#include "itkOrientImageFilter.h"
#include "itkSpatialOrientationAdapter.h"
#include "itkImageDuplicator.h"
+#include "itkRelabelComponentImageFilter.h"
+
#include <fcntl.h>
//--------------------------------------------------------------------
SetForegroundValue(1);
SetMinimalComponentSize(100);
VerboseRegionGrowingFlagOff();
+ RemoveSmallLabelBeforeSeparationFlagOn();
// Step 1 default values
SetUpperThreshold(-300);
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);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Separate Left/Right lungs");
- PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
+ PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
// Initial label
working_mask = Labelize<MaskImageType>(working_mask,
GetBackgroundValue(),
statisticsImageFilter->SetInput(working_mask);
statisticsImageFilter->Update();
unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum();
- working_mask = statisticsImageFilter->GetOutput();
-
+ working_mask = statisticsImageFilter->GetOutput();
PrintMemory(GetVerboseMemoryFlag(), "After count label");
+
+ // If already 2 labels, but a too big differences, remove the
+ // smalest one (sometimes appends with the stomach
+ if (initialNumberOfLabels >1) {
+ if (GetRemoveSmallLabelBeforeSeparationFlag()) {
+ typedef itk::RelabelComponentImageFilter<MaskImageType, MaskImageType> RelabelFilterType;
+ typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+ relabelFilter->SetInput(working_mask);
+ relabelFilter->SetMinimumObjectSize(10);
+ relabelFilter->Update();
+ const std::vector<float> & a = relabelFilter->GetSizeOfObjectsInPhysicalUnits();
+ std::vector<MaskImagePixelType> remove_label;
+ for(unsigned int i=1; i<a.size(); i++) {
+ if (a[i] < 0.5*a[0]) { // more than 0.5 difference
+ remove_label.push_back(i+1); // label zero is BG
+ }
+ }
+ working_mask =
+ clitk::RemoveLabels<MaskImageType>(working_mask, GetBackgroundValue(), remove_label);
+ statisticsImageFilter->SetInput(working_mask);
+ statisticsImageFilter->Update();
+ initialNumberOfLabels = statisticsImageFilter->GetMaximum();
+ }
+ }
// Decompose the first label
if (initialNumberOfLabels<2) {
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();
+ slicer->SetDirectionCollapseToIdentity();
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;