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
// clitk
#include "clitkSetBackgroundImageFilter.h"
+#include "clitkSliceBySliceRelativePositionFilter.h"
+#include "clitkCropLikeImageFilter.h"
+#include "clitkMemoryUsage.h"
// itk
#include <itkConnectedComponentImageFilter.h>
#include <itkRelabelComponentImageFilter.h>
#include <itkBinaryThresholdImageFilter.h>
#include <itkPasteImageFilter.h>
+#include <itkStatisticsLabelMapFilter.h>
+#include <itkBinaryBallStructuringElement.h>
+#include <itkBinaryDilateImageFilter.h>
+#include <itkConstantPadImageFilter.h>
+#include <itkImageSliceIteratorWithIndex.h>
+#include <itkBinaryMorphologicalOpeningImageFilter.h>
+#include <itkImageDuplicator.h>
+#include <itkSignedMaurerDistanceMapImageFilter.h>
-//--------------------------------------------------------------------
-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);
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template<class ImageType, class TMaskImageType>
-typename ImageType::Pointer
-clitk::SetBackground(typename ImageType::ConstPointer input,
- typename TMaskImageType::ConstPointer mask,
- typename TMaskImageType::PixelType maskBG,
- typename ImageType::PixelType outValue) {
- typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType> 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 ImageType>
-int clitk::GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
- typename ImageType::PixelType BG,
- bool isFullyConnected) {
- // Connected Component label
- typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
- typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
- connectFilter->SetInput(input);
- connectFilter->SetBackgroundValue(BG);
- connectFilter->SetFullyConnected(isFullyConnected);
- connectFilter->Update();
-
- // Return result
- return connectFilter->GetObjectCount();
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::Labelize(typename ImageType::Pointer input,
- typename ImageType::PixelType BG,
- bool isFullyConnected,
- int minimalComponentSize) {
- // Connected Component label
- typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> 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<ImageType, ImageType> 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 ImageType>
-typename ImageType::Pointer
-clitk::RemoveLabels(typename ImageType::Pointer input,
- typename ImageType::PixelType BG,
- std::vector<typename ImageType::PixelType> & labelsToRemove) {
- typename ImageType::Pointer working_image = input;
- for (unsigned int i=0; i <labelsToRemove.size(); i++) {
- typedef clitk::SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
- typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template<class ImageType, class TMaskImageType>
+ typename ImageType::Pointer
+ SetBackground(const ImageType * input,
+ const TMaskImageType * mask,
+ typename TMaskImageType::PixelType maskBG,
+ typename ImageType::PixelType outValue,
+ bool inPlace) {
+ typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
+ SetBackgroundImageFilterType;
+ typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
+ = SetBackgroundImageFilterType::New();
+ // if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
+ setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
setBackgroundFilter->SetInput(input);
- setBackgroundFilter->SetInput2(input);
- setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
- setBackgroundFilter->SetOutsideValue(BG);
+ setBackgroundFilter->SetInput2(mask);
+ setBackgroundFilter->SetMaskValue(maskBG);
+ setBackgroundFilter->SetOutsideValue(outValue);
setBackgroundFilter->Update();
- working_image = setBackgroundFilter->GetOutput();
+ return setBackgroundFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ int GetNumberOfConnectedComponentLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ bool isFullyConnected) {
+ // Connected Component label
+ typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
+ typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+ connectFilter->SetInput(input);
+ connectFilter->SetBackgroundValue(BG);
+ connectFilter->SetFullyConnected(isFullyConnected);
+ connectFilter->Update();
+
+ // Return result
+ return connectFilter->GetObjectCount();
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ /*
+ Warning : in this cas, we consider outputType like inputType, not
+ InternalImageType. Be sure it fits.
+ */
+ template<class ImageType>
+ typename ImageType::Pointer
+ Labelize(const ImageType * input,
+ typename ImageType::PixelType BG,
+ bool isFullyConnected,
+ int minimalComponentSize) {
+ // InternalImageType for storing large number of component
+ typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
+
+ // Connected Component label
+ typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
+ typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+ // connectFilter->ReleaseDataFlagOn();
+ connectFilter->SetInput(input);
+ connectFilter->SetBackgroundValue(BG);
+ connectFilter->SetFullyConnected(isFullyConnected);
+
+ // Sort by size and remove too small area.
+ typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
+ typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+ // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
+ relabelFilter->SetInput(connectFilter->GetOutput());
+ relabelFilter->SetMinimumObjectSize(minimalComponentSize);
+ relabelFilter->Update();
+
+ // Return result
+ typename ImageType::Pointer output = relabelFilter->GetOutput();
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ /*
+ Warning : in this cas, we consider outputType like inputType, not
+ InternalImageType. Be sure it fits.
+ */
+ template<class ImageType>
+ typename ImageType::Pointer
+ LabelizeAndCountNumberOfObjects(const ImageType * input,
+ typename ImageType::PixelType BG,
+ bool isFullyConnected,
+ int minimalComponentSize,
+ int & nb) {
+ // InternalImageType for storing large number of component
+ typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
+
+ // Connected Component label
+ typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
+ typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+ // connectFilter->ReleaseDataFlagOn();
+ connectFilter->SetInput(input);
+ connectFilter->SetBackgroundValue(BG);
+ connectFilter->SetFullyConnected(isFullyConnected);
+
+ // Sort by size and remove too small area.
+ typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
+ typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+ // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
+ relabelFilter->SetInput(connectFilter->GetOutput());
+ relabelFilter->SetMinimumObjectSize(minimalComponentSize);
+ relabelFilter->Update();
+
+ nb = relabelFilter->GetNumberOfObjects();
+ // DD(relabelFilter->GetOriginalNumberOfObjects());
+ // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
+
+ // Return result
+ typename ImageType::Pointer output = relabelFilter->GetOutput();
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ RemoveLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ std::vector<typename ImageType::PixelType> & labelsToRemove) {
+ assert(labelsToRemove.size() != 0);
+ typename ImageType::Pointer working_image;// = input;
+ for (unsigned int i=0; i <labelsToRemove.size(); i++) {
+ typedef SetBackgroundImageFilter<ImageType, ImageType> 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 ImageType>
+ typename ImageType::Pointer
+ KeepLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ typename ImageType::PixelType firstKeep,
+ typename ImageType::PixelType lastKeep,
+ bool useLastKeep) {
+ typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> 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 ImageType>
+ typename ImageType::Pointer
+ LabelizeAndSelectLabels(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG,
+ bool isFullyConnected,
+ int minimalComponentSize,
+ LabelizeParameters<typename ImageType::PixelType> * param)
+ {
+ typename ImageType::Pointer working_image;
+ working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
+ if (param->GetLabelsToRemove().size() != 0)
+ working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
+ working_image = KeepLabels<ImageType>(working_image,
+ BG, FG,
+ param->GetFirstKeep(),
+ param->GetLastKeep(),
+ param->GetUseLastKeep());
+ return working_image;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class MaskImageType>
+ typename MaskImageType::Pointer
+ SliceBySliceRelativePosition(const MaskImageType * input,
+ const MaskImageType * object,
+ int direction,
+ double threshold,
+ std::string orientation,
+ bool uniqueConnectedComponent,
+ double spacing,
+ bool autocropFlag,
+ bool singleObjectCCL)
+ {
+ typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
+ typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
+ sliceRelPosFilter->VerboseStepFlagOff();
+ sliceRelPosFilter->WriteStepFlagOff();
+ sliceRelPosFilter->SetInput(input);
+ sliceRelPosFilter->SetInputObject(object);
+ sliceRelPosFilter->SetDirection(direction);
+ sliceRelPosFilter->SetFuzzyThreshold(threshold);
+ sliceRelPosFilter->AddOrientationTypeString(orientation);
+ sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
+ sliceRelPosFilter->SetIntermediateSpacing(spacing);
+ sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
+ sliceRelPosFilter->ObjectCCLSelectionFlagOff();
+ sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
+ // sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
+ sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
+ sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
+ sliceRelPosFilter->Update();
+ return sliceRelPosFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class MaskImageType>
+ typename MaskImageType::Pointer
+ SliceBySliceRelativePosition(const MaskImageType * input,
+ const MaskImageType * object,
+ int direction,
+ double threshold,
+ double angle,
+ bool inverseflag,
+ bool uniqueConnectedComponent,
+ double spacing,
+ bool autocropFlag,
+ bool singleObjectCCL)
+ {
+ typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
+ typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
+ sliceRelPosFilter->VerboseStepFlagOff();
+ sliceRelPosFilter->WriteStepFlagOff();
+ sliceRelPosFilter->SetInput(input);
+ sliceRelPosFilter->SetInputObject(object);
+ sliceRelPosFilter->SetDirection(direction);
+ sliceRelPosFilter->SetFuzzyThreshold(threshold);
+ // sliceRelPosFilter->AddOrientationTypeString(orientation);
+ sliceRelPosFilter->AddAnglesInRad(angle, 0.0);
+ sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
+ sliceRelPosFilter->SetIntermediateSpacing(spacing);
+ sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
+ sliceRelPosFilter->ObjectCCLSelectionFlagOff();
+ sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
+ sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
+ sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
+ sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
+ sliceRelPosFilter->Update();
+ return sliceRelPosFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ bool
+ FindExtremaPointInAGivenDirection(const ImageType * input,
+ typename ImageType::PixelType bg,
+ int direction, bool opposite,
+ typename ImageType::PointType & point)
+ {
+ typename ImageType::PointType dummy;
+ return FindExtremaPointInAGivenDirection(input, bg, direction,
+ opposite, dummy, 0, point);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ 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 & point)
+ {
+ /*
+ 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();
+ typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
+ if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
+ bool found=false;
+ while (!iter.IsAtEnd()) {
+ if (iter.Get() != bg) {
+ bool test = iter.GetIndex()[direction] > max[direction];
+ if (opposite) test = !test;
+ if (test) {
+ typename ImageType::PointType p;
+ input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
+ if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
+ max = iter.GetIndex();
+ found = true;
+ }
+ }
+ }
+ ++iter;
+ }
+ if (!found) return false;
+ input->TransformIndexToPhysicalPoint(max, point);
+ return true;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageRemoveGreaterThan(const ImageType * image,
+ int dim, double min, bool autoCrop,
+ typename ImageType::PixelType BG)
+ {
+ return CropImageAlongOneAxis<ImageType>(image, dim,
+ image->GetOrigin()[dim],
+ min,
+ autoCrop, BG);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageRemoveLowerThan(const ImageType * image,
+ int dim, double max, bool autoCrop,
+ typename ImageType::PixelType BG)
+ {
+ typename ImageType::PointType p;
+ image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
+ image->GetLargestPossibleRegion().GetSize(), p);
+ // Add GetSpacing because remove Lower or equal than
+ // DD(max);
+ // DD(p);
+ // DD(max+image->GetSpacing()[dim]);
+ return CropImageAlongOneAxis<ImageType>(image, dim, max+image->GetSpacing()[dim], p[dim], autoCrop, BG);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageAlongOneAxis(const ImageType * image,
+ int dim, double min, double max,
+ bool autoCrop, typename ImageType::PixelType BG)
+ {
+ // Compute region size
+ typename ImageType::RegionType region;
+ typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
+ typename ImageType::PointType p = image->GetOrigin();
+ if (min > p[dim]) p[dim] = min; // Check if not outside the image
+ typename ImageType::IndexType start;
+ image->TransformPhysicalPointToIndex(p, start);
+ double m = image->GetOrigin()[dim] + size[dim]*image->GetSpacing()[dim];
+ if (max > m) p[dim] = m; // Check if not outside the image
+ else p[dim] = max;
+ typename ImageType::IndexType end;
+ image->TransformPhysicalPointToIndex(p, end);
+ size[dim] = abs(end[dim]-start[dim]);
+ region.SetIndex(start);
+ region.SetSize(size);
+
+ // Perform Crop
+ typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(image);
+ cropFilter->SetRegionOfInterest(region);
+ cropFilter->Update();
+ typename ImageType::Pointer result = cropFilter->GetOutput();
+
+ // Auto Crop
+ if (autoCrop) {
+ result = AutoCrop<ImageType>(result, BG);
+ }
+ return result;
}
- return working_image;
-}
-//--------------------------------------------------------------------
+ //--------------------------------------------------------------------
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::KeepLabels(typename ImageType::Pointer input,
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ ComputeCentroids(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 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, class LabelType>
+ typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
+ ComputeLabelMap(const ImageType * image,
typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- typename ImageType::PixelType firstKeep,
- typename ImageType::PixelType lastKeep,
- bool useLastKeep) {
- typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> 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 ImageType>
-typename ImageType::Pointer
-clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
+ 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,
typename ImageType::PixelType BG,
- typename ImageType::PixelType FG,
- bool isFullyConnected,
- int minimalComponentSize,
- LabelizeParameters<typename ImageType::PixelType> * param)
-{
- typename ImageType::Pointer working_image;
- working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
- working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
- working_image = KeepLabels<ImageType>(working_image,
- BG, FG,
- param->GetFirstKeep(),
- param->GetLastKeep(),
- param->GetUseLastKeep());
- return working_image;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::EnlargeImageLike(typename ImageType::Pointer input,
- typename ImageType::Pointer like,
- typename ImageType::PixelType backgroundValue)
-{
- if (!HaveSameSpacing<ImageType, ImageType>(input, like)) {
- FATAL("Images must have the same spacing");
- }
-
- typename ImageType::Pointer output = ImageType::New();
- typename ImageType::SizeType size;
- for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
- size[i] = lrint((like->GetLargestPossibleRegion().GetSize()[i]*like->GetSpacing()[i])/
- (double)like->GetSpacing()[i]);
- }
- // DD(size);
- typename ImageType::RegionType region;
- region.SetSize(size);
- output->SetRegions(region);
- output->SetSpacing(like->GetSpacing());
- output->SetOrigin(like->GetOrigin());
- output->Allocate();
- output->FillBuffer(backgroundValue);
- typedef itk::PasteImageFilter<ImageType,ImageType> PasteFilterType;
- typename PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
- typename PasteFilterType::InputImageIndexType index;
- for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
- index[i] = lrint((input->GetOrigin()[i] - like->GetOrigin()[i])/(double)input->GetSpacing()[i]);
- }
- // DD(index);
- pasteFilter->SetSourceImage(input);
- pasteFilter->SetDestinationImage(output);
- pasteFilter->SetDestinationIndex(index);
- pasteFilter->SetSourceRegion(input->GetLargestPossibleRegion());
- pasteFilter->Update();
- return pasteFilter->GetOutput();
-}
-//--------------------------------------------------------------------
+ double distanceMax)
+ {
+ // Which direction ? Increasing or decreasing.
+ int d=1;
+ if (inverse) d=-1;
+
+ // Transform to pixel index
+ typename ImageType::IndexType index;
+ input->TransformPhysicalPointToIndex(p, index);
+
+ // Loop while inside the mask;
+ while (input->GetPixel(index) != BG) {
+ index[dimension] += d;
+ }
+
+ // Transform back to Physical Units
+ typename ImageType::PointType result;
+ input->TransformIndexToPhysicalPoint(index, result);
+
+ // Check that is is not too far away
+ double distance = p.EuclideanDistanceTo(result);
+ if (distance > distanceMax) {
+ result = p; // Get back to initial value
+ }
+
+ return result;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class PointType>
+ bool
+ IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
+ {
+ // Look at the position of point 'like' according to the AB line
+ double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
+ bool negative = s<0;
+
+ // Look the C position
+ s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+
+ if (negative && (s<=0)) return true;
+ if (!negative && (s>=0)) return true;
+ return false;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ /* 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][extremaDirection] += margin;
+ B[i][extremaDirection] += 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;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Clone(const ImageType * input) {
+ typedef itk::ImageDuplicator<ImageType> DuplicatorType;
+ typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
+ duplicator->SetInputImage(input);
+ duplicator->Update();
+ return duplicator->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ /* Consider an input object, start at A, for each slice (dim1):
+ - compute the intersection between the AB line and the current slice
+ - remove what is at lower or greater according to dim2 of this point
+ - stop at B
+ */
+ 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)
+
+ {
+ // Extract slices
+ typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+ typedef typename SliceType::Pointer SlicePointer;
+ std::vector<SlicePointer> slices;
+ clitk::ExtractSlices<ImageType>(input, dim1, slices);
+
+ // Start at slice that contains A, and stop at B
+ typename ImageType::IndexType Ap;
+ typename ImageType::IndexType Bp;
+ input->TransformPhysicalPointToIndex(A, Ap);
+ input->TransformPhysicalPointToIndex(B, Bp);
+
+ // Determine slice largest region
+ typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
+ typename SliceType::SizeType size = region.GetSize();
+ typename SliceType::IndexType index = region.GetIndex();
+
+ // Line slope
+ double a = (Bp[dim2]-Ap[dim2])/(Bp[dim1]-Ap[dim1]);
+ double b = Ap[dim2];
+
+ // Loop from slice A to slice B
+ for(uint i=0; i<(Bp[dim1]-Ap[dim1]); i++) {
+ // Compute intersection between line AB and current slice for the dim2
+ double p = a*i+b;
+ // Change region (lower than dim2)
+ if (removeLowerPartFlag) {
+ size[dim2] = p-Ap[dim2];
+ }
+ else {
+ size[dim2] = slices[0]->GetLargestPossibleRegion().GetSize()[dim2]-p;
+ index[dim2] = p;
+ }
+ region.SetSize(size);
+ region.SetIndex(index);
+ // Fill region with BG (simple region iterator)
+ FillRegionWithValue<SliceType>(slices[i+Ap[dim1]], BG, region);
+ /*
+ typedef itk::ImageRegionIterator<SliceType> IteratorType;
+ IteratorType iter(slices[i+Ap[dim1]], region);
+ iter.GoToBegin();
+ while (!iter.IsAtEnd()) {
+ iter.Set(BG);
+ ++iter;
+ }
+ */
+ // Loop
+ }
+
+ // Merge slices
+ typename ImageType::Pointer output;
+ output = clitk::JoinSlices<ImageType>(slices, input, dim1);
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ /* Consider an input object, slice by slice, use the point A and set
+ pixel to BG according to their position relatively to A
+ */
+ 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)
+
+ {
+ // Extract slices
+ typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+ typedef typename SliceType::Pointer SlicePointer;
+ std::vector<SlicePointer> slices;
+ clitk::ExtractSlices<ImageType>(input, sliceDim, slices);
+
+ // Start at slice that contains A
+ typename ImageType::IndexType Ap;
+
+ // Determine slice largest region
+ typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
+ typename SliceType::SizeType size = region.GetSize();
+ typename SliceType::IndexType index = region.GetIndex();
+
+ // Loop from slice A to slice B
+ for(uint i=0; i<A.size(); i++) {
+ input->TransformPhysicalPointToIndex(A[i], Ap);
+ uint sliceIndex = Ap[2] - input->GetLargestPossibleRegion().GetIndex()[2];
+ if ((sliceIndex < 0) || (sliceIndex >= slices.size())) {
+ continue; // do not consider this slice
+ }
+
+ // Compute region for BG
+ if (removeGreaterThanXFlag) {
+ index[0] = Ap[0];
+ size[0] = region.GetSize()[0]-(index[0]-region.GetIndex()[0]);
+ }
+ else {
+ index[0] = region.GetIndex()[0];
+ size[0] = Ap[0] - index[0];
+ }
+
+ if (removeGreaterThanYFlag) {
+ index[1] = Ap[1];
+ size[1] = region.GetSize()[1]-(index[1]-region.GetIndex()[1]);
+ }
+ else {
+ index[1] = region.GetIndex()[1];
+ size[1] = Ap[1] - index[1];
+ }
+
+ // Set region
+ region.SetSize(size);
+ region.SetIndex(index);
+
+ // Fill region with BG (simple region iterator)
+ FillRegionWithValue<SliceType>(slices[sliceIndex], BG, region);
+ // Loop
+ }
+
+ // Merge slices
+ typename ImageType::Pointer output;
+ output = clitk::JoinSlices<ImageType>(slices, input, sliceDim);
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region)
+ {
+ typedef itk::ImageRegionIterator<ImageType> IteratorType;
+ IteratorType iter(input, region);
+ iter.GoToBegin();
+ while (!iter.IsAtEnd()) {
+ iter.Set(value);
+ ++iter;
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min,
+ typename ImageType::PointType & max)
+ {
+ typedef typename ImageType::PointType PointType;
+ typedef typename ImageType::IndexType IndexType;
+ IndexType min_i, max_i;
+ min_i = input->GetLargestPossibleRegion().GetIndex();
+ for(uint i=0; i<ImageType::ImageDimension; i++)
+ max_i[i] = input->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
+ input->TransformIndexToPhysicalPoint(min_i, min);
+ input->TransformIndexToPhysicalPoint(max_i, max);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename itk::Image<float, ImageType::ImageDimension>::Pointer
+ DistanceMap(const ImageType * input, typename ImageType::PixelType BG)//,
+ // typename itk::Image<float, ImageType::ImageDimension>::Pointer dmap)
+ {
+ typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
+ typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, FloatImageType> DistanceMapFilterType;
+ typename DistanceMapFilterType::Pointer filter = DistanceMapFilterType::New();
+ filter->SetInput(input);
+ filter->SetUseImageSpacing(true);
+ filter->SquaredDistanceOff();
+ filter->SetBackgroundValue(BG);
+ filter->Update();
+ return filter->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ 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)
+ {
+ // Extract slices
+ typedef typename itk::Image<typename ImageType::PixelType, 2> SliceType;
+ typedef typename SliceType::Pointer SlicePointer;
+ std::vector<SlicePointer> slices_s1;
+ std::vector<SlicePointer> slices_s2;
+ clitk::ExtractSlices<ImageType>(S1, sliceDimension, slices_s1);
+ clitk::ExtractSlices<ImageType>(S2, sliceDimension, slices_s2);
+
+ assert(slices_s1.size() == slices_s2.size());
+
+ // Prepare dmap
+ typedef itk::Image<float,2> FloatImageType;
+ typedef itk::SignedMaurerDistanceMapImageFilter<SliceType, FloatImageType> DistanceMapFilterType;
+ std::vector<typename FloatImageType::Pointer> dmaps1;
+ std::vector<typename FloatImageType::Pointer> dmaps2;
+ typename FloatImageType::Pointer dmap;
+
+ // loop on slices
+ for(uint i=0; i<slices_s1.size(); i++) {
+ // Compute dmap for S1 *TO PUT IN FONCTION*
+ dmap = clitk::DistanceMap<SliceType>(slices_s1[i], BG);
+ dmaps1.push_back(dmap);
+ writeImage<FloatImageType>(dmap, "dmap1.mha");
+ // Compute dmap for S2
+ dmap = clitk::DistanceMap<SliceType>(slices_s2[i], BG);
+ dmaps2.push_back(dmap);
+ writeImage<FloatImageType>(dmap, "dmap2.mha");
+
+ // Look in S2 for the point the closest to S1
+ typename SliceType::PointType p = ComputeClosestPoint<SliceType>(slices_s1[i], dmaps2[i], BG);
+ typename ImageType::PointType p3D;
+ clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S1, i, p3D);
+ A.push_back(p3D);
+
+ // Look in S2 for the point the closest to S1
+ p = ComputeClosestPoint<SliceType>(slices_s2[i], dmaps1[i], BG);
+ clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S2, i, p3D);
+ B.push_back(p3D);
+
+ }
+
+ // Debug dmap
+ /*
+ typedef itk::Image<float,3> FT;
+ FT::Pointer f = FT::New();
+ typename FT::Pointer d1 = clitk::JoinSlices<FT>(dmaps1, S1, 2);
+ typename FT::Pointer d2 = clitk::JoinSlices<FT>(dmaps2, S2, 2);
+ writeImage<FT>(d1, "d1.mha");
+ writeImage<FT>(d2, "d2.mha");
+ */
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::PointType
+ ComputeClosestPoint(const ImageType * input,
+ const itk::Image<float, ImageType::ImageDimension> * dmap,
+ typename ImageType::PixelType & BG)
+ {
+ // Loop dmap + S2, if FG, get min
+ typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
+ typedef itk::ImageRegionConstIteratorWithIndex<ImageType> ImageIteratorType;
+ typedef itk::ImageRegionConstIterator<FloatImageType> DMapIteratorType;
+ ImageIteratorType iter1(input, input->GetLargestPossibleRegion());
+ DMapIteratorType iter2(dmap, dmap->GetLargestPossibleRegion());
+
+ iter1.GoToBegin();
+ iter2.GoToBegin();
+ double dmin = 100000.0;
+ typename ImageType::IndexType indexmin;
+ while (!iter1.IsAtEnd()) {
+ if (iter1.Get() != BG) {
+ double d = iter2.Get();
+ if (d<dmin) {
+ indexmin = iter1.GetIndex();
+ dmin = d;
+ }
+ }
+ ++iter1;
+ ++iter2;
+ }
+
+ // Convert in Point
+ typename ImageType::PointType p;
+ input->TransformIndexToPhysicalPoint(indexmin, p);
+ return p;
+ }
+ //--------------------------------------------------------------------
+
+
+
+
+} // end of namespace
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff