void SampleGradHistogram(double *pt, double radius, typename TImage::Pointer image, arma::ivec& samples)
{
typedef TImage ImageType;
int radius_pix[3]; //radius in voxels, to be calculated
radius_pix[0] = std::ceil(radius / image->GetSpacing()[0]);
radius_pix[1] = std::ceil(radius / image->GetSpacing()[1]);
radius_pix[2] = std::ceil(radius / image->GetSpacing()[2]);
#ifdef DEBUG_MESSAGES_HOG
std::cout << "Requested point: " << pt[0] << ", " << pt[1] << ", " << pt[2] << std::endl;
std::cout << "Neighborhood size in mm: " << radius << std::endl;
std::cout << "Neighborhood size in pix: " << radius_pix[0] << ", " << radius_pix[1] << ", " << radius_pix[2] << std::endl;
#endif
if (radius_pix[0] == 0 || radius_pix[1] == 0 || radius_pix[2] == 0) {
std::cout << "One of the neighborhood dimensions is zero. Please correct the radius. Aborting." << std::endl;
return;
}
//transform the point from physical s1pace
typename ImageType::PointType point;
point[0] = pt[0];
point[1] = pt[1];
point[2] = pt[2];
typename ImageType::IndexType pt_pix;
image->TransformPhysicalPointToIndex(point, pt_pix);
//define the region around the point of interest
typename ImageType::IndexType rgn_idx = {
{pt_pix[0] - radius_pix[0], pt_pix[1] - radius_pix[1], pt_pix[2] - radius_pix[2]}};
typename ImageType::SizeType rgn_size = {
{2 * radius_pix[0] + 1, 2 * radius_pix[1] + 1, 2 * radius_pix[2] + 1}};
//crop the region so that it is inside
rgn_idx[0] = std::max(rgn_idx[0], image->GetLargestPossibleRegion().GetIndex(0));
rgn_idx[1] = std::max(rgn_idx[1], image->GetLargestPossibleRegion().GetIndex(1));
rgn_idx[2] = std::max(rgn_idx[2], image->GetLargestPossibleRegion().GetIndex(2));
//set it first as a corner for comparison and then undo that operation
rgn_size[0] = std::min(rgn_size[0]+rgn_idx[0], image->GetLargestPossibleRegion().GetSize(0))-rgn_idx[0];
rgn_size[1] = std::min(rgn_size[1]+rgn_idx[1], image->GetLargestPossibleRegion().GetSize(1))-rgn_idx[1];
rgn_size[2] = std::min(rgn_size[2]+rgn_idx[2], image->GetLargestPossibleRegion().GetSize(2))-rgn_idx[2];
typename ImageType::RegionType window(rgn_idx, rgn_size);
#ifdef DEBUG_MESSAGES_HOG
std::cout << "Region: " << window << std::endl;
#endif
samples.set_size(rgn_size[0]*rgn_size[1]*rgn_size[2]);
samples.zeros();
// itk::ImageRegionConstIterator<typename GradientFilterType::OutputImageType> imageIterator(gradient_filter->GetOutput(), window);
itk::ImageRegionConstIterator<ImageType> imageIterator(image, window);
imageIterator.GoToBegin();
int i=0;
while (!imageIterator.IsAtEnd()) {
// Get the value of the current pixel
typename ImageType::PixelType val = imageIterator.Get();
//std::cout << val << std::endl;
samples[i++] = val;
++imageIterator;
}
}
void SampleStatistics(double *pt, double radius, typename TImage::Pointer image, arma::vec& features)
{
features.set_size(4); //just four features for now
features.zeros();
typedef TImage ImageType;
int radius_pix[3]; //radius in voxels, to be calculated
radius_pix[0] = std::ceil(radius / image->GetSpacing()[0]);
radius_pix[1] = std::ceil(radius / image->GetSpacing()[1]);
radius_pix[2] = std::ceil(radius / image->GetSpacing()[2]);
#ifdef DEBUG_MESSAGES_HOG
std::cout << "Requested point: " << pt[0] << ", " << pt[1] << ", " << pt[2] << std::endl;
std::cout << "Neighborhood size in mm: " << radius << std::endl;
std::cout << "Neighborhood size in pix: " << radius_pix[0] << ", " << radius_pix[1] << ", " << radius_pix[2] << std::endl;
#endif
if (radius_pix[0] == 0 || radius_pix[1] == 0 || radius_pix[2] == 0) {
std::cout << "One of the neighborhood dimensions is zero. Please correct the radius. Aborting." << std::endl;
return;
}
//transform the point from physical s1pace
typename ImageType::PointType point;
point[0] = pt[0];
point[1] = pt[1];
point[2] = pt[2];
typename ImageType::IndexType pt_pix;
image->TransformPhysicalPointToIndex(point, pt_pix);
//define the region around the point of interest
typename ImageType::IndexType rgn_idx = {
{pt_pix[0] - radius_pix[0], pt_pix[1] - radius_pix[1], pt_pix[2] - radius_pix[2]}};
typename ImageType::SizeType rgn_size = {
{2 * radius_pix[0] + 1, 2 * radius_pix[1] + 1, 2 * radius_pix[2] + 1}};
//crop the region so that it is inside
rgn_idx[0] = std::max(rgn_idx[0], image->GetLargestPossibleRegion().GetIndex(0));
rgn_idx[1] = std::max(rgn_idx[1], image->GetLargestPossibleRegion().GetIndex(1));
rgn_idx[2] = std::max(rgn_idx[2], image->GetLargestPossibleRegion().GetIndex(2));
//set it first as a corner for comparison and then undo that operation
rgn_size[0] = std::min(rgn_size[0]+rgn_idx[0], image->GetLargestPossibleRegion().GetSize(0))-rgn_idx[0];
rgn_size[1] = std::min(rgn_size[1]+rgn_idx[1], image->GetLargestPossibleRegion().GetSize(1))-rgn_idx[1];
rgn_size[2] = std::min(rgn_size[2]+rgn_idx[2], image->GetLargestPossibleRegion().GetSize(2))-rgn_idx[2];
typename ImageType::RegionType window(rgn_idx, rgn_size);
#ifdef DEBUG_MESSAGES_HOG
std::cout << "Region: " << window << std::endl;
#endif
itk::ImageRegionConstIterator<ImageType> imageIterator(image, window);
imageIterator.GoToBegin();
const int nvoxels = rgn_size[0]*rgn_size[1]*rgn_size[2];
arma::vec voxels;
voxels.set_size(nvoxels);
voxels.zeros();
long int i=0;
while (!imageIterator.IsAtEnd()) {
// Get the value of the current pixel
typename ImageType::PixelType val = imageIterator.Get();
//std::cout << val << std::endl;
voxels[i++] = val;
++imageIterator;
}
//do the statistics
const double mean = arma::mean(voxels);
const double std = arma::stddev(voxels);
double E3 = 0; //Accumulate expectation of (X-u)^3
double E4 = 0; //Accumulate expectation of (X-u)^4
for(int i=0; i<voxels.size(); i++)
{
const double diff = voxels[i] - mean;
const double k = diff*diff*diff/nvoxels;
E3 += k; //cubed
E4 += diff*k; //4th power
}
features[0] = mean;
features[1] = std;
features[2] = E3/(std*std*std); //skewness
features[3] = E3/(std*std*std*std); //kurtosis
}