#include "clitkSliceBySliceRelativePositionFilter.h"
// itk
-#include <deque>
#include <itkStatisticsLabelMapFilter.h>
#include <itkLabelImageToStatisticsLabelMapFilter.h>
#include <itkRegionOfInterestImageFilter.h>
#include <itkBinaryThresholdImageFilter.h>
#include <itkImageSliceConstIteratorWithIndex.h>
+#include <itkBinaryThinningImageFilter.h>
// itk ENST
#include "RelativePositionPropImageFilter.h"
clitk::ExtractLymphStationsFilter<TImageType>::
ExtractLymphStationsFilter():
clitk::FilterBase(),
+ clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
itk::ImageToImageFilter<TImageType, TImageType>()
{
this->SetNumberOfRequiredInputs(1);
SetBackgroundValueTrachea(0);
SetBackgroundValue(0);
SetForegroundValue(1);
-
SetIntermediateSpacing(6);
- SetFuzzyThreshold1(0.6);
+ SetFuzzyThreshold1(0.6);
+ m_CarinaZPositionInMMIsSet = false;
}
//--------------------------------------------------------------------
clitk::ExtractLymphStationsFilter<TImageType>::
SetInputMediastinumLabelImage(const TImageType * image, ImagePixelType bg) {
this->SetNthInput(0, const_cast<TImageType *>(image));
- m_BackgroundValueMediastinum = bg;
- SetCarenaZPositionInMM(image->GetOrigin()[2]+image->GetLargestPossibleRegion().GetSize()[2]*image->GetSpacing()[2]);
- SetMiddleLobeBronchusZPositionInMM(image->GetOrigin()[2]);
- // DD(m_CarenaZPositionInMM);
-// DD(m_MiddleLobeBronchusZPositionInMM);
+ SetBackgroundValueMediastinum(bg);
}
//--------------------------------------------------------------------
clitk::ExtractLymphStationsFilter<TImageType>::
SetInputTracheaLabelImage(const TImageType * image, ImagePixelType bg) {
this->SetNthInput(1, const_cast<TImageType *>(image));
- m_BackgroundValueTrachea = bg;
+ SetBackgroundValueTrachea(bg);
}
//--------------------------------------------------------------------
SetVerboseStep_GGO(mArgsInfo);
SetWriteStep_GGO(mArgsInfo);
SetVerboseWarningOff_GGO(mArgsInfo);
- SetCarenaZPositionInMM_GGO(mArgsInfo);
+ SetAFDBFilename_GGO(mArgsInfo);
+ SetCarinaZPositionInMM_GGO(mArgsInfo);
+ m_CarinaZPositionInMMIsSet = false;
SetMiddleLobeBronchusZPositionInMM_GGO(mArgsInfo);
SetIntermediateSpacing_GGO(mArgsInfo);
SetFuzzyThreshold1_GGO(mArgsInfo);
- //SetBackgroundValueMediastinum_GGO(mArgsInfo);
}
//--------------------------------------------------------------------
// Get input
m_mediastinum = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(0));
m_trachea = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(1));
-
+
+ // Get landmarks information
+ if (!m_CarinaZPositionInMMIsSet) {
+ ImagePointType carina;
+ LoadAFDB();
+ GetAFDB()->GetPoint3D("Carena", carina);
+ DD(carina);
+ m_CarinaZPositionInMM = carina[2];
+ }
+ DD(m_CarinaZPositionInMM);
+
// ----------------------------------------------------------------
// ----------------------------------------------------------------
// Superior limit = carena
// Inferior limit = origine middle lobe bronchus
- StartNewStep("Inf/Sup limits with carena/bronchus");
+ StartNewStep("Inf/Sup mediastinum limits with carena/bronchus");
ImageRegionType region = m_mediastinum->GetLargestPossibleRegion(); DD(region);
ImageSizeType size = region.GetSize();
ImageIndexType index = region.GetIndex();
- DD(m_CarenaZPositionInMM);
+ DD(m_CarinaZPositionInMM);
DD(m_MiddleLobeBronchusZPositionInMM);
index[2] = floor((m_MiddleLobeBronchusZPositionInMM - m_mediastinum->GetOrigin()[2]) / m_mediastinum->GetSpacing()[2]);
- size[2] = ceil((m_CarenaZPositionInMM-m_MiddleLobeBronchusZPositionInMM) / m_mediastinum->GetSpacing()[2]);
+ size[2] = ceil((m_CarinaZPositionInMM-m_MiddleLobeBronchusZPositionInMM) / m_mediastinum->GetSpacing()[2]);
region.SetSize(size);
region.SetIndex(index);
DD(region);
// ----------------------------------------------------------------
// ----------------------------------------------------------------
// Separate trachea in two CCL
- StartNewStep("Separate trachea");
+ StartNewStep("Separate trachea under carena");
// DD(region);
ImageRegionType trachea_region = m_trachea->GetLargestPossibleRegion();
for(int i=0; i<3; i++) {
// Labelize and consider two main labels
m_working_trachea = Labelize<ImageType>(m_working_trachea, 0, true, 1);
- StopCurrentStep<ImageType>(m_working_trachea);
-
+
// Detect wich label is at Left
typedef itk::ImageSliceConstIteratorWithIndex<ImageType> SliceIteratorType;
SliceIteratorType iter(m_working_trachea, m_working_trachea->GetLargestPossibleRegion());
iter.GoToBegin();
bool stop = false;
ImagePixelType leftLabel;
+ ImagePixelType rightLabel;
while (!stop) {
if (iter.Get() != m_BackgroundValueTrachea) {
// DD(iter.GetIndex());
}
++iter;
}
+ if (leftLabel == 1) rightLabel = 2;
+ else rightLabel = 1;
DD((int)leftLabel);
-
- /*
- // Relative position
- StartNewStep("Left/Right limits with trachea");
-
- // Select LeftLabel (set label 1 to 0)
- ImagePointer temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, 1, 0);
- writeImage<ImageType>(temp, "temp1.mhd");
-
- // Left relative position
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<TImageType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInput(m_working_image);
- relPosFilter->SetInputObject(temp);
- relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
- relPosFilter->Update();
- m_working_image = relPosFilter->GetOutput();
-
- // Select RightLabel (set label 2 to 0)
- temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, 2, 0);
- writeImage<ImageType>(temp, "temp2.mhd");
+ DD((int)rightLabel);
- // Left relative position
- relPosFilter = RelPosFilterType::New();
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOn();
- relPosFilter->WriteStepOn();
- relPosFilter->SetInput(m_working_image);
- relPosFilter->SetInputObject(temp);
- relPosFilter->SetOrientationType(RelPosFilterType::LeftTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
- relPosFilter->Update();
- m_working_image = relPosFilter->GetOutput();
+ // End step
+ StopCurrentStep<ImageType>(m_working_trachea);
+
+ //-----------------------------------------------------
+ /* DD("TEST Skeleton");
+ typedef itk::BinaryThinningImageFilter<ImageType, ImageType> SkeletonFilterType;
+ typename SkeletonFilterType::Pointer skeletonFilter = SkeletonFilterType::New();
+ skeletonFilter->SetInput(m_working_trachea);
+ skeletonFilter->Update();
+ writeImage<ImageType>(skeletonFilter->GetOutput(), "skel.mhd");
+ writeImage<ImageType>(skeletonFilter->GetThinning(), "skel2.mhd");
*/
//-----------------------------------------------------
- StartNewStep("Left/Right limits with trachea (slice by slice");
-
- // Select LeftLabel (set label 1 to 0)
- ImagePointer temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, 1, 0);
+ StartNewStep("Left limits with bronchus (slice by slice)");
+ // Select LeftLabel (set right label to 0)
+ ImagePointer temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, rightLabel, 0);
writeImage<ImageType>(temp, "temp1.mhd");
- /*
- - écrire utilisation de filter SliceBySliceRelPosFilter (combine in a 3D)
- - filter SliceBySliceRelPosFilter + combine in a 3D
- - resampling, affine transfo to pair the slices
- - extract list of images (ecrire utilisation de ExtractSliceFilter)
- */
-
typedef clitk::SliceBySliceRelativePositionFilter<ImageType> SliceRelPosFilterType;
typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
sliceRelPosFilter->SetInput(m_working_image);
sliceRelPosFilter->SetInputObject(temp);
sliceRelPosFilter->SetDirection(2);
+ sliceRelPosFilter->SetFuzzyThreshold(0.6);
+ sliceRelPosFilter->SetOrientationType(SliceRelPosFilterType::RelPosFilterType::RightTo);
sliceRelPosFilter->Update();
m_working_image = sliceRelPosFilter->GetOutput();
writeImage<ImageType>(m_working_image, "afterslicebyslice.mhd");
- /*
-
- itk::ImageSliceConstIteratorWithIndex<ImageType> it(temp, temp->GetRequestedRegion());
- itk::ImageRegionIterator<SliceType> * ot;
- typename SliceType::Pointer slice;
- it.SetFirstDirection(0);
- it.SetSecondDirection(1);
- it.GoToBegin();
- typename SliceType::RegionType mSliceRegion;
- typename SliceType::IndexType mSliceIndex;
- typename SliceType::SizeType mSliceSize;
- typename SliceType::SpacingType mSliceSpacing;
- typename SliceType::PointType mSliceOrigin;
- mSliceIndex[0] = temp->GetLargestPossibleRegion().GetIndex()[0];
- mSliceIndex[1] = temp->GetLargestPossibleRegion().GetIndex()[1];
- mSliceSize[0] = temp->GetLargestPossibleRegion().GetSize()[0];
- mSliceSize[1] = temp->GetLargestPossibleRegion().GetSize()[1];
- mSliceSpacing[0] = temp->GetSpacing()[0];
- mSliceSpacing[1] = temp->GetSpacing()[1];
- mSliceOrigin[0] = temp->GetOrigin()[0];
- mSliceOrigin[1] = temp->GetOrigin()[1];
- mSliceRegion.SetIndex(mSliceIndex);
- mSliceRegion.SetSize(mSliceSize);
- int i=0;
- while( !it.IsAtEnd() ) {
- // DD(i);
- slice = SliceType::New();
- slice->SetRegions(mSliceRegion);
- slice->SetOrigin(mSliceOrigin);
- slice->SetSpacing(mSliceSpacing);
- slice->Allocate();
- ot = new itk::ImageRegionIterator<SliceType>(slice, slice->GetLargestPossibleRegion());
- ot->GoToBegin();
- // DD(it.GetIndex());
- while(!it.IsAtEndOfSlice()) {
- // DD(ot->GetIndex());
- while(!it.IsAtEndOfLine()) {
- ot->Set(it.Get());
- ++it;
- ++(*ot);
- }
- it.NextLine();
- }
- mImageSlices.push_back(slice);
- it.NextSlice();
- ++i;
- }
- writeImage<SliceType>(mImageSlices[10], "slice.mhd");
-
- // Perform RelPos by slice
- for(int i=0; i<mImageSlices.size(); i++) {
- DD(i);
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<SliceType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- // relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInput(m_working_image);
- relPosFilter->SetInputObject(temp);
- relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
- relPosFilter->Update();
- m_working_image = relPosFilter->GetOutput();
- }
+ //-----------------------------------------------------
+ StartNewStep("Right limits with bronchus (slice by slice)");
+ // Select LeftLabel (set right label to 0)
+ temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, leftLabel, 0);
+ writeImage<ImageType>(temp, "temp2.mhd");
+
+ sliceRelPosFilter = SliceRelPosFilterType::New();
+ sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ sliceRelPosFilter->VerboseStepOn();
+ sliceRelPosFilter->WriteStepOn();
+ sliceRelPosFilter->SetInput(m_working_image);
+ sliceRelPosFilter->SetInputObject(temp);
+ sliceRelPosFilter->SetDirection(2);
+ sliceRelPosFilter->SetFuzzyThreshold(0.6);
+ sliceRelPosFilter->SetOrientationType(SliceRelPosFilterType::RelPosFilterType::LeftTo);
+ sliceRelPosFilter->Update();
+ m_working_image = sliceRelPosFilter->GetOutput();
+ writeImage<ImageType>(m_working_image, "afterslicebyslice.mhd");
+
- */
-
DD("end");
m_output = m_working_image;
StopCurrentStep<ImageType>(m_output);
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff