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
#include <itkBinaryDilateImageFilter.h>
#include <itkConstantPadImageFilter.h>
#include <itkImageSliceIteratorWithIndex.h>
+#include <itkBinaryMorphologicalOpeningImageFilter.h>
namespace clitk {
/*
loop over input pixels, store the index in the fg that is max
according to the given direction.
- */
+ */
typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
IteratorType iter(input, input->GetLargestPossibleRegion());
iter.GoToBegin();
//--------------------------------------------------------------------
template<class ImageType>
typename ImageType::Pointer
- CropImageAbove(const ImageType * image,
+ CropImageRemoveGreaterThan(const ImageType * image,
int dim, double min, bool autoCrop,
typename ImageType::PixelType BG)
{
//--------------------------------------------------------------------
template<class ImageType>
typename ImageType::Pointer
- CropImageBelow(const ImageType * image,
+ CropImageRemoveLowerThan(const ImageType * image,
int dim, double max, bool autoCrop,
typename ImageType::PixelType BG)
{
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 BG
+ //DS FIXME (not useful ! to change ..)
+ for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
+ int label = labelMap->GetLabels()[i];
+ centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ 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>::Convert2DTo3DList(const MapPoint2DType & map,
+ PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
const ImageType * image,
VectorPoint3DType & list)
{
}
//--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ 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
//--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ 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,
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);
//--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ /* Consider an input object, for each slice, find the extrema
+ position according to a given direction and build a line segment
+ passing throught this point in a given direction. Output is a
+ vector of line (from point A to B), for each slice;
+ */
+ 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)
+ {
+ // Type of a slice
+ typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+
+ // Build the list of slices
+ std::vector<typename SliceType::Pointer> slices;
+ clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
+
+ // Build the list of 2D points
+ std::map<int, typename SliceType::PointType> position2D;
+ for(uint i=0; i<slices.size(); i++) {
+ typename SliceType::PointType p;
+ bool found =
+ clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
+ extremaDirection, extremaOppositeFlag, p);
+ if (found) {
+ position2D[i] = p;
+ }
+ }
+
+ // Convert 2D points in slice into 3D points
+ clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
+
+ // Create additional point just right to the previous ones, on the
+ // given lineDirection, in order to create a horizontal/vertical line.
+ for(uint i=0; i<A.size(); i++) {
+ typename ImageType::PointType p = A[i];
+ p[lineDirection] += 10;
+ B.push_back(p);
+ // Margins ?
+ A[i][1] += margin;
+ B[i][1] += margin;
+ }
+
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ SliceBySliceKeepMainCCL(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG) {
+
+ // Extract slices
+ const int d = ImageType::ImageDimension-1;
+ typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
+ std::vector<typename SliceType::Pointer> slices;
+ clitk::ExtractSlices<ImageType>(input, d, slices);
+
+ // Labelize and keep the main one
+ std::vector<typename SliceType::Pointer> o;
+ for(uint i=0; i<slices.size(); i++) {
+ o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
+ o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
+ }
+
+ // Join slices
+ typename ImageType::Pointer output;
+ output = clitk::JoinSlices<ImageType>(o, input, d);
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+
} // end of namespace
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff