#include "clitkCommon.h"
#include "clitkAutoCropFilter.h"
#include "clitkLabelizeParameters.h"
+#include "clitkExtractSliceFilter.h"
// itk
#include <itkBoundingBox.h>
+#include <itkJoinSeriesImageFilter.h>
+#include <itkChangeInformationImageFilter.h>
-namespace clitk {
+/*
+ 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.
+*/
- //--------------------------------------------------------------------
- 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);
+namespace clitk {
//--------------------------------------------------------------------
- template<class ImageType>
- void ComputeRegionFromBB(typename ImageType::Pointer image,
- const typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb,
- typename ImageType::RegionType & region);
- //--------------------------------------------------------------------
template<class TInternalImageType, class TMaskInternalImageType>
typename TInternalImageType::Pointer
SetBackground(const TInternalImageType * input,
//--------------------------------------------------------------------
template<class ImageType>
- int GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
+ int GetNumberOfConnectedComponentLabels(const ImageType * input,
typename ImageType::PixelType BG,
bool isFullyConnected);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class TImageType>
typename TImageType::Pointer
- Labelize(const TImageType * 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) {
+ AutoCrop(const ImageType * input,
+ typename ImageType::PixelType BG,
+ const bool useBorderFlag=false) {
typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
autoCropFilter->SetInput(input);
autoCropFilter->SetBackgroundValue(BG);
+ autoCropFilter->SetUseBorder(useBorderFlag);
autoCropFilter->Update();
return autoCropFilter->GetOutput();
}
//--------------------------------------------------------------------
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,
int minimalComponentSize,
LabelizeParameters<typename TImageType::PixelType> * param);
- //--------------------------------------------------------------------
- template<class ImageType>
- typename ImageType::Pointer
- ResizeImageLike(typename ImageType::Pointer input,
- typename ImageType::Pointer like,
- typename ImageType::PixelType BG);
-
//--------------------------------------------------------------------
template<class MaskImageType>
std::string orientation,
bool uniqueConnectedComponent=false,
double spacing=-1,
- bool notflag=false);
+ bool autocropflag=true,
+ bool singleObjectCCL=true);
+ template<class MaskImageType>
+ typename MaskImageType::Pointer
+ SliceBySliceRelativePosition(const MaskImageType * input,
+ const MaskImageType * object,
+ int direction,
+ double threshold,
+ double angle,
+ bool inverseflag,
+ 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
//--------------------------------------------------------------------
template<class ImageType>
typename ImageType::Pointer
- CropImageAlongOneAxis(typename ImageType::Pointer image,
+ 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(typename ImageType::Pointer image,
- int dim, double min,
- bool autoCrop = false,
- typename ImageType::PixelType BG=0);
+ CropImageRemoveGreaterThan(const ImageType * image,
+ int dim, double min, bool autoCrop = false,
+ typename ImageType::PixelType BG=0);
template<class ImageType>
typename ImageType::Pointer
- CropImageBelow(typename ImageType::Pointer image,
- int dim, double max,
- bool autoCrop = false,
- typename ImageType::PixelType BG=0);
+ CropImageRemoveLowerThan(const ImageType * image,
+ int dim, double max,bool autoCrop = false,
+ typename ImageType::PixelType BG=0);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
+ template<class ImageType, class LabelType>
+ typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
+ ComputeLabelMap(const ImageType * image,
+ typename ImageType::PixelType BG,
+ bool computePerimeterFlag=false);
+ template<class ImageType>
+ void
+ ComputeCentroids(const ImageType * image,
+ typename ImageType::PixelType BG,
+ std::vector<typename ImageType::PointType> & centroids);
template<class ImageType>
void
- ComputeCentroids(typename ImageType::Pointer image,
+ ComputeCentroids2(const ImageType * image,
typename ImageType::PixelType BG,
std::vector<typename ImageType::PointType> & centroids);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class ImageType>
void
- ExtractSlices(typename ImageType::Pointer image,
- int dim,
- std::vector< typename itk::Image<typename ImageType::PixelType,
- ImageType::ImageDimension-1>::Pointer > & slices);
+ 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>
typename ImageType::Pointer
JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
- ImageType::ImageDimension-1>::Pointer > & slices,
- typename ImageType::Pointer input,
- int dim);
+ ImageType::ImageDimension-1>::Pointer > & slices,
+ const itk::ImageBase<ImageType::ImageDimension> * input, //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();
+ }
//--------------------------------------------------------------------
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;
+ typedef std::vector<PointType2D> VectorPoint2DType;
+
public:
static void Convert2DTo3D(const PointType2D & p2D,
- ImagePointer image,
+ const ImageType * image,
const int slice,
PointType3D & p3D);
- static void Convert2DTo3DList(const MapPoint2DType & map,
- ImagePointer image,
+ static void Convert2DMapTo3DList(const MapPoint2DType & map,
+ const ImageType * image,
VectorPoint3DType & list);
+ static void Convert2DListTo3DList(const VectorPoint2DType & p,
+ int slice,
+ const ImageType * image,
+ VectorPoint3DType & list);
};
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class ImageType>
typename ImageType::Pointer
- Dilate(typename ImageType::Pointer image,
- double radiusInMM,
- typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- bool extendSupport);
+ Dilate(const ImageType * image, double radiusInMM,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool extendSupport);
template<class ImageType>
typename ImageType::Pointer
- Dilate(typename ImageType::Pointer image,
- typename ImageType::SizeType radius,
- typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- bool extendSupport);
+ 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(typename ImageType::Pointer image,
- typename ImageType::PointType radiusInMM,
- typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- bool extendSupport);
+ Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool extendSupport);
+ //--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Opening(const ImageType * image, typename ImageType::SizeType radius,
+ typename ImageType::PixelType BG, typename ImageType::PixelType FG);
+ //--------------------------------------------------------------------
+
//--------------------------------------------------------------------
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) \
+#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,
+ bool keepIfEqual=false);
+ template<class ImageType>
+ void
+ SliceBySliceSetBackgroundFromLineSeparation_pt(ImageType * input,
+ std::vector<typename ImageType::PointType> & lA,
+ std::vector<typename ImageType::PointType> & lB,
+ typename ImageType::PixelType BG,
+ typename ImageType::PointType offsetToKeep,
+ bool keepIfEqual=false);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void AndNot(ImageType * input,
+ const ImageType * object,
+ typename ImageType::PixelType BG=0);
+ template<class ImageType>
+ void And(ImageType * input,
+ const ImageType * object,
+ typename ImageType::PixelType BG=0);
+ template<class ImageType>
+ void Or(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);
+ template<class ImageType>
+ void
+ SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1,
+ const ImageType * S2,
+ typename ImageType::PixelType BG,
+ int sliceDimension,
+ std::vector<typename ImageType::PointType> & A,
+ std::vector<typename ImageType::PointType> & B);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ SliceBySliceKeepMainCCL(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Clone(const ImageType * input);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ SliceBySliceSetBackgroundFromSingleLine(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PointType & A,
+ typename ImageType::PointType & B,
+ int dim1, int dim2, bool removeLowerPartFlag);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ SliceBySliceSetBackgroundFromPoints(const ImageType * input,
+ typename ImageType::PixelType BG,
+ int sliceDim,
+ std::vector<typename ImageType::PointType> & A,
+ bool removeGreaterThanXFlag,
+ bool removeGreaterThanYFlag);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ FillRegionWithValue(ImageType * input, typename ImageType::PixelType value,
+ typename ImageType::RegionType & region);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min,
+ typename ImageType::PointType & max);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename itk::Image<float, ImageType::ImageDimension>::Pointer//void
+ DistanceMap(const ImageType * input, typename ImageType::PixelType BG);//,
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::PointType
+ ComputeClosestPoint(const ImageType * input,
+ const itk::Image<float, ImageType::ImageDimension> * dmap,
+ typename ImageType::PixelType & BG);
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ RemoveNegativeIndexFromRegion(ImageType * input);
+ //--------------------------------------------------------------------
+
-}
+} // end clitk namespace
#include "clitkSegmentationUtils.txx"
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff