// ------------------------------------------------------------------------
void createLabelImage(const SeriesTransform &series,
const ImageType::Pointer &reference,
const LevelSetType::Pointer &levelSet,
const std::vector<int> &roiOffset,
ImageType::Pointer &label,
unsigned int instance)
{
// initialise the label image
createOutput(series.images[instance], label);
// create the level set interpolator
typedef itk::LinearInterpolateImageFunction<LevelSetType> InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetInputImage(levelSet);
// iterate through the output
itk::ImageRegionIterator<ImageType> it(label, label->GetLargestPossibleRegion());
it.GoToBegin();
while(!it.IsAtEnd())
{
ImageType::IndexType index = it.GetIndex();
ImageType::PointType p1, p2;
// get the point in the level set space
label->TransformIndexToPhysicalPoint(index, p1);
transformPointToPatient(reference, series, roiOffset, p1, p2);
// interpolate the level set value
if(interpolator->IsInsideBuffer(p2))
{
float val = interpolator->Evaluate(p2);
if(val >= 0) it.Set(1);
}
++it;
}
}
//calculate segmentation values
bool CTImageTreeItem::internalGetSegmentationValues( SegmentationValues &values) const {
//get ITK image
ImageType::Pointer image = getITKImage();
if (image.IsNull())
return false;
//get buffered region of the image
ImageType::RegionType ctregion = image->GetBufferedRegion();
//define an iterator for the binary segment
typedef itk::ImageRegionConstIteratorWithIndex< BinaryImageType > BinaryIteratorType;
//get binary segment
BinaryImageTreeItem::ImageType::Pointer segment = values.m_segment->getITKImage();
if (segment.IsNull())
return false;
/* typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( "test.dcm" );
writer->SetInput( image );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception catched !" << std::endl;
std::cerr << excep << std::endl;
}
*/
//create a binary iterator for the segment and its buffered region
BinaryIteratorType binIter( segment, segment->GetBufferedRegion() );
ImageType::PointType point;
//The Accumulators Framework is framework for performing incremental calculations
using namespace boost::accumulators;
//http://boost-sandbox.sourceforge.net/libs/accumulators/doc/html/accumulators/user_s_guide.html#accumulators.user_s_guide.the_accumulators_framework
accumulator_set<double,features<tag::count, tag::min, tag::mean, tag::max, tag::variance> > acc;
//check selected accuracy
if (values.m_accuracy == SegmentationValues::SimpleAccuracy) {
ImageType::IndexType index;
//iterate over the pixel of the binary segment
for(binIter.GoToBegin(); !binIter.IsAtEnd(); ++binIter) {
//if actual value = 255
if (binIter.Value() == BinaryPixelOn) {
//transforms the index to a physical point in the binary segment
segment->TransformIndexToPhysicalPoint(binIter.GetIndex(),point);
//transform that point to an index of the CT image
image->TransformPhysicalPointToIndex(point, index);
//check if that index is inside the CT region
if (ctregion.IsInside(index)) {
//get the pixel value at the index
int t = image->GetPixel(index);
//check if pixel value != -2048
if (isRealHUvalue(t)) {
//accumulate pixel value
acc( t );
}
}
}
}
//check selected accuracy
} else if (values.m_accuracy == SegmentationValues::PreventDoubleSamplingAccuracy) {
ImageType::IndexType index;
//definition for a set of indices, which can be compared
typedef std::set< ImageType::IndexType, IndexCompareFunctor > IndexSetType;
IndexSetType indexSet;
//iterate over the pixel of the binary segment
for(binIter.GoToBegin(); !binIter.IsAtEnd(); ++binIter) {
//if actual value = 255
if (binIter.Value() == BinaryPixelOn) {
//transforms the index to a physical point in the binary segment
segment->TransformIndexToPhysicalPoint(binIter.GetIndex(),point);
//transform that point to an index of the CT image
image->TransformPhysicalPointToIndex(point, index);
//check if that index is inside the CT region
if (ctregion.IsInside(index)) {
std::pair<IndexSetType::iterator,IndexSetType::iterator> ret;
//
ret = indexSet.equal_range(index);
//If x does not match any key in the container, the range returned has a length of zero,
//with both iterators pointing to the nearest value greater than x, if any,
//or to set::end if x is greater than all the elements in the container.
if (ret.first == ret.second) {
indexSet.insert(ret.first, index);
//get the pixel value at the index
int t = image->GetPixel(index);
//check if pixel value != -2048
if (isRealHUvalue(t)) {
//accumulate pixel value
acc( t );
}
}
}
}
}
//check selected accuracy
} else if (values.m_accuracy == SegmentationValues::InterpolatedAccuracy) {
//define an interpolate function
typedef itk::LinearInterpolateImageFunction< CTImageType > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
//set input to the interpolator
interpolator->SetInputImage( image );
InterpolatorType::ContinuousIndexType index;
//iterate over the pixel of the binary segment
for(binIter.GoToBegin(); !binIter.IsAtEnd(); ++binIter) {
//if actual value = 255
if (binIter.Value() == BinaryPixelOn) {
//transforms the index to a physical point in the binary segment
segment->TransformIndexToPhysicalPoint(binIter.GetIndex(),point);
//transform that point to an index of the CT image
image->TransformPhysicalPointToContinuousIndex(point, index);
//check if the index is inside the buffer of the interpolator
if (interpolator->IsInsideBuffer(index)) {
//Returns the linearly interpolated image intensity
int t = interpolator->EvaluateAtContinuousIndex(index);
//check if pixel value != -2048
if (isRealHUvalue(t)) {
//accumulate pixel value
acc( t );
}
}
}
}
}
//set sample count, min, mean, max and standard deviation
//from the accumulated intensities
values.m_sampleCount = count( acc );
values.m_min = min( acc );
values.m_mean = mean( acc );
values.m_max = max( acc );
values.m_stddev = std::sqrt( variance( acc ) );
//set the image modification time
values.m_mtime = segment->GetMTime();
const_cast<CTImageTreeItem*>(this)->m_segmentationValueCache[ values.m_segment ] = values;
return values.m_sampleCount > 0;
}