Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- 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
+// clitk
#include "clitkCommon.h"
#include "clitkAutoCropFilter.h"
#include "clitkLabelizeParameters.h"
+
+// itk
#include <itkBoundingBox.h>
+#include <itkJoinSeriesImageFilter.h>
+
+/*
+ According to
+ http://answerpot.com/showthread.php?357451-Itk::SmartPointer%20-%20problem%20making%20code%20const-correct
+ it is better to take raw pointer as argument instead of SmartPointer.
+*/
namespace clitk {
//--------------------------------------------------------------------
template<class ImageType>
- void ComputeBBFromImageRegion(typename ImageType::Pointer image,
+ void ComputeBBFromImageRegion(const ImageType * image,
typename ImageType::RegionType region,
typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb);
+ ImageType::ImageDimension>::Pointer bb);
//--------------------------------------------------------------------
template<int Dimension>
//--------------------------------------------------------------------
template<class ImageType>
- void ComputeRegionFromBB(typename ImageType::Pointer image,
+ void ComputeRegionFromBB(const ImageType * image,
const typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb,
+ ImageType::ImageDimension>::Pointer bb,
typename ImageType::RegionType & region);
//--------------------------------------------------------------------
template<class TInternalImageType, class TMaskInternalImageType>
typename TInternalImageType::Pointer
- SetBackground(typename TInternalImageType::ConstPointer input,
- typename TMaskInternalImageType::ConstPointer mask,
+ SetBackground(const TInternalImageType * input,
+ const TMaskInternalImageType * mask,
typename TMaskInternalImageType::PixelType maskBG,
- typename TInternalImageType::PixelType outValue);
+ typename TInternalImageType::PixelType outValue,
+ bool inPlace);
//--------------------------------------------------------------------
-
+
//--------------------------------------------------------------------
- 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 ImageType>
+ int GetNumberOfConnectedComponentLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ bool isFullyConnected);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class TImageType>
typename TImageType::Pointer
- Labelize(typename TImageType::Pointer input,
- typename TImageType::PixelType BG,
- bool isFullyConnected,
- int minimalComponentSize);
+ Labelize(const TImageType * input, typename TImageType::PixelType BG,
+ bool isFullyConnected, int minimalComponentSize);
+ template<class TImageType>
+ typename TImageType::Pointer
+ LabelizeAndCountNumberOfObjects(const TImageType * input,
+ typename TImageType::PixelType BG,
+ bool isFullyConnected,
+ int minimalComponentSize,
+ int & nb);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class ImageType>
typename ImageType::Pointer
- RemoveLabels(typename ImageType::Pointer input,
+ RemoveLabels(const ImageType * input,
typename ImageType::PixelType BG,
std::vector<typename ImageType::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();
+ typename ImageType::Pointer
+ AutoCrop(const ImageType * input,
+ typename ImageType::PixelType BG) {
+ typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
+ typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
+ autoCropFilter->SetInput(input);
+ autoCropFilter->SetBackgroundValue(BG);
+ autoCropFilter->Update();
+ return autoCropFilter->GetOutput();
}
-
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class TImageType>
typename TImageType::Pointer
- KeepLabels(typename TImageType::Pointer input,
+ KeepLabels(const TImageType * input,
typename TImageType::PixelType BG,
typename TImageType::PixelType FG,
typename TImageType::PixelType firstKeep,
//--------------------------------------------------------------------
template<class TImageType>
typename TImageType::Pointer
- LabelizeAndSelectLabels(typename TImageType::Pointer input,
+ LabelizeAndSelectLabels(const TImageType * input,
typename TImageType::PixelType BG,
typename TImageType::PixelType FG,
bool isFullyConnected,
//--------------------------------------------------------------------
template<class ImageType>
typename ImageType::Pointer
- EnlargeImageLike(typename ImageType::Pointer input,
- typename ImageType::Pointer like,
- typename ImageType::PixelType BG);
+ ResizeImageLike(const ImageType * input,
+ const itk::ImageBase<ImageType::ImageDimension> * like,
+ typename ImageType::PixelType BG);
+
+
+ //--------------------------------------------------------------------
+ template<class MaskImageType>
+ typename MaskImageType::Pointer
+ SliceBySliceRelativePosition(const MaskImageType * input,
+ const MaskImageType * object,
+ int direction,
+ double threshold,
+ std::string orientation,
+ bool uniqueConnectedComponent=false,
+ double spacing=-1,
+ bool autocropflag=true,
+ bool singleObjectCCL=true);
+
+ //--------------------------------------------------------------------
+ // In a binary image, search for the point belonging to the FG that
+ // is the most exterma in the direction 'direction' (or in the
+ // opposite if notFlag is given).
+ template<class ImageType>
+ bool
+ FindExtremaPointInAGivenDirection(const ImageType * input,
+ typename ImageType::PixelType bg,
+ int direction, bool opposite,
+ typename ImageType::PointType & p);
+
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ // Same as above but check that the found point is not more than
+ // 'distanceMax' away from 'refPoint'
+ 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 & p);
+
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageAlongOneAxis(const ImageType * image,
+ int dim, double min, double max,
+ bool autoCrop = false,
+ typename ImageType::PixelType BG=0);
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageAbove(const ImageType * image,
+ int dim, double min, bool autoCrop = false,
+ typename ImageType::PixelType BG=0);
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageBelow(const ImageType * image,
+ int dim, double max,bool autoCrop = false,
+ typename ImageType::PixelType BG=0);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ ComputeCentroids(const ImageType * image,
+ typename ImageType::PixelType BG,
+ std::vector<typename ImageType::PointType> & centroids);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ ExtractSlices(const ImageType * image, int dim,
+ std::vector< typename itk::Image<typename ImageType::PixelType,
+ ImageType::ImageDimension-1>::Pointer > & slices);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
+ ImageType::ImageDimension-1>::Pointer > & slices,
+ const ImageType * 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();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ // Set of tools to manage 3D points and 2D points in slices
+ template<class ImageType>
+ class PointsUtils
+ {
+ typedef typename ImageType::PointType PointType3D;
+ typedef typename ImageType::IndexType IndexType3D;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef itk::Image<PixelType, 2> SliceType;
+ typedef typename SliceType::PointType PointType2D;
+ typedef typename SliceType::IndexType IndexType2D;
+
+ typedef std::map<int, PointType2D> MapPoint2DType;
+ typedef std::vector<PointType3D> VectorPoint3DType;
+ public:
+ static void Convert2DTo3D(const PointType2D & p2D,
+ const ImageType * image,
+ const int slice,
+ PointType3D & p3D);
+ static void Convert2DTo3DList(const MapPoint2DType & map,
+ const ImageType * image,
+ VectorPoint3DType & list);
+ };
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
+ std::string filename);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Dilate(const ImageType * image, double radiusInMM,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool 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);
+ template<class ImageType>
+ typename ImageType::Pointer
+ Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool extendSupport);
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ValueType, class VectorType>
+ void ConvertOption(std::string optionName, uint given,
+ ValueType * values, VectorType & p,
+ uint dim, bool required);
+#define ConvertOptionMacro(OPTIONNAME, VAR, DIM, REQUIRED) \
+ ConvertOption(#OPTIONNAME, OPTIONNAME##_given, OPTIONNAME##_arg, VAR, DIM, REQUIRED);
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ 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);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void AndNot(ImageType * input,
+ const ImageType * object,
+ typename ImageType::PixelType BG=0);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Binarize(const ImageType * input,
+ typename ImageType::PixelType lower,
+ typename ImageType::PixelType upper,
+ typename ImageType::PixelType BG=0,
+ typename ImageType::PixelType FG=1);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ GetMinMaxPointPosition(const ImageType * input,
+ typename ImageType::PointType & min,
+ typename ImageType::PointType & max);
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::PointType
+ FindExtremaPointInAGivenLine(const ImageType * input,
+ int dimension, bool inverse,
+ typename ImageType::PointType p,
+ typename ImageType::PixelType BG,
+ double distanceMax);
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class PointType>
+ bool
+ IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ 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);
+ //--------------------------------------------------------------------
+
+
}
#include "clitkSegmentationUtils.txx"
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff