#include "itkImageIteratorWithIndex.h"
#include "itkBinaryMorphologicalOpeningImageFilter.h"
#include "itkBinaryMorphologicalClosingImageFilter.h"
+#include "itkConstantPadImageFilter.h"
+#include <itkBinaryBallStructuringElement.h>
+#include "itkStatisticsLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkLabelImageToShapeLabelMapFilter.h"
+#include "itkLabelMapToLabelImageFilter.h"
+#include "itkExtractImageFilter.h"
+#include "itkOrientImageFilter.h"
+#include "itkSpatialOrientationAdapter.h"
+#include "itkImageDuplicator.h"
+#include "itkRelabelComponentImageFilter.h"
+
+#include <fcntl.h>
//--------------------------------------------------------------------
template <class ImageType>
SetForegroundValue(1);
SetMinimalComponentSize(100);
VerboseRegionGrowingFlagOff();
+ RemoveSmallLabelBeforeSeparationFlagOn();
// Step 1 default values
SetUpperThreshold(-300);
SetLabelizeParameters1(p1);
// Step 2 default values
- SetUpperThresholdForTrachea(-900);
+ SetTracheaSeedAlgorithm(0);
+ SetUpperThresholdForTrachea(-700);
SetMultiplierForTrachea(5);
SetThresholdStepSizeForTrachea(64);
SetNumberOfSlicesToSkipBeforeSearchingSeed(0);
TracheaVolumeMustBeCheckedFlagOn();
+ SetNumSlices(50);
+ SetMaxElongation(0.5);
+ SetSeedPreProcessingThreshold(-400);
+
// Step 3 default values
SetNumberOfHistogramBins(500);
// Step 6
FillHolesFlagOn();
+ AutoCropOn();
}
//--------------------------------------------------------------------
StartNewStep("Set background to initial image");
working_input = SetBackground<ImageType, MaskImageType>
(working_input, patient, GetPatientMaskBackgroundValue(), -1000, true);
+
+ // Pad images with air to prevent patient touching the image border
+ static const unsigned int Dim = ImageType::ImageDimension;
+ typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
+ typename PadFilterType::Pointer padFilter = PadFilterType::New();
+ padFilter->SetInput(working_input);
+ padFilter->SetConstant(-1000);
+ typename ImageType::SizeType bounds;
+ for (unsigned i = 0; i < Dim - 1; ++i)
+ bounds[i] = 1;
+ bounds[Dim - 1] = 0;
+ padFilter->SetPadLowerBound(bounds);
+ padFilter->SetPadUpperBound(bounds);
+ padFilter->Update();
+ working_input = padFilter->GetOutput();
+
StopCurrentStep<ImageType>(working_input);
PrintMemory(GetVerboseMemoryFlag(), "After set bg"); // OK, additional mem = 0
StartNewStep("Search for the trachea");
SearchForTrachea();
PrintMemory(GetVerboseMemoryFlag(), "After SearchForTrachea");
+ if (m_Seeds.empty()) {
+ clitkExceptionMacro("No seeds for trachea... Aborting.");
+ }
//--------------------------------------------------------------------
//--------------------------------------------------------------------
//--------------------------------------------------------------------
PrintMemory(GetVerboseMemoryFlag(), "before autocropfilter");
if (m_Seeds.size() != 0) { // if ==0 ->no trachea found
- trachea = clitk::AutoCrop<MaskImageType>(trachea, GetBackgroundValue());
+ if (GetAutoCrop())
+ trachea = clitk::AutoCrop<MaskImageType>(trachea, GetBackgroundValue());
+ else
+ {
+ // Remove Padding region
+ typedef itk::CropImageFilter<MaskImageType, MaskImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(trachea);
+ cropFilter->SetLowerBoundaryCropSize(bounds);
+ cropFilter->SetUpperBoundaryCropSize(bounds);
+ cropFilter->Update();
+ trachea = cropFilter->GetOutput();
+ }
StopCurrentStep<MaskImageType>(trachea);
PrintMemory(GetVerboseMemoryFlag(), "after delete trachea");
}
//--------------------------------------------------------------------
StartNewStep("Cropping lung");
PrintMemory(GetVerboseMemoryFlag(), "Before Autocropfilter");
- working_mask = clitk::AutoCrop<MaskImageType>(working_mask, GetBackgroundValue());
+ if (GetAutoCrop())
+ working_mask = clitk::AutoCrop<MaskImageType>(working_mask, GetBackgroundValue());
+ else
+ {
+ // Remove Padding region
+ typedef itk::CropImageFilter<MaskImageType, MaskImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(working_mask);
+ cropFilter->SetLowerBoundaryCropSize(bounds);
+ cropFilter->SetUpperBoundaryCropSize(bounds);
+ cropFilter->Update();
+ working_mask = cropFilter->GetOutput();
+ }
StopCurrentStep<MaskImageType>(working_mask);
//--------------------------------------------------------------------
StopCurrentStep<MaskImageType>(working_mask);
}
- //--------------------------------------------------------------------
- //--------------------------------------------------------------------
- StartNewStep("Separate Left/Right lungs");
+ if (GetSeparateLungsFlag()) {
+ //--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ StartNewStep("Separate Left/Right lungs");
PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
- // Initial label
- working_mask = Labelize<MaskImageType>(working_mask,
- GetBackgroundValue(),
- false,
- GetMinimalComponentSize());
-
- PrintMemory(GetVerboseMemoryFlag(), "After Labelize");
-
- // Count the labels
- typedef itk::StatisticsImageFilter<MaskImageType> StatisticsImageFilterType;
- typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
- statisticsImageFilter->SetInput(working_mask);
- statisticsImageFilter->Update();
- unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum();
- working_mask = statisticsImageFilter->GetOutput();
+ // Initial label
+ working_mask = Labelize<MaskImageType>(working_mask,
+ GetBackgroundValue(),
+ false,
+ GetMinimalComponentSize());
+
+ PrintMemory(GetVerboseMemoryFlag(), "After Labelize");
+
+ // Count the labels
+ typedef itk::StatisticsImageFilter<MaskImageType> StatisticsImageFilterType;
+ typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
+ statisticsImageFilter->SetInput(working_mask);
+ statisticsImageFilter->Update();
+ unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum();
+ 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()) {
+ DD(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();
+ }
+ }
- PrintMemory(GetVerboseMemoryFlag(), "After count label");
-
- // Decompose the first label
- static const unsigned int Dim = ImageType::ImageDimension;
- if (initialNumberOfLabels<2) {
- // Structuring element radius
- typename ImageType::SizeType radius;
- for (unsigned int i=0;i<Dim;i++) radius[i]=1;
- typedef clitk::DecomposeAndReconstructImageFilter<MaskImageType,MaskImageType> DecomposeAndReconstructFilterType;
- typename DecomposeAndReconstructFilterType::Pointer decomposeAndReconstructFilter=DecomposeAndReconstructFilterType::New();
- decomposeAndReconstructFilter->SetInput(working_mask);
- decomposeAndReconstructFilter->SetVerbose(false);
- decomposeAndReconstructFilter->SetRadius(radius);
- decomposeAndReconstructFilter->SetMaximumNumberOfLabels(2);
- decomposeAndReconstructFilter->SetMinimumObjectSize(this->GetMinimalComponentSize());
- decomposeAndReconstructFilter->SetMinimumNumberOfIterations(1);
- decomposeAndReconstructFilter->SetBackgroundValue(this->GetBackgroundValue());
- decomposeAndReconstructFilter->SetForegroundValue(this->GetForegroundValue());
- decomposeAndReconstructFilter->SetFullyConnected(true);
- decomposeAndReconstructFilter->SetNumberOfNewLabels(1);
- decomposeAndReconstructFilter->Update();
- working_mask = decomposeAndReconstructFilter->GetOutput();
+ // Decompose the first label
+ if (initialNumberOfLabels<2) {
+ // Structuring element radius
+ typename ImageType::SizeType radius;
+ for (unsigned int i=0;i<Dim;i++) radius[i]=1;
+ typedef clitk::DecomposeAndReconstructImageFilter<MaskImageType,MaskImageType> DecomposeAndReconstructFilterType;
+ typename DecomposeAndReconstructFilterType::Pointer decomposeAndReconstructFilter=DecomposeAndReconstructFilterType::New();
+ decomposeAndReconstructFilter->SetInput(working_mask);
+ decomposeAndReconstructFilter->SetVerbose(false);
+ decomposeAndReconstructFilter->SetRadius(radius);
+ decomposeAndReconstructFilter->SetMaximumNumberOfLabels(2);
+ decomposeAndReconstructFilter->SetMinimumObjectSize(this->GetMinimalComponentSize());
+ decomposeAndReconstructFilter->SetMinimumNumberOfIterations(1);
+ decomposeAndReconstructFilter->SetBackgroundValue(this->GetBackgroundValue());
+ decomposeAndReconstructFilter->SetForegroundValue(this->GetForegroundValue());
+ decomposeAndReconstructFilter->SetFullyConnected(true);
+ decomposeAndReconstructFilter->SetNumberOfNewLabels(1);
+ decomposeAndReconstructFilter->Update();
+ working_mask = decomposeAndReconstructFilter->GetOutput();
+ }
+ PrintMemory(GetVerboseMemoryFlag(), "After decomposeAndReconstructFilter");
}
- PrintMemory(GetVerboseMemoryFlag(), "After decomposeAndReconstructFilter");
// Retain labels ('1' is largset lung, so right. '2' is left)
typedef itk::ThresholdImageFilter<MaskImageType> ThresholdImageFilterType;
}
//--------------------------------------------------------------------
+
+bool is_orientation_superior(itk::SpatialOrientation::ValidCoordinateOrientationFlags orientation)
+{
+ itk::SpatialOrientation::CoordinateTerms sup = itk::SpatialOrientation::ITK_COORDINATE_Superior;
+ bool primary = (orientation & 0x0000ff) == sup;
+ bool secondary = ((orientation & 0x00ff00) >> 8) == sup;
+ bool tertiary = ((orientation & 0xff0000) >> 16) == sup;
+ return primary || secondary || tertiary;
+}
+
+//--------------------------------------------------------------------
+template <class ImageType>
+bool
+clitk::ExtractLungFilter<ImageType>::
+SearchForTracheaSeed2(int numberOfSlices)
+{
+ if (m_Seeds.size() == 0) { // try to find seed (if not zero, it is given by user)
+ if (GetVerboseRegionGrowingFlag())
+ std::cout << "SearchForTracheaSeed2(" << numberOfSlices << ", " << GetMaxElongation() << ")" << std::endl;
+
+ typedef unsigned char MaskPixelType;
+ typedef itk::Image<MaskPixelType, ImageType::ImageDimension> MaskImageType;
+ typedef itk::Image<typename MaskImageType::PixelType, 2> MaskImageType2D;
+ typedef itk::BinaryThresholdImageFilter<ImageType, MaskImageType> ThresholdFilterType;
+ typedef itk::BinaryBallStructuringElement<MaskPixelType, MaskImageType::ImageDimension> KernelType;
+ typedef itk::BinaryMorphologicalClosingImageFilter<MaskImageType, MaskImageType, KernelType> ClosingFilterType;
+ typedef itk::BinaryMorphologicalOpeningImageFilter<MaskImageType, MaskImageType, KernelType> OpeningFilterType;
+ typedef itk::ExtractImageFilter<MaskImageType, MaskImageType2D> SlicerFilterType;
+ typedef itk::ConnectedComponentImageFilter<MaskImageType2D, MaskImageType2D> LabelFilterType;
+ typedef itk::ShapeLabelObject<MaskPixelType, MaskImageType2D::ImageDimension> ShapeLabelType;
+ typedef itk::LabelMap<ShapeLabelType> LabelImageType;
+ typedef itk::LabelImageToShapeLabelMapFilter<MaskImageType2D, LabelImageType> ImageToLabelMapFilterType;
+ typedef itk::LabelMapToLabelImageFilter<LabelImageType, MaskImageType2D> LabelMapToImageFilterType;
+ typedef itk::ImageFileWriter<MaskImageType2D> FileWriterType;
+
+ // threshold to isolate airawys and lungs
+ typename ThresholdFilterType::Pointer threshold = ThresholdFilterType::New();
+ threshold->SetLowerThreshold(-2000);
+ threshold->SetUpperThreshold(GetSeedPreProcessingThreshold());
+ threshold->SetInput(working_input);
+ threshold->Update();
+
+ KernelType kernel_closing, kernel_opening;
+
+ // remove small noise
+ typename OpeningFilterType::Pointer opening = OpeningFilterType::New();
+ kernel_opening.SetRadius(1);
+ opening->SetKernel(kernel_opening);
+ opening->SetInput(threshold->GetOutput());
+ opening->Update();
+
+ typename SlicerFilterType::Pointer slicer = SlicerFilterType::New();
+#if ITK_VERSION_MAJOR >= 4
+ slicer->SetDirectionCollapseToIdentity();
+#endif
+ slicer->SetInput(opening->GetOutput());
+
+ // label result
+ typename LabelFilterType::Pointer label_filter = LabelFilterType::New();
+ label_filter->SetInput(slicer->GetOutput());
+
+ // extract shape information from labels
+ typename ImageToLabelMapFilterType::Pointer label_to_map_filter = ImageToLabelMapFilterType::New();
+ label_to_map_filter->SetInput(label_filter->GetOutput());
+
+ typename LabelMapToImageFilterType::Pointer map_to_label_filter = LabelMapToImageFilterType::New();
+ typename FileWriterType::Pointer writer = FileWriterType::New();
+
+ typename ImageType::IndexType index;
+ typename ImageType::RegionType region = working_input->GetLargestPossibleRegion();
+ typename ImageType::SizeType size = region.GetSize();
+ typename ImageType::SpacingType spacing = working_input->GetSpacing();
+ typename ImageType::PointType origin = working_input->GetOrigin();
+
+ int nslices = min(numberOfSlices, size[2]);
+ int start = 0, increment = 1;
+ itk::SpatialOrientationAdapter orientation;
+ typename ImageType::DirectionType dir = working_input->GetDirection();
+ if (!is_orientation_superior(orientation.FromDirectionCosines(dir))) {
+ start = size[2]-1;
+ increment = -1;
+ }
+
+ typename MaskImageType::PointType image_centre;
+ image_centre[0] = size[0]/2;
+ image_centre[1] = size[1]/2;
+ image_centre[2] = 0;
+
+ typedef InternalIndexType SeedType;
+ SeedType trachea_centre, shape_centre, max_e_centre, prev_e_centre;
+ typedef std::list<SeedType> PointListType;
+ typedef std::list<PointListType> SequenceListType;
+ PointListType* current_sequence = NULL;
+ SequenceListType sequence_list;
+
+ prev_e_centre.Fill(0);
+ std::ostringstream file_name;
+ index[0] = index[1] = 0;
+ size[0] = size[1] = 512;
+ size[2] = 0;
+ while (nslices--) {
+ index[2] = start;
+ start += increment;
+
+ region.SetIndex(index);
+ region.SetSize(size);
+ slicer->SetExtractionRegion(region);
+ slicer->Update();
+ label_filter->SetInput(slicer->GetOutput());
+ label_filter->Update();
+
+ label_to_map_filter->SetInput(label_filter->GetOutput());
+ label_to_map_filter->Update();
+ typename LabelImageType::Pointer label_map = label_to_map_filter->GetOutput();
+
+ if (GetWriteStepFlag()) {
+ map_to_label_filter->SetInput(label_map);
+ writer->SetInput(map_to_label_filter->GetOutput());
+ file_name.str("");
+ file_name << "labels_";
+ file_name.width(3);
+ file_name.fill('0');
+ file_name << index[2] << ".mhd";
+ writer->SetFileName(file_name.str().c_str());
+ writer->Update();
+ }
+
+ typename ShapeLabelType::Pointer shape, max_e_shape;
+ double max_elongation = GetMaxElongation();
+ double max_size = size[0]*size[1]/128;
+ double max_e = 0;
+ int nshapes = 0;
+ unsigned int nlables = label_map->GetNumberOfLabelObjects();
+ 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++;
+ shape_centre[0] = (shape->GetCentroid()[0] - origin[0])/spacing[0];
+ shape_centre[1] = (shape->GetCentroid()[1] - origin[1])/spacing[1];
+ shape_centre[2] = index[2];
+ //double d = 1 - (shape_centre - image_centre).Magnitude()/max_dist;
+ double dx = shape_centre[0] - image_centre[0];
+ double d = 1 - dx*2/size[0];
+ e = e + d;
+ if (e > max_e)
+ {
+ max_e = e;
+ max_e_shape = shape;
+ max_e_centre = shape_centre;
+ }
+ }
+ }
+ }
+
+ if (nshapes > 0)
+ {
+ itk::Point<typename SeedType::IndexValueType, ImageType::ImageDimension> p1, p2;
+ p1[0] = max_e_centre[0];
+ p1[1] = max_e_centre[1];
+ p1[2] = max_e_centre[2];
+
+ p2[0] = prev_e_centre[0];
+ p2[1] = prev_e_centre[1];
+ p2[2] = prev_e_centre[2];
+
+ double mag = (p2 - p1).GetNorm();
+ if (GetVerboseRegionGrowingFlag()) {
+ cout.precision(3);
+ cout << index[2] << ": ";
+ cout << "region(" << max_e_centre[0] << ", " << max_e_centre[1] << ", " << max_e_centre[2] << "); ";
+ cout << "prev_region(" << prev_e_centre[0] << ", " << prev_e_centre[1] << ", " << prev_e_centre[2] << "); ";
+ cout << "mag(" << mag << "); " << endl;
+ }
+
+ if (mag > 5)
+ {
+ PointListType point_list;
+ point_list.push_back(max_e_centre);
+ sequence_list.push_back(point_list);
+ current_sequence = &sequence_list.back();
+ }
+ else if (current_sequence)
+ current_sequence->push_back(max_e_centre);
+
+ prev_e_centre= max_e_centre;
+ }
+ else {
+ if (GetVerboseRegionGrowingFlag()) {
+ cout << "No shapes found at slice " << index[2] << std::endl;
+ }
+ }
+ }
+
+ size_t longest = 0;
+ for (typename SequenceListType::iterator s = sequence_list.begin(); s != sequence_list.end(); s++)
+ {
+ if (s->size() > longest)
+ {
+ longest = s->size();
+ trachea_centre = s->front();
+ }
+ }
+
+ if (longest > 0) {
+ if (GetVerboseRegionGrowingFlag())
+ std::cout << "seed at: " << trachea_centre << std::endl;
+ m_Seeds.push_back(trachea_centre);
+ }
+ }
+ return (m_Seeds.size() != 0);
+}
+//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
template <class ImageType>
void
f->SetUpper(GetUpperThresholdForTrachea());
f->SetMinimumLowerThreshold(-2000);
// f->SetMaximumUpperThreshold(0); // MAYBE TO CHANGE ???
- f->SetMaximumUpperThreshold(-800); // MAYBE TO CHANGE ???
+ f->SetMaximumUpperThreshold(-300); // MAYBE TO CHANGE ???
f->SetAdaptLowerBorder(false);
f->SetAdaptUpperBorder(true);
f->SetMinimumSize(5000);
//--------------------------------------------------------------------
template <class ImageType>
-void
+void
clitk::ExtractLungFilter<ImageType>::
SearchForTrachea()
{
// compute trachea volume
// if volume not plausible -> skip more slices and restart
+ bool has_seed;
bool stop = false;
double volume = 0.0;
int skip = GetNumberOfSlicesToSkipBeforeSearchingSeed();
while (!stop) {
- stop = SearchForTracheaSeed(skip);
- if (stop) {
+ stop = true;
+ if (GetTracheaSeedAlgorithm() == 0)
+ has_seed = SearchForTracheaSeed(skip);
+ else
+ has_seed = SearchForTracheaSeed2(GetNumSlices());
+
+ if (has_seed) {
TracheaRegionGrowing();
volume = ComputeTracheaVolume()/1000; // assume mm3, so divide by 1000 to get cc
if (GetWriteStepFlag()) {
if (GetTracheaVolumeMustBeCheckedFlag()) {
if ((volume > 10) && (volume < 65 )) { // depend on image size ...
// Typical volume 22.59 cm 3 (± 7.69 cm 3 ) [ Leader 2004 ]
- if (GetVerboseStepFlag()) {
+ if (GetVerboseStepFlag())
+ {
std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl;
}
- stop = true;
}
- else {
- if (GetVerboseStepFlag()) {
- std::cout << "\t The volume of the trachea (" << volume
- << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds."
- << std::endl;
- }
- skip += 5;
- stop = false;
- // empty the list of seed
- m_Seeds.clear();
+ else
+ if (GetTracheaSeedAlgorithm() == 0) {
+ if (GetVerboseStepFlag()) {
+ std::cout << "\t The volume of the trachea (" << volume
+ << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds."
+ << std::endl;
+ }
+ skip += 5;
+ stop = false;
+ // empty the list of seed
+ m_Seeds.clear();
+ }
+ if (skip > 0.5 * working_input->GetLargestPossibleRegion().GetSize()[2]) {
+ // we want to skip more than a half of the image, it is probably a bug
+ std::cerr << "2 : Number of slices to skip to find trachea too high = " << skip << std::endl;
+ stop = true;
}
}
else {
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff