--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ======================================================================-====*/
+
+#ifndef CLITKSEGMENTATIONFUNCTIONS_H
+#define CLITKSEGMENTATIONFUNCTIONS_H
+
+#include "clitkAutoCropFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template<class TInternalImageType, class TMaskInternalImageType>
+ typename TInternalImageType::Pointer
+ SetBackground(typename TInternalImageType::ConstPointer input,
+ typename TMaskInternalImageType::ConstPointer mask,
+ typename TMaskInternalImageType::PixelType maskBG,
+ typename TInternalImageType::PixelType outValue);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class TInternalImageType, class TMaskInternalImageType>
+ typename TInternalImageType::Pointer
+ SetBackground(typename TInternalImageType::Pointer input,
+ typename TMaskInternalImageType::Pointer mask,
+ typename TMaskInternalImageType::PixelType maskBG,
+ typename TInternalImageType::PixelType outValue) {
+ return SetBackground<TInternalImageType, TMaskInternalImageType>
+ (static_cast<typename TInternalImageType::ConstPointer>(input),
+ static_cast<typename TMaskInternalImageType::ConstPointer>(mask),
+ maskBG, outValue);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class TImageType>
+ typename TImageType::Pointer
+ Labelize(typename TImageType::Pointer input,
+ typename TImageType::PixelType BG,
+ bool isFullyConnected,
+ int minimalComponentSize);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class TImageType>
+ typename TImageType::Pointer
+ RemoveLabels(typename TImageType::Pointer input,
+ typename TImageType::PixelType BG,
+ std::vector<typename TImageType::PixelType> & labelsToRemove);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ AutoCrop(typename ImageType::Pointer input,
+ typename ImageType::PixelType BG) {
+ typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
+ typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
+ autoCropFilter->SetInput(input);
+ autoCropFilter->Update();
+ return autoCropFilter->GetOutput();
+ }
+
+ //--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ template<class TImageType>
+ typename TImageType::Pointer
+ KeepLabels(typename TImageType::Pointer input,
+ typename TImageType::PixelType BG,
+ typename TImageType::PixelType FG,
+ typename TImageType::PixelType firstKeep,
+ typename TImageType::PixelType lastKeep,
+ bool useLastKeep);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class TImageType>
+ typename TImageType::Pointer
+ LabelizeAndSelectLabels(typename TImageType::Pointer input,
+ typename TImageType::PixelType BG,
+ typename TImageType::PixelType FG,
+ bool isFullyConnected,
+ int minimalComponentSize,
+ LabelizeParameters<typename TImageType::PixelType> * param);
+}
+//--------------------------------------------------------------------
+
+#include "clitkSegmentationFunctions.txx"
+//--------------------------------------------------------------------
+
+#endif
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - 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>
+
+//--------------------------------------------------------------------
+template<class TImageType, class TMaskImageType>
+typename TImageType::Pointer
+clitk::SetBackground(typename TImageType::ConstPointer input,
+ typename TMaskImageType::ConstPointer mask,
+ typename TMaskImageType::PixelType maskBG,
+ typename TImageType::PixelType outValue) {
+ typedef clitk::SetBackgroundImageFilter<TImageType, TMaskImageType, TImageType> 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 TImageType>
+typename TImageType::Pointer
+clitk::Labelize(typename TImageType::Pointer input,
+ typename TImageType::PixelType BG,
+ bool isFullyConnected,
+ int minimalComponentSize) {
+
+ // Connected Component label
+ typedef itk::ConnectedComponentImageFilter<TImageType, TImageType> 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<TImageType, TImageType> 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 TImageType>
+typename TImageType::Pointer
+clitk::RemoveLabels(typename TImageType::Pointer input,
+ typename TImageType::PixelType BG,
+ std::vector<typename TImageType::PixelType> & labelsToRemove) {
+ typename TImageType::Pointer working_image = input;
+ for (unsigned int i=0; i <labelsToRemove.size(); i++) {
+ typedef clitk::SetBackgroundImageFilter<TImageType, TImageType> 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 TImageType>
+typename TImageType::Pointer
+clitk::KeepLabels(typename TImageType::Pointer input,
+ typename TImageType::PixelType BG,
+ typename TImageType::PixelType FG,
+ typename TImageType::PixelType firstKeep,
+ typename TImageType::PixelType lastKeep,
+ bool useLastKeep) {
+ typedef itk::BinaryThresholdImageFilter<TImageType, TImageType> 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 TImageType>
+typename TImageType::Pointer
+clitk::LabelizeAndSelectLabels(typename TImageType::Pointer input,
+ typename TImageType::PixelType BG,
+ typename TImageType::PixelType FG,
+ bool isFullyConnected,
+ int minimalComponentSize,
+ LabelizeParameters<typename TImageType::PixelType> * param)
+{
+ typename TImageType::Pointer working_image;
+ working_image = Labelize<TImageType>(input, BG, isFullyConnected, minimalComponentSize);
+ working_image = RemoveLabels<TImageType>(working_image, BG, param->GetLabelsToRemove());
+ working_image = KeepLabels<TImageType>(working_image,
+ BG, FG,
+ param->GetFirstKeep(),
+ param->GetLastKeep(),
+ param->GetUseLastKeep());
+ return working_image;
+}
+//--------------------------------------------------------------------
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ======================================================================-====*/
+
+#ifndef CLITKSEGMENTATIONUTILS_H
+#define CLITKSEGMENTATIONUTILS_H
+
+#include "clitkCommon.h"
+#include <itkBoundingBox.h>
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void ComputeBBFromImageRegion(typename ImageType::Pointer image,
+ typename ImageType::RegionType region,
+ typename itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension>::Pointer bb);
+
+ //--------------------------------------------------------------------
+ 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);
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void ComputeRegionFromBB(typename ImageType::Pointer image,
+ const typename itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension>::Pointer bb,
+ typename ImageType::RegionType & region);
+
+}
+
+#include "clitkSegmentationUtils.txx"
+
+#endif
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+======================================================================-====*/
+
+//--------------------------------------------------------------------
+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] = 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++) {
+ regionSize[i] = floor((maxs[i] - mins[i])/image->GetSpacing()[i]);
+ }
+
+ // Create region
+ region.SetIndex(regionStart);
+ region.SetSize(regionSize);
+ }
+ //--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff