+ bool computePerimeterFlag)
+ {
+ static const unsigned int Dim = ImageType::ImageDimension;
+ typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
+ typedef itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
+ typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
+ typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
+ typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
+ imageToLabelFilter->SetBackgroundValue(BG);
+ imageToLabelFilter->SetInput(image);
+ statFilter->SetInput(imageToLabelFilter->GetOutput());
+ statFilter->SetComputePerimeter(computePerimeterFlag);
+ statFilter->Update();
+ return statFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ ComputeCentroids2(const ImageType * image,
+ typename ImageType::PixelType BG,
+ std::vector<typename ImageType::PointType> & centroids)
+ {
+ typedef long LabelType;
+ static const unsigned int Dim = ImageType::ImageDimension;
+ typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
+ typedef itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
+ typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
+ typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
+ typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
+ imageToLabelFilter->SetBackgroundValue(BG);
+ imageToLabelFilter->SetInput(image);
+ statFilter->SetInput(imageToLabelFilter->GetOutput());
+ statFilter->Update();
+ typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
+
+ centroids.clear();
+ typename ImageType::PointType dummy;
+ centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
+ for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
+ centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
+ }
+
+ for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
+ DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
+ DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
+ DD(labelMap->GetLabelObject(i)->GetRoundness ());
+
+ // search for the point on the boundary alog PA
+
+ }
+
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
+ const ImageType * image,
+ const int slice,
+ PointType3D & p3D)
+ {
+ IndexType3D index3D;
+ index3D[0] = index3D[1] = 0;
+ index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
+ image->TransformIndexToPhysicalPoint(index3D, p3D);
+ p3D[0] = p2D[0];
+ p3D[1] = p2D[1];
+ // p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
+ // + image->GetOrigin()[2];
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
+ const ImageType * image,
+ VectorPoint3DType & list)
+ {
+ typename MapPoint2DType::const_iterator iter = map.begin();
+ while (iter != map.end()) {
+ PointType3D p;
+ Convert2DTo3D(iter->second, image, iter->first, p);
+ list.push_back(p);
+ ++iter;
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D,
+ int slice,
+ const ImageType * image,
+ VectorPoint3DType & list)
+ {
+ for(uint i=0; i<p2D.size(); i++) {
+ PointType3D p;
+ Convert2DTo3D(p2D[i], image, slice, p);
+ list.push_back(p);
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
+ std::string filename)
+ {
+ std::ofstream os;
+ openFileForWriting(os, filename);
+ os << "LANDMARKS1" << std::endl;
+ for(uint i=0; i<points.size(); i++) {
+ const typename ImageType::PointType & p = points[i];
+ // Write it in the file
+ os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
+ }
+ os.close();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Dilate(const ImageType * image, double radiusInMM,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool extendSupport)
+ {
+ typename ImageType::SizeType r;
+ for(uint i=0; i<ImageType::ImageDimension; i++)
+ r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
+ return Dilate<ImageType>(image, r, BG, FG, 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)
+ {
+ typename ImageType::SizeType r;
+ for(uint i=0; i<ImageType::ImageDimension; i++)
+ r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
+ return Dilate<ImageType>(image, r, BG, FG, 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)
+ {
+ // Create kernel for dilatation
+ typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
+ ImageType::ImageDimension> KernelType;
+ KernelType structuringElement;
+ structuringElement.SetRadius(radius);
+ structuringElement.CreateStructuringElement();
+
+ typename ImageType::Pointer output;
+ if (extendSupport) {
+ typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
+ typename PadFilterType::Pointer padFilter = PadFilterType::New();
+ padFilter->SetInput(image);
+ typename ImageType::SizeType lower;
+ typename ImageType::SizeType upper;
+ for(uint i=0; i<3; i++) {
+ lower[i] = upper[i] = 2*(radius[i]+1);
+ }
+ padFilter->SetPadLowerBound(lower);
+ padFilter->SetPadUpperBound(upper);
+ padFilter->Update();
+ output = padFilter->GetOutput();
+ }
+
+ // Dilate filter
+ typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
+ typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
+ dilateFilter->SetBackgroundValue(BG);
+ dilateFilter->SetForegroundValue(FG);
+ dilateFilter->SetBoundaryToForeground(false);
+ dilateFilter->SetKernel(structuringElement);
+ if (extendSupport) dilateFilter->SetInput(output);
+ else dilateFilter->SetInput(image);
+ dilateFilter->Update();
+ return dilateFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Opening(const ImageType * image, typename ImageType::SizeType radius,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG)
+ {
+ // Kernel
+ typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
+ ImageType::ImageDimension> KernelType;
+ KernelType structuringElement;
+ structuringElement.SetRadius(radius);
+ structuringElement.CreateStructuringElement();
+
+ // Filter
+ typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
+ typename OpeningFilterType::Pointer open = OpeningFilterType::New();
+ open->SetInput(image);
+ open->SetBackgroundValue(BG);
+ open->SetForegroundValue(FG);
+ open->SetKernel(structuringElement);
+ open->Update();
+ return open->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+
+ //--------------------------------------------------------------------
+ template<class ValueType, class VectorType>
+ void ConvertOption(std::string optionName, uint given,
+ ValueType * values, VectorType & p,
+ uint dim, bool required)
+ {
+ if (required && (given == 0)) {
+ clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
+ << dim << " values.");
+ }
+ if (given == 1) {
+ for(uint i=0; i<dim; i++) p[i] = values[0];
+ return;
+ }
+ if (given == dim) {
+ for(uint i=0; i<dim; i++) p[i] = values[i];
+ return;
+ }
+ if (given == 0) return;
+ clitkExceptionMacro("The option --" << optionName << " must have 1 or "
+ << dim << " values.");
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ /*
+ http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
+ Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
+ (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
+ This will equal zero if the point C is on the line formed by
+ points A and B, and will have a different sign depending on the
+ side. Which side this is depends on the orientation of your (x,y)
+ coordinates, but you can plug test values for A,B and C into this
+ formula to determine whether negative values are to the left or to
+ the right.
+ => to accelerate, start with formula, when change sign -> stop and fill
+
+ offsetToKeep = is used to determine which side of the line we
+ keep. The point along the mainDirection but 'offsetToKeep' mm away
+ is kept.
+
+ */
+ 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)
+ {
+ assert((mainDirection==0) || (mainDirection==1));
+ typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
+ SliceIteratorType siter = SliceIteratorType(input, input->GetLargestPossibleRegion());
+ siter.SetFirstDirection(0);
+ siter.SetSecondDirection(1);
+ siter.GoToBegin();
+ uint i=0;
+ typename ImageType::PointType A;
+ typename ImageType::PointType B;
+ typename ImageType::PointType C;
+ assert(lA.size() == lB.size());
+ while ((i<lA.size()) && (!siter.IsAtEnd())) {
+ // Check that the current slice correspond to the current point
+ input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
+ if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
+ }
+ else {
+ // Define A,B,C points
+ A = lA[i];
+ B = lB[i];
+ C = A;
+ // Check that the line is not a point (A=B)
+ bool p = (A[0] == B[0]) && (A[1] == B[1]);
+
+ if (!p) {
+ C[mainDirection] += offsetToKeep; // I know I must keep this point
+ double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+ bool isPositive = s<0;
+ while (!siter.IsAtEndOfSlice()) {
+ while (!siter.IsAtEndOfLine()) {
+ // Very slow, I know ... but image should be very small
+ input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
+ double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+ if (s == 0) siter.Set(BG); // on the line, we decide to remove
+ if (isPositive) {
+ if (s > 0) siter.Set(BG);
+ }
+ else {
+ if (s < 0) siter.Set(BG);
+ }
+ ++siter;
+ }
+ siter.NextLine();
+ } // end loop slice
+ }
+
+ ++i;
+ } // End of current slice
+ siter.NextSlice();
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ AndNot(ImageType * input,
+ const ImageType * object,
+ typename ImageType::PixelType BG)
+ {
+ typename ImageType::Pointer o;
+ bool resized=false;
+ if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
+ o = clitk::ResizeImageLike<ImageType>(object, input, BG);
+ resized = true;
+ }
+
+ typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+ typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
+ boolFilter->InPlaceOn();
+ boolFilter->SetInput1(input);
+ if (resized) boolFilter->SetInput2(o);
+ else boolFilter->SetInput2(object);
+ boolFilter->SetBackgroundValue1(BG);
+ boolFilter->SetBackgroundValue2(BG);
+ boolFilter->SetOperationType(BoolFilterType::AndNot);
+ boolFilter->Update();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ And(ImageType * input,
+ const ImageType * object,
+ typename ImageType::PixelType BG)
+ {
+ typename ImageType::Pointer o;
+ bool resized=false;
+ if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
+ o = clitk::ResizeImageLike<ImageType>(object, input, BG);
+ resized = true;
+ }
+
+ typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+ typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
+ boolFilter->InPlaceOn();
+ boolFilter->SetInput1(input);
+ if (resized) boolFilter->SetInput2(o);
+ else boolFilter->SetInput2(object);
+ boolFilter->SetBackgroundValue1(BG);
+ boolFilter->SetBackgroundValue2(BG);
+ boolFilter->SetOperationType(BoolFilterType::And);
+ boolFilter->Update();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ Or(ImageType * input,
+ const ImageType * object,
+ typename ImageType::PixelType BG)
+ {
+ typename ImageType::Pointer o;
+ bool resized=false;
+ if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
+ o = clitk::ResizeImageLike<ImageType>(object, input, BG);
+ resized = true;
+ }
+
+ typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+ typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
+ boolFilter->InPlaceOn();
+ boolFilter->SetInput1(input);
+ if (resized) boolFilter->SetInput2(o);
+ else boolFilter->SetInput2(object);
+ boolFilter->SetBackgroundValue1(BG);
+ boolFilter->SetBackgroundValue2(BG);
+ boolFilter->SetOperationType(BoolFilterType::Or);
+ boolFilter->Update();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Binarize(const ImageType * input,
+ typename ImageType::PixelType lower,
+ typename ImageType::PixelType upper,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG)
+ {
+ typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
+ typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
+ binarizeFilter->SetInput(input);
+ binarizeFilter->InPlaceOff();
+ binarizeFilter->SetLowerThreshold(lower);
+ binarizeFilter->SetUpperThreshold(upper);
+ binarizeFilter->SetInsideValue(FG);
+ binarizeFilter->SetOutsideValue(BG);
+ binarizeFilter->Update();
+ return binarizeFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ GetMinMaxPointPosition(const ImageType * input,
+ typename ImageType::PointType & min,
+ typename ImageType::PointType & max)
+ {
+ typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
+ input->TransformIndexToPhysicalPoint(index, min);
+ index = index+input->GetLargestPossibleRegion().GetSize();
+ input->TransformIndexToPhysicalPoint(index, max);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::PointType
+ FindExtremaPointInAGivenLine(const ImageType * input,
+ int dimension,
+ bool inverse,
+ typename ImageType::PointType p,