- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+ ======================================================================-====*/
+
+// clitk
+#include "clitkSetBackgroundImageFilter.h"
+
+// itk
+#include <itkConnectedComponentImageFilter.h>
+#include <itkRelabelComponentImageFilter.h>
+#include <itkBinaryThresholdImageFilter.h>
+#include <itkPasteImageFilter.h>
//--------------------------------------------------------------------
template<class ImageType>
void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image,
- typename ImageType::RegionType region,
- typename itk::BoundingBox<unsigned long,
+ 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] = region.GetSize()[i];
+ lastIndex[i] = firstIndex[i]+region.GetSize()[i];
}
typedef itk::BoundingBox<unsigned long,
//--------------------------------------------------------------------
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) {
+ 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;
//--------------------------------------------------------------------
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);
+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++) {
- regionSize[i] = floor((maxs[i] - mins[i])/image->GetSpacing()[i]);
- }
+ // 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]);
+ }
- // Create region
- region.SetIndex(regionStart);
- region.SetSize(regionSize);
+ // Create region
+ region.SetIndex(regionStart);
+ region.SetSize(regionSize);
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType, class TMaskImageType>
+typename ImageType::Pointer
+clitk::SetBackground(//typename ImageType::ConstPointer input,
+ const ImageType * input,
+ const TMaskImageType * mask,
+ typename TMaskImageType::PixelType maskBG,
+ typename ImageType::PixelType outValue) {
+ typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType> SetBackgroundImageFilterType;
+ typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+ 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();
+
+ // Return result
+ return connectFilter->GetObjectCount();
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::Labelize(typename ImageType::Pointer 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->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->InPlaceOn();
+ relabelFilter->SetInput(connectFilter->GetOutput());
+ relabelFilter->SetMinimumObjectSize(minimalComponentSize);
+ relabelFilter->Update();
+
+ // Return result
+ return relabelFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+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(typename ImageType::Pointer 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::EnlargeImageLike(typename ImageType::Pointer input,
+ typename ImageType::Pointer like,
+ typename ImageType::PixelType backgroundValue)
+{
+ if (!HaveSameSpacing<ImageType, ImageType>(input, like)) {
+ FATAL("Images must have the same spacing");
+ }
+
+ typename ImageType::Pointer output = ImageType::New();
+ typename ImageType::SizeType size;
+ for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
+ size[i] = lrint((like->GetLargestPossibleRegion().GetSize()[i]*like->GetSpacing()[i])/
+ (double)like->GetSpacing()[i]);
+ }
+ // DD(size);
+ typename ImageType::RegionType region;
+ region.SetSize(size);
+ output->SetRegions(region);
+ output->SetSpacing(like->GetSpacing());
+ output->SetOrigin(like->GetOrigin());
+ output->Allocate();
+ output->FillBuffer(backgroundValue);
+ typedef itk::PasteImageFilter<ImageType,ImageType> PasteFilterType;
+ typename PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
+ typename PasteFilterType::InputImageIndexType index;
+ for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
+ index[i] = lrint((input->GetOrigin()[i] - like->GetOrigin()[i])/(double)input->GetSpacing()[i]);
+ }
+ // DD(index);
+ pasteFilter->SetSourceImage(input);
+ pasteFilter->SetDestinationImage(output);
+ pasteFilter->SetDestinationIndex(index);
+ pasteFilter->SetSourceRegion(input->GetLargestPossibleRegion());
+ pasteFilter->Update();
+ return pasteFilter->GetOutput();
+}
+//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff