namespace clitk {
- //--------------------------------------------------------------------
- template<class ImageType>
- void ComputeBBFromImageRegion(const ImageType * 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] = firstIndex[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 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 ComputeRegionFromBB(const ImageType * 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] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
- }
-
- // Create region
- region.SetIndex(regionStart);
- region.SetSize(regionSize);
- }
- //--------------------------------------------------------------------
-
//--------------------------------------------------------------------
template<class ImageType, class TMaskImageType>
typename ImageType::Pointer
//--------------------------------------------------------------------
- template<class ImageType>
- typename ImageType::Pointer
- ResizeImageLike(const ImageType * input,
- const itk::ImageBase<ImageType::ImageDimension> * like,
- typename ImageType::PixelType backgroundValue)
+ 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 CropLikeImageFilter<ImageType> CropFilterType;
- typename CropFilterType::Pointer cropFilter = CropFilterType::New();
- cropFilter->SetInput(input);
- cropFilter->SetCropLikeImage(like);
- cropFilter->SetBackgroundValue(backgroundValue);
- cropFilter->Update();
- return cropFilter->GetOutput();
+ 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();
}
//--------------------------------------------------------------------
const MaskImageType * object,
int direction,
double threshold,
- std::string orientation,
+ double angle,
+ bool inverseflag,
bool uniqueConnectedComponent,
double spacing,
bool autocropFlag,
bool singleObjectCCL)
{
- typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
+ typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
sliceRelPosFilter->VerboseStepFlagOff();
sliceRelPosFilter->WriteStepFlagOff();
sliceRelPosFilter->SetInputObject(object);
sliceRelPosFilter->SetDirection(direction);
sliceRelPosFilter->SetFuzzyThreshold(threshold);
- sliceRelPosFilter->AddOrientationTypeString(orientation);
+ // 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->SetInverseOrientationFlag(inverseflag);
sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
sliceRelPosFilter->Update();
++iter;
}
if (!found) return false;
- input->TransformIndexToPhysicalPoint(max, point);
+ input->TransformIndexToPhysicalPoint(max, point); // half of the pixel
return true;
}
//--------------------------------------------------------------------
int dim, double max, bool autoCrop,
typename ImageType::PixelType BG)
{
- typename ImageType::PointType p;
+ typename ImageType::PointType p;
+
image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
image->GetLargestPossibleRegion().GetSize(), p);
+
return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
}
//--------------------------------------------------------------------
// Compute region size
typename ImageType::RegionType region;
typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
- typename ImageType::PointType p = image->GetOrigin();
- p[dim] = min;
+
+ // Starting index
+ typename ImageType::PointType p = image->GetOrigin(); // not at pixel center !
+ if (min > p[dim]) p[dim] = min; // Check if not outside the image
typename ImageType::IndexType start;
image->TransformPhysicalPointToIndex(p, start);
- p[dim] = max;
+
+ // Size of the region
+ // -1 because last point is size -1
+ double m = image->GetOrigin()[dim] + (size[dim]-1)*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]);
+ size[dim] = abs(end[dim]-start[dim])+1;// +1 because we want to include the point.
+
+ // Set region
region.SetIndex(start);
region.SetSize(size);
{
assert((mainDirection==0) || (mainDirection==1));
typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
- SliceIteratorType siter = SliceIteratorType(input,
- input->GetLargestPossibleRegion());
+ SliceIteratorType siter = SliceIteratorType(input, input->GetLargestPossibleRegion());
siter.SetFirstDirection(0);
siter.SetSecondDirection(1);
siter.GoToBegin();
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]);
// 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");
+ //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");
+ //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);
iter2.GoToBegin();
double dmin = 100000.0;
typename ImageType::IndexType indexmin;
+ indexmin.Fill(0);
while (!iter1.IsAtEnd()) {
if (iter1.Get() != BG) {
double d = iter2.Get();
//--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ RemoveNegativeIndexFromRegion(ImageType * input) {
+ typedef itk::ChangeInformationImageFilter< ImageType > InfoFilterType;
+ typename InfoFilterType::Pointer indexChangeFilter = InfoFilterType::New();
+ indexChangeFilter->ChangeRegionOn();
+ // The next line is commented because not exist in itk 3
+ // typename InfoFilterType::OutputImageOffsetValueType indexShift[3];
+ long indexShift[3];
+ typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
+ for(uint i=0;i<ImageType::ImageDimension; i++)
+ indexShift[i] = (index[i]<0 ? -index[i]:0);
+ typename ImageType::PointType origin;
+ for(uint i=0;i<ImageType::ImageDimension; i++)
+ origin[i] = input->GetOrigin()[i] - indexShift[i]*input->GetSpacing()[i];
+ indexChangeFilter->SetOutputOffset( indexShift );
+ indexChangeFilter->SetInput(input);
+ indexChangeFilter->SetOutputOrigin(origin);
+ indexChangeFilter->ChangeOriginOn();
+ indexChangeFilter->Update();
+ return indexChangeFilter->GetOutput();
+ }
+ //--------------------------------------------------------------------
} // end of namespace
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff