TracheaVolumeMustBeCheckedFlagOn();
SetNumSlices(50);
SetMaxElongation(0.5);
- SetSeedPreProcessingThreshold(-400);
-
+ SetSeedPreProcessingThreshold(-400);
// Step 3 default values
SetNumberOfHistogramBins(500);
template <class ImageType>
void
clitk::ExtractLungFilter<ImageType>::
-AddSeed(InternalIndexType s)
+//AddSeed(InternalIndexType s)
+AddSeed(InputImagePointType s)
+{
+ m_SeedsInMM.push_back(s);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLungFilter<ImageType>::
+AddSeedInPixels(InternalIndexType s)
{
m_Seeds.push_back(s);
}
// smalest one (sometimes appends with the stomach
if (initialNumberOfLabels >1) {
if (GetRemoveSmallLabelBeforeSeparationFlag()) {
- DD(GetRemoveSmallLabelBeforeSeparationFlag());
typedef itk::RelabelComponentImageFilter<MaskImageType, MaskImageType> RelabelFilterType;
typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
relabelFilter->SetInput(working_mask);
it.GoToBegin();
while (!it.IsAtEnd()) {
if(it.Get() < GetUpperThresholdForTrachea() ) {
- AddSeed(it.GetIndex());
+ AddSeedInPixels(it.GetIndex());
// DD(it.GetIndex());
}
++it;
opening->Update();
typename SlicerFilterType::Pointer slicer = SlicerFilterType::New();
-#if ITK_VERSION_MAJOR >= 4
slicer->SetDirectionCollapseToIdentity();
-#endif
slicer->SetInput(opening->GetOutput());
// label result
for (unsigned int j = 0; j < nlables; j++) {
shape = label_map->GetNthLabelObject(j);
if (shape->Size() > 150 && shape->Size() <= max_size) {
-#if ITK_VERSION_MAJOR < 4
- double e = 1 - 1/shape->GetBinaryElongation();
-#else
double e = 1 - 1/shape->GetElongation();
-#endif
//double area = 1 - r->Area() ;
if (e < max_elongation) {
nshapes++;
f->SetVerbose(GetVerboseRegionGrowingFlag());
for(unsigned int i=0; i<m_Seeds.size();i++) {
f->AddSeed(m_Seeds[i]);
- // DD(m_Seeds[i]);
+ //DD(m_Seeds[i]);
}
f->Update();
PrintMemory(GetVerboseMemoryFlag(), "After RG update");
// compute trachea volume
// if volume not plausible -> skip more slices and restart
+ // If initial seed, convert from mm to pixels
+ if (m_SeedsInMM.size() > 0) {
+ for(unsigned int i=0; i<m_SeedsInMM.size(); i++) {
+ InputImageIndexType index;
+ working_input->TransformPhysicalPointToIndex(m_SeedsInMM[i], index);
+ m_Seeds.push_back(index);
+ }
+ }
+
bool has_seed;
bool stop = false;
double volume = 0.0;