+ // Create region
+ region.SetIndex(regionStart);
+ region.SetSize(regionSize);
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType, class TMaskImageType>
+typename ImageType::Pointer
+clitk::SetBackground(typename ImageType::ConstPointer input,
+ typename TMaskImageType::ConstPointer 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>
+typename ImageType::Pointer
+clitk::Labelize(typename ImageType::Pointer input,
+ typename ImageType::PixelType BG,
+ bool isFullyConnected,
+ int minimalComponentSize) {
+
+ // Connected Component label
+ typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> 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<ImageType, 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");