2] = (image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
- + image->GetOrigin()[2];
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-void
-clitk::PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map,
- ImagePointer image,
- VectorPoint3DType & list)
-{
- typename MapPoint2DType::const_iterator iter = map.begin();
- while (iter != map.end()) {
- PointType3D p;
- Convert2DTo3D(iter->second, image, iter->first, p);
- list.push_back(p);
- ++iter;
- }
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template<class ImageType>
-void
-clitk::WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
- std::string filename)
-{
- std::ofstream os;
- openFileForWriting(os, filename);
- os << "LANDMARKS1" << std::endl;
- for(uint i=0; i<points.size(); i++) {
- const typename ImageType::PointType & p = points[i];
- // Write it in the file
- os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
- }
- os.close();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::Dilate(typename ImageType::Pointer image,
- double radiusInMM,
- typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- bool extendSupport)
-{
- typename ImageType::SizeType r;
- for(uint i=0; i<ImageType::ImageDimension; i++)
- r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
- return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::Dilate(typename ImageType::Pointer image,
- typename ImageType::PointType radiusInMM,
- typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- bool extendSupport)
-{
- typename ImageType::SizeType r;
- for(uint i=0; i<ImageType::ImageDimension; i++)
- r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
- return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::Dilate(typename ImageType::Pointer image,
- typename ImageType::SizeType radius,
- typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- bool extendSupport)
-{
- // Create kernel for dilatation
- typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
- ImageType::ImageDimension> KernelType;
- KernelType structuringElement;
- structuringElement.SetRadius(radius);
- structuringElement.CreateStructuringElement();
-
- if (extendSupport) {
- typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
- typename PadFilterType::Pointer padFilter = PadFilterType::New();
- padFilter->SetInput(image);
- typename ImageType::SizeType lower;
- typename ImageType::SizeType upper;
- for(uint i=0; i<3; i++) {
- lower[i] = upper[i] = 2*(radius[i]+1);
+ // Auto Crop
+ if (autoCrop) {
+ result = AutoCrop<ImageType>(result, BG);
+ }
+ return result;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ ComputeCentroids(const ImageType * image,
+ typename ImageType::PixelType BG,
+ std::vector<typename ImageType::PointType> & centroids)
+ {
+ typedef long LabelType;
+ static const unsigned int Dim = ImageType::ImageDimension;
+ typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
+ typedef itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
+ typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
+ typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
+ typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
+ imageToLabelFilter->SetBackgroundValue(BG);
+ imageToLabelFilter->SetInput(image);
+ statFilter->SetInput(imageToLabelFilter->GetOutput());
+ statFilter->Update();
+ typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
+
+ centroids.clear();
+ typename ImageType::PointType dummy;
+ centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
+ for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
+ centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ ExtractSlices(const ImageType * image, int direction,
+ std::vector<typename itk::Image<typename ImageType::PixelType,
+ ImageType::ImageDimension-1>::Pointer > & slices)
+ {
+ typedef ExtractSliceFilter<ImageType> ExtractSliceFilterType;
+ typedef typename ExtractSliceFilterType::SliceType SliceType;
+ typename ExtractSliceFilterType::Pointer
+ extractSliceFilter = ExtractSliceFilterType::New();
+ extractSliceFilter->SetInput(image);
+ extractSliceFilter->SetDirection(direction);
+ extractSliceFilter->Update();
+ extractSliceFilter->GetOutputSlices(slices);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
+ const ImageType * image,
+ const int slice,
+ PointType3D & p3D)
+ {
+ IndexType3D index3D;
+ index3D[0] = index3D[1] = 0;
+ index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
+ image->TransformIndexToPhysicalPoint(index3D, p3D);
+ p3D[0] = p2D[0];
+ p3D[1] = p2D[1];
+ // p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
+ // + image->GetOrigin()[2];
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map,
+ const ImageType * image,
+ VectorPoint3DType & list)
+ {
+ typename MapPoint2DType::const_iterator iter = map.begin();
+ while (iter != map.end()) {
+ PointType3D p;
+ Convert2DTo3D(iter->second, image, iter->first, p);
+ list.push_back(p);
+ ++iter;
+ }
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
+ std::string filename)
+ {
+ std::ofstream os;
+ openFileForWriting(os, filename);
+ os << "LANDMARKS1" << std::endl;
+ for(uint i=0; i<points.size(); i++) {
+ const typename ImageType::PointType & p = points[i];
+ // Write it in the file
+ os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
+ }
+ os.close();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Dilate(const ImageType * image, double radiusInMM,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool extendSupport)
+ {
+ typename ImageType::SizeType r;
+ for(uint i=0; i<ImageType::ImageDimension; i++)
+ r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
+ return Dilate<ImageType>(image, r, BG, FG, extendSupport);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool extendSupport)
+ {
+ typename ImageType::SizeType r;
+ for(uint i=0; i<ImageType::ImageDimension; i++)
+ r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
+ return Dilate<ImageType>(image, r, BG, FG, extendSupport);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Dilate(const ImageType * image, typename ImageType::SizeType radius,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool extendSupport)
+ {
+ // Create kernel for dilatation
+ typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
+ ImageType::ImageDimension> KernelType;
+ KernelType structuringElement;
+ structuringElement.SetRadius(radius);
+ structuringElement.CreateStructuringElement();
+
+ typename ImageType::Pointer output;
+ if (extendSupport) {
+ typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
+ typename PadFilterType::Pointer padFilter = PadFilterType::New();
+ padFilter->SetInput(image);
+ typename ImageType::SizeType lower;
+ typename ImageType::SizeType upper;
+ for(uint i=0; i<3; i++) {
+ lower[i] = upper[i] = 2*(radius[i]+1);
+ }
+ padFilter->SetPadLowerBound(lower);
+ padFilter->SetPadUpperBound(upper);
+ padFilter->Update();
+ output = padFilter->GetOutput();
}
- padFilter->SetPadLowerBound(lower);
- padFilter->SetPadUpperBound(upper);
- padFilter->Update();
- image = padFilter->GetOutput();
- }
-
- // Dilate filter
- typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
- typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
- dilateFilter->SetBackgroundValue(BG);
- dilateFilter->SetForegroundValue(FG);
- dilateFilter->SetBoundaryToForeground(false);
- dilateFilter->SetKernel(structuringElement);
- dilateFilter->SetInput(image);
- dilateFilter->Update();
- return image = dilateFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ValueType, class VectorType>
-void clitk::ConvertOption(std::string optionName, uint given,
- ValueType * values, VectorType & p,
- uint dim, bool required)
-{
- if (required && (given == 0)) {
- clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
+
+ // Dilate filter
+ typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
+ typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
+ dilateFilter->SetBackgroundValue(BG);
+ dilateFilter->SetForegroundValue(FG);
+ dilateFilter->SetBoundaryToForeground(false);
+ dilateFilter->SetKernel(structuringElement);
+ dilateFilter->SetInput(output);
+ dilateFilter->Update();
+ return dilateFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ValueType, class VectorType>
+ void ConvertOption(std::string optionName, uint given,
+ ValueType * values, VectorType & p,
+ uint dim, bool required)
+ {
+ if (required && (given == 0)) {
+ clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
+ << dim << " values.");
+ }
+ if (given == 1) {
+ for(uint i=0; i<dim; i++) p[i] = values[0];
+ return;
+ }
+ if (given == dim) {
+ for(uint i=0; i<dim; i++) p[i] = values[i];
+ return;
+ }
+ if (given == 0) return;
+ clitkExceptionMacro("The option --" << optionName << " must have 1 or "
<< dim << " values.");
}
- if (given == 1) {
- for(uint i=0; i<dim; i++) p[i] = values[0];
- return;
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ /*
+ http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
+ Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
+ (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
+ This will equal zero if the point C is on the line formed by
+ points A and B, and will have a different sign depending on the
+ side. Which side this is depends on the orientation of your (x,y)
+ coordinates, but you can plug test values for A,B and C into this
+ formula to determine whether negative values are to the left or to
+ the right.
+ => to accelerate, start with formula, when change sign -> stop and fill
+
+ offsetToKeep = is used to determine which side of the line we
+ keep. The point along the mainDirection but 'offsetToKeep' mm away
+ is kept.
+
+ */
+ template<class ImageType>
+ void
+ SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
+ std::vector<typename ImageType::PointType> & lA,
+ std::vector<typename ImageType::PointType> & lB,
+ typename ImageType::PixelType BG,
+ int mainDirection,
+ double offsetToKeep)
+ {
+ typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
+ SliceIteratorType siter = SliceIteratorType(input,
+ input->GetLargestPossibleRegion());
+ siter.SetFirstDirection(0);
+ siter.SetSecondDirection(1);
+ siter.GoToBegin();
+ uint i=0;
+ typename ImageType::PointType A;
+ typename ImageType::PointType B;
+ typename ImageType::PointType C;
+ assert(lA.size() == lB.size());
+ while ((i<lA.size()) && (!siter.IsAtEnd())) {
+ // Check that the current slice correspond to the current point
+ input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
+ // DD(C);
+ // DD(i);
+ // DD(lA[i]);
+ if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
+ }
+ else {
+ // Define A,B,C points
+ A = lA[i];
+ B = lB[i];
+ C = A;
+ // DD(A);
+ // DD(B);
+ // DD(C);
+
+ // Check that the line is not a point (A=B)
+ bool p = (A[0] == B[0]) && (A[1] == B[1]);
+
+ if (!p) {
+ C[mainDirection] += offsetToKeep; // I know I must keep this point
+ double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+ bool isPositive = s<0;
+ while (!siter.IsAtEndOfSlice()) {
+ while (!siter.IsAtEndOfLine()) {
+ // Very slow, I know ... but image should be very small
+ input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
+ double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+ if (s == 0) siter.Set(BG); // on the line, we decide to remove
+ if (isPositive) {
+ if (s > 0) siter.Set(BG);
+ }
+ else {
+ if (s < 0) siter.Set(BG);
+ }
+ ++siter;
+ }
+ siter.NextLine();
+ } // end loop slice
+ }
+
+ ++i;
+ } // End of current slice
+ siter.NextSlice();
+ }
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ AndNot(ImageType * input,
+ const ImageType * object,
+ typename ImageType::PixelType BG)
+ {
+ typename ImageType::Pointer o;
+ bool resized=false;
+ if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
+ o = clitk::ResizeImageLike<ImageType>(object, input, BG);
+ resized = true;
+ }
+
+ typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+ typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
+ boolFilter->InPlaceOn();
+ boolFilter->SetInput1(input);
+ if (resized) boolFilter->SetInput2(o);
+ else boolFilter->SetInput2(object);
+ boolFilter->SetBackgroundValue1(BG);
+ boolFilter->SetBackgroundValue2(BG);
+ boolFilter->SetOperationType(BoolFilterType::AndNot);
+ boolFilter->Update();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Binarize(const ImageType * input,
+ typename ImageType::PixelType lower,
+ typename ImageType::PixelType upper,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG)
+ {
+ typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
+ typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
+ binarizeFilter->SetInput(input);
+ binarizeFilter->SetLowerThreshold(lower);
+ binarizeFilter->SetUpperThreshold(upper);
+ binarizeFilter->SetInsideValue(FG);
+ binarizeFilter->SetOutsideValue(BG);
+ binarizeFilter->Update();
+ return binarizeFilter->GetOutput();
}
- if (given == dim) {
- for(uint i=0; i<dim; i++) p[i] = values[i];
- return;
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ GetMinMaxPointPosition(const ImageType * input,
+ typename ImageType::PointType & min,
+ typename ImageType::PointType & max)
+ {
+ typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
+ input->TransformIndexToPhysicalPoint(index, min);
+ index = index+input->GetLargestPossibleRegion().GetSize();
+ input->TransformIndexToPhysicalPoint(index, max);
}
- if (given == 0) return;
- clitkExceptionMacro("The option --" << optionName << " must have 1 or "
- << dim << " values.");
-}
-//--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::PointType
+ FindExtremaPointInAGivenLine(const ImageType * input,
+ int dimension,
+ bool inverse,
+ typename ImageType::PointType p,
+ typename ImageType::PixelType BG,
+ double distanceMax)
+ {
+ // Which direction ? Increasing or decreasing.
+ int d=1;
+ if (inverse) d=-1;
+
+ // Transform to pixel index
+ typename ImageType::IndexType index;
+ input->TransformPhysicalPointToIndex(p, index);
+
+ // Loop while inside the mask;
+ while (input->GetPixel(index) != BG) {
+ index[dimension] += d;
+ }
+
+ // Transform back to Physical Units
+ typename ImageType::PointType result;
+ input->TransformIndexToPhysicalPoint(index, result);
+
+ // Check that is is not too far away
+ double distance = p.EuclideanDistanceTo(result);
+ if (distance > distanceMax) {
+ result = p; // Get back to initial value
+ }
+
+ return result;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class PointType>
+ bool
+ IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
+ {
+ // Look at the position of point 'like' according to the AB line
+ double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
+ bool negative = s<0;
+
+ // Look the C position
+ s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+
+ if (negative && (s<=0)) return true;
+ if (!negative && (s>=0)) return true;
+ return false;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ /* Consider an input object, for each slice, find the extrema
+ position according to a given direction and build a line segment
+ passing throught this point in a given direction. Output is a
+ vector of line (from point A to B), for each slice;
+ */
+ template<class ImageType>
+ void
+ SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
+ typename ImageType::PixelType BG,
+ int sliceDimension,
+ int extremaDirection,
+ bool extremaOppositeFlag,
+ int lineDirection,
+ double margin,
+ std::vector<typename ImageType::PointType> & A,
+ std::vector<typename ImageType::PointType> & B)
+ {
+ // Type of a slice
+ typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+
+ // Build the list of slices
+ std::vector<typename SliceType::Pointer> slices;
+ clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
+
+ // Build the list of 2D points
+ std::map<int, typename SliceType::PointType> position2D;
+ for(uint i=0; i<slices.size(); i++) {
+ typename SliceType::PointType p;
+ bool found =
+ clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
+ extremaDirection, extremaOppositeFlag, p);
+ if (found) {
+ position2D[i] = p;
+ }
+ }
+
+ // Convert 2D points in slice into 3D points
+ clitk::PointsUtils<ImageType>::Convert2DTo3DList(position2D, input, A);
+
+ // Create additional point just right to the previous ones, on the
+ // given lineDirection, in order to create a horizontal/vertical line.
+ for(uint i=0; i<A.size(); i++) {
+ typename ImageType::PointType p = A[i];
+ p[lineDirection] += 10;
+ B.push_back(p);
+ // Margins ?
+ A[i][1] += margin;
+ B[i][1] += margin;
+ }
+
+ }
+ //--------------------------------------------------------------------
+
+} // end of namespace
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff