SetBackground(const TInternalImageType * input,
const TMaskInternalImageType * mask,
typename TMaskInternalImageType::PixelType maskBG,
- typename TInternalImageType::PixelType outValue);
+ typename TInternalImageType::PixelType outValue,
+ bool inPlace);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// In a binary image, search for the point belonging to the FG that
// is the most exterma in the direction 'direction' (or in the
- // opposite if notFlag is given). if 'point' and 'distanceMax' are
- // given, do not consider points that are away from 'point' more
- // than 'distanceMax'
- template<class SliceType>
- typename SliceType::PointType
- FindExtremaPointInAGivenDirection(const SliceType * input,
- typename SliceType::PixelType bg,
- int direction,
- bool notFlag,
- typename SliceType::PointType point,
- double distanceMax);
+ // opposite if notFlag is given).
+ template<class ImageType>
+ bool
+ FindExtremaPointInAGivenDirection(const ImageType * input,
+ typename ImageType::PixelType bg,
+ int direction, bool opposite,
+ typename ImageType::PointType & p);
+
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ // Same as above but check that the found point is not more than
+ // 'distanceMax' away from 'refPoint'
+ template<class ImageType>
+ bool
+ FindExtremaPointInAGivenDirection(const ImageType * input,
+ typename ImageType::PixelType bg,
+ int direction, bool opposite,
+ typename ImageType::PointType refPoint,
+ double distanceMax,
+ typename ImageType::PointType & p);
//--------------------------------------------------------------------
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);
+ template<class ImageType>
+ typename ImageType::Pointer
+ CropImageBelow(typename ImageType::Pointer image,
+ int dim, double max,
+ bool autoCrop = false,
+ typename ImageType::PixelType BG=0);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ ComputeCentroids(typename ImageType::Pointer 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);
+ //--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
+ 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);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ // Set of tools to manage 3D points and 2D points in slices
+ template<class ImageType>
+ class PointsUtils
+ {
+ typedef typename ImageType::PointType PointType3D;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef itk::Image<PixelType, 2> SliceType;
+ typedef typename SliceType::PointType PointType2D;
+
+ typedef std::map<int, PointType2D> MapPoint2DType;
+ typedef std::vector<PointType3D> VectorPoint3DType;
+ public:
+ static void Convert2DTo3D(const PointType2D & p2D,
+ ImagePointer image,
+ const int slice,
+ PointType3D & p3D);
+ static void Convert2DTo3DList(const MapPoint2DType & map,
+ ImagePointer image,
+ VectorPoint3DType & list);
+ };
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void
+ WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
+ std::string filename);
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Dilate(typename ImageType::Pointer 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);
+ 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);
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ template<class ValueType, class VectorType>
+ void ConvertOption(std::string optionName, uint given,
+ ValueType * values, VectorType & p,
+ uint dim, bool required);
+#define ConvertOptionMacro(OPTIONNAME, VAR, DIM, REQUIRED) \
+ ConvertOption(#OPTIONNAME, OPTIONNAME##_given, OPTIONNAME##_arg, VAR, DIM, REQUIRED);
+
}
#include "clitkSegmentationUtils.txx"
#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>
//--------------------------------------------------------------------
template<class ImageType>
//--------------------------------------------------------------------
template<class ImageType, class TMaskImageType>
typename ImageType::Pointer
-clitk::SetBackground(//typename ImageType::ConstPointer input,
- const ImageType * input,
+clitk::SetBackground(const ImageType * input,
const TMaskImageType * mask,
typename TMaskImageType::PixelType maskBG,
- typename ImageType::PixelType outValue) {
- typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType> SetBackgroundImageFilterType;
- typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+ typename ImageType::PixelType outValue,
+ bool inPlace) {
+ typedef clitk::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(mask);
setBackgroundFilter->SetMaskValue(maskBG);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
+/*
+ Warning : in this cas, we consider outputType like inputType, not
+ InternalImageType. Be sure it fits.
+ */
template<class ImageType>
typename ImageType::Pointer
clitk::Labelize(const ImageType * input,
// 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->InPlaceOn();
+ // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
relabelFilter->SetInput(connectFilter->GetOutput());
relabelFilter->SetMinimumObjectSize(minimalComponentSize);
relabelFilter->Update();
// Return result
- return relabelFilter->GetOutput();
+ typename ImageType::Pointer output = relabelFilter->GetOutput();
+ return output;
}
//--------------------------------------------------------------------
std::string orientation,
bool uniqueConnectedComponent,
double spacing,
- bool notflag)
+ bool inverseflag)
{
typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
- sliceRelPosFilter->VerboseStepOff();
- sliceRelPosFilter->WriteStepOff();
+ sliceRelPosFilter->VerboseStepFlagOff();
+ sliceRelPosFilter->WriteStepFlagOff();
sliceRelPosFilter->SetInput(input);
sliceRelPosFilter->SetInputObject(object);
sliceRelPosFilter->SetDirection(direction);
sliceRelPosFilter->SetFuzzyThreshold(threshold);
- sliceRelPosFilter->SetOrientationTypeString(orientation);
+ sliceRelPosFilter->AddOrientationTypeString(orientation);
sliceRelPosFilter->SetResampleBeforeRelativePositionFilter((spacing != -1));
sliceRelPosFilter->SetIntermediateSpacing(spacing);
sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
- sliceRelPosFilter->SetNotFlag(notflag);
+ sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
// sliceRelPosFilter->SetAutoCropFlag(true); ??
sliceRelPosFilter->Update();
return sliceRelPosFilter->GetOutput();
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template<class SliceType>
-typename SliceType::PointType
-clitk::FindExtremaPointInAGivenDirection(const SliceType * input,
- typename SliceType::PixelType bg,
- int direction,
- bool notFlag,
- typename SliceType::PointType point,
- double distanceMax)
+template<class ImageType>
+bool
+clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
+ typename ImageType::PixelType bg,
+ int direction, bool opposite,
+ typename ImageType::PointType & point)
+{
+ typename ImageType::PointType dummy;
+ return clitk::FindExtremaPointInAGivenDirection(input, bg, direction,
+ opposite, dummy, 0, point);
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType>
+bool
+clitk::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<SliceType> IteratorType;
+ typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
IteratorType iter(input, input->GetLargestPossibleRegion());
iter.GoToBegin();
- typename SliceType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
- if (notFlag) max = max+input->GetLargestPossibleRegion().GetSize();
+ 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 (notFlag) test = !test;
+ if (opposite) test = !test;
if (test) {
- typename SliceType::PointType p;
+ typename ImageType::PointType p;
input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
- if ((distanceMax==0) || (p.EuclideanDistanceTo(point) < distanceMax)) {
+ if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
max = iter.GetIndex();
+ found = true;
}
}
}
++iter;
}
- typename SliceType::PointType p;
- input->TransformIndexToPhysicalPoint(max, p);
- return p;
+ if (!found) return false;
+ input->TransformIndexToPhysicalPoint(max, point);
+ return true;
}
//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::CropImageAbove(typename ImageType::Pointer image,
+ int dim, double min,
+ bool autoCrop,
+ typename ImageType::PixelType BG)
+{
+ return clitk::CropImageAlongOneAxis<ImageType>(image, dim,
+ image->GetOrigin()[dim],
+ min,
+ autoCrop, BG);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::CropImageBelow(typename ImageType::Pointer image,
+ int dim, double max,
+ bool autoCrop,
+ typename ImageType::PixelType BG)
+{
+ typename ImageType::PointType p;
+ image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
+ image->GetLargestPossibleRegion().GetSize(), p);
+ return clitk::CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
template<class ImageType>
typename ImageType::Pointer
size[dim] = fabs(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->SetRegionOfInterest(region);
cropFilter->Update();
typename ImageType::Pointer result = cropFilter->GetOutput();
+
// Auto Crop
if (autoCrop) {
result = clitk::AutoCrop<ImageType>(result, BG);
return result;
}
//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void
+clitk::ComputeCentroids(typename ImageType::Pointer 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());
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void
+clitk::ExtractSlices(typename ImageType::Pointer image,
+ int direction,
+ std::vector<typename itk::Image<typename ImageType::PixelType,
+ ImageType::ImageDimension-1>::Pointer > & slices)
+{
+ typedef clitk::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
+clitk::JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
+ ImageType::ImageDimension-1>::Pointer > & slices,
+ typename ImageType::Pointer 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();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void
+clitk::PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p,
+ ImagePointer image,
+ const int slice,
+ PointType3D & p3D)
+{
+ p3D[0] = p[0];
+ p3D[1] = p[1];
+ p3D[2] = (image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
+ + image->GetOrigin()[2];
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void
+clitk::PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map,
+ ImagePointer 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
+clitk::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
+clitk::Dilate(typename ImageType::Pointer 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 clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::Dilate(typename ImageType::Pointer 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 clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::Dilate(typename ImageType::Pointer 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();
+
+ 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();
+ image = 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);
+ dilateFilter->SetInput(image);
+ dilateFilter->Update();
+ return image = dilateFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ValueType, class VectorType>
+void clitk::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.");
+}
+//--------------------------------------------------------------------
+
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff