++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);
- // 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);
+
+ 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();
+
+ // 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);
- double m = image->GetOrigin()[dim] + size[dim]*image->GetSpacing()[dim];
+
+ // 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);
std::vector<typename ImageType::PointType> & lB,
typename ImageType::PixelType BG,
int mainDirection,
- double offsetToKeep)
+ double offsetToKeep,
+ bool keepIfEqual)
{
assert((mainDirection==0) || (mainDirection==1));
+ typename ImageType::PointType offset;
+ offset[0] = offset[1] = offset[2] = 0.0;
+ offset[mainDirection] = offsetToKeep;
+ SliceBySliceSetBackgroundFromLineSeparation_pt<ImageType>(input, lA, lB, BG, offset, keepIfEqual);
+ }
+ template<class ImageType>
+ void
+ SliceBySliceSetBackgroundFromLineSeparation_pt(ImageType * input,
+ std::vector<typename ImageType::PointType> & lA,
+ std::vector<typename ImageType::PointType> & lB,
+ typename ImageType::PixelType BG,
+ typename ImageType::PointType offsetToKeep,
+ bool keepIfEqual)
+ {
typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
SliceIteratorType siter = SliceIteratorType(input, input->GetLargestPossibleRegion());
siter.SetFirstDirection(0);
// 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
+ // FIXME : if not the same slices, should advance i or slice (not done yet)
+ // clitkExceptionMacro("Error list of point and slice do not start at the same location");
}
else {
// Define A,B,C points
bool p = (A[0] == B[0]) && (A[1] == B[1]);
if (!p) {
- C[mainDirection] += offsetToKeep; // I know I must keep this point
+ //C[mainDirection] += offsetToKeep; // I know I must keep this point
+ C[0] += offsetToKeep[0];
+ C[1] += offsetToKeep[1];
+ //C[2] += offsetToKeep[2];
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);
+ if (siter.Get() != BG) { // do only if not BG
+ // 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) {
+ if (!keepIfEqual) 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;
}
// 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);
}
- // 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");
+ // 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");
*/
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff