#include <itkRegionOfInterestImageFilter.h>
#include <itkBinaryThresholdImageFilter.h>
#include <itkImageSliceConstIteratorWithIndex.h>
+#include <itkImageSliceIteratorWithIndex.h>
#include <itkBinaryThinningImageFilter.h>
// itk ENST
clitk::ExtractLymphStationsFilter<TImageType>::
ExtractLymphStationsFilter():
clitk::FilterBase(),
- itk::ImageToImageFilter<TImageType, TImageType>()
+ clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+ itk::ImageToImageFilter<TImageType, MaskImageType>()
{
this->SetNumberOfRequiredInputs(1);
- SetBackgroundValueMediastinum(0);
- SetBackgroundValueTrachea(0);
SetBackgroundValue(0);
SetForegroundValue(1);
- SetIntermediateSpacing(6);
- SetFuzzyThreshold1(0.6);
+ // Station 8
+ SetDistanceMaxToAnteriorPartOfTheSpine(10);
+ MaskImagePointType p;
+ p[0] = 15; p[1] = 2; p[2] = 1;
+ SetEsophagusDiltationForAnt(p);
+ p[0] = 5; p[1] = 10; p[2] = 1;
+ SetEsophagusDiltationForRight(p);
+ SetFuzzyThresholdForS8(0.5);
+
+ // Station 7
+ SetFuzzyThreshold(0.5);
+ SetStation7Filename("station7.mhd");
}
//--------------------------------------------------------------------
template <class TImageType>
void
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);
+GenerateOutputInformation() {
+ // Get inputs
+ LoadAFDB();
+ m_Input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
+ m_Mediastinum = GetAFDB()->template GetImage <MaskImageType>("Mediastinum");
+
+ // Extract Station8
+ StartNewStep("Station 8");
+ StartSubStep();
+ ExtractStation_8();
+ StopSubStep();
+
+ // Compute some interesting points in trachea
+ // ( ALTERNATIVE -> SKELETON ANALYSIS ?
+ // Pb : not sufficient for mostXX points ... )
+
+ /* ==> todo (but why ???)
+ ComputeTracheaCentroidsAboveCarina();
+ ComputeBronchusExtremaPointsBelowCarina();
+ */
+
+ if (0) { // temporary suppress
+ // Extract Station7
+ StartNewStep("Station 7");
+ StartSubStep();
+ ExtractStation_7();
+ StopSubStep();
+
+ // Extract Station4RL
+ StartNewStep("Station 4RL");
+ StartSubStep();
+ //ExtractStation_4RL();
+ StopSubStep();
+ }
+
+
+ //
+ // typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BFilter;
+ //BFilter::Pointer merge = BFilter::New();
+ // writeImage<MaskImageType>(m_Output, "ouput.mhd");
+ //writeImage<MaskImageType>(m_Working_Support, "ws.mhd");
+ /*merge->SetInput1(m_Station7);
+ merge->SetInput2(m_Station4RL); // support
+ merge->SetOperationType(BFilter::AndNot); CHANGE OPERATOR
+ merge->SetForegroundValue(4);
+ merge->Update();
+ m_Output = merge->GetOutput();
+ */
}
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-SetInputTracheaLabelImage(const TImageType * image, ImagePixelType bg) {
- this->SetNthInput(1, const_cast<TImageType *>(image));
- m_BackgroundValueTrachea = bg;
+GenerateInputRequestedRegion() {
+ DD("GenerateInputRequestedRegion (nothing?)");
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template <class TImageType>
-template<class ArgsInfoType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-SetArgsInfo(ArgsInfoType mArgsInfo)
-{
- SetVerboseOption_GGO(mArgsInfo);
- SetVerboseStep_GGO(mArgsInfo);
- SetWriteStep_GGO(mArgsInfo);
- SetVerboseWarningOff_GGO(mArgsInfo);
- SetCarenaZPositionInMM_GGO(mArgsInfo);
- SetMiddleLobeBronchusZPositionInMM_GGO(mArgsInfo);
- SetIntermediateSpacing_GGO(mArgsInfo);
- SetFuzzyThreshold1_GGO(mArgsInfo);
- //SetBackgroundValueMediastinum_GGO(mArgsInfo);
+GenerateData() {
+ DD("GenerateData, graft output");
+
+ // Final Step -> graft output (if SetNthOutput => redo)
+ this->GraftOutput(m_ListOfStations["8"]);
}
//--------------------------------------------------------------------
-
+
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateOutputInformation() {
- // Superclass::GenerateOutputInformation();
-
- // Get input
- m_mediastinum = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(0));
- m_trachea = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(1));
-
- // ----------------------------------------------------------------
- // ----------------------------------------------------------------
- // Superior limit = carena
- // Inferior limit = origine middle lobe 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_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]);
- region.SetSize(size);
- region.SetIndex(index);
- DD(region);
- typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
- typename CropFilterType::Pointer cropFilter = CropFilterType::New();
- cropFilter->SetInput(m_mediastinum);
- cropFilter->SetRegionOfInterest(region);
- cropFilter->Update();
- m_working_image = cropFilter->GetOutput();
- // Auto Crop (because following rel pos is faster)
- m_working_image = clitk::AutoCrop<ImageType>(m_working_image, 0);
- StopCurrentStep<ImageType>(m_working_image);
- m_output = m_working_image;
-
- // ----------------------------------------------------------------
- // ----------------------------------------------------------------
- // Separate trachea in two CCL
- StartNewStep("Separate trachea under carena");
- // DD(region);
- ImageRegionType trachea_region = m_trachea->GetLargestPossibleRegion();
- for(int i=0; i<3; i++) {
- index[i] = floor(((index[i]*m_mediastinum->GetSpacing()[i])+m_mediastinum->GetOrigin()[i]
- -m_trachea->GetOrigin()[i])/m_trachea->GetSpacing()[i]);
- // DD(index[i]);
- size[i] = ceil((size[i]*m_mediastinum->GetSpacing()[i])/m_trachea->GetSpacing()[i]);
- // DD(size[i]);
- if (index[i] < 0) {
- size[i] += index[i];
- index[i] = 0;
- }
- if (size[i]+index[i] > (trachea_region.GetSize()[i] + trachea_region.GetIndex()[i])) {
- size[i] = trachea_region.GetSize()[i] + trachea_region.GetIndex()[i] - index[i];
- }
- }
- // DD(index);
- // DD(size);
- region.SetIndex(index);
- region.SetSize(size);
- // typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
- // typename CropFilterType::Pointer
- cropFilter = CropFilterType::New();
- // m_trachea.Print(std::cout);
- cropFilter->SetInput(m_trachea);
- cropFilter->SetRegionOfInterest(region);
- cropFilter->Update();
- m_working_trachea = cropFilter->GetOutput();
-
- // Labelize and consider two main labels
- m_working_trachea = Labelize<ImageType>(m_working_trachea, 0, true, 1);
-
- // Detect wich label is at Left
- typedef itk::ImageSliceConstIteratorWithIndex<ImageType> SliceIteratorType;
- SliceIteratorType iter(m_working_trachea, m_working_trachea->GetLargestPossibleRegion());
- iter.SetFirstDirection(0);
- iter.SetSecondDirection(1);
- iter.GoToBegin();
- bool stop = false;
- ImagePixelType leftLabel;
- ImagePixelType rightLabel;
- while (!stop) {
- if (iter.Get() != m_BackgroundValueTrachea) {
- // DD(iter.GetIndex());
- // DD((int)iter.Get());
- leftLabel = iter.Get();
- stop = true;
- }
- ++iter;
- }
- if (leftLabel == 1) rightLabel = 2;
- else rightLabel = 1;
- DD((int)leftLabel);
- DD((int)rightLabel);
+ExtractStation_8() {
- // 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");
- */
+ // Check if m_ListOfStations["8"] exist. If yes -> use it as initial
+ // support instead of m_Mediastinum
+ if (m_ListOfStations["8"]) {
+ DD("Station 8 support already exist -> use it");
+ m_Working_Support = m_ListOfStations["8"];
+ }
+ else m_Working_Support = m_Mediastinum;
- //-----------------------------------------------------
- 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");
-
- typedef clitk::SliceBySliceRelativePositionFilter<ImageType> SliceRelPosFilterType;
- typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
- sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- sliceRelPosFilter->VerboseStepOn();
- sliceRelPosFilter->WriteStepOn();
- sliceRelPosFilter->SetInput(m_working_image);
- sliceRelPosFilter->SetInputObject(temp);
- sliceRelPosFilter->SetDirection(2);
- sliceRelPosFilter->SetFuzzyThreshold(0.5);
- sliceRelPosFilter->SetOrientationType(SliceRelPosFilterType::RelPosFilterType::RightTo);
- sliceRelPosFilter->Update();
- m_working_image = sliceRelPosFilter->GetOutput();
- writeImage<ImageType>(m_working_image, "afterslicebyslice.mhd");
-
-
- //-----------------------------------------------------
- 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(0.5);
- 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);
-
- // Set output image information (required)
- ImagePointer outputImage = this->GetOutput(0);
- outputImage->SetRegions(m_working_image->GetLargestPossibleRegion());
- outputImage->SetOrigin(m_working_image->GetOrigin());
- outputImage->SetRequestedRegion(m_working_image->GetLargestPossibleRegion());
- DD("end2");
+ ExtractStation_8_SI_Limits();
+ ExtractStation_8_AP_Limits();
+ // ExtractStation_8_LR_Limits();
}
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateInputRequestedRegion() {
- DD("GenerateInputRequestedRegion");
- // Call default
- Superclass::GenerateInputRequestedRegion();
- // Following needed because output region can be greater than input (trachea)
- ImagePointer mediastinum = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(0));
- ImagePointer trachea = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(1));
- mediastinum->SetRequestedRegion(mediastinum->GetLargestPossibleRegion());
- trachea->SetRequestedRegion(trachea->GetLargestPossibleRegion());
+ExtractStation_7() {
+ if (m_ListOfStations["7"]) {
+ DD("Station 7 support already exist -> use it");
+ m_Working_Support = m_ListOfStations["7"];
+ }
+ else m_Working_Support = m_Mediastinum;
+ ExtractStation_7_SI_Limits();
+ ExtractStation_7_RL_Limits();
+ ExtractStation_7_Posterior_Limits();
}
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateData() {
- DD("GenerateData");
- // Final Step -> graft output (if SetNthOutput => redo)
- this->GraftOutput(m_output);
+ExtractStation_4RL() {
+ /*
+ WARNING ONLY 4R FIRST !!! (not same inf limits)
+ */
+ ExtractStation_4RL_SI_Limits();
+ ExtractStation_4RL_LR_Limits();
+ ExtractStation_4RL_AP_Limits();
}
//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+FindExtremaPointsInBronchus(MaskImagePointer input,
+ int direction,
+ double distance_max_from_center_point,
+ ListOfPointsType & LR,
+ ListOfPointsType & Ant,
+ ListOfPointsType & Post)
+{
+
+ // Other solution ==> with auto bounding box ! (but pb to prevent to
+ // be too distant from the center point
+
+ // Extract slices
+ std::vector<typename MaskSliceType::Pointer> slices;
+ clitk::ExtractSlices<MaskImageType>(input, 2, slices);
+ // Loop on slices
+ bool found;
+ for(uint i=0; i<slices.size(); i++) {
+ /*
+ // Keep main CCL
+ slices[i] = Labelize<MaskSliceType>(slices[i], 0, true, 10);
+ slices[i] = KeepLabels<MaskSliceType>(slices[i],
+ GetBackgroundValue(),
+ GetForegroundValue(), 1, 1, true);
+ */
+
+ // ------- Find rightmost or leftmost point -------
+ MaskSliceType::PointType LRMost;
+ found =
+ clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
+ GetBackgroundValue(),
+ 0, // axis XY
+ (direction==0?false:true), // right or left according to direction
+ LRMost);
+ // ------- Find postmost point -------
+ MaskSliceType::PointType postMost;
+ found =
+ clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
+ GetBackgroundValue(),
+ 1, false, LRMost,
+ distance_max_from_center_point,
+ postMost);
+ // ------- Find antmost point -------
+ MaskSliceType::PointType antMost;
+ found =
+ clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
+ GetBackgroundValue(),
+ 1, true, LRMost,
+ distance_max_from_center_point,
+ antMost);
+ // Only add point if found
+ if (found) {
+ // ------- Convert 2D to 3D points --------
+ MaskImageType::PointType p;
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(LRMost, input, i, p);
+ LR.push_back(p);
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(antMost, input, i, p);
+ Ant.push_back(p);
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(postMost, input, i, p);
+ Post.push_back(p);
+ }
+ }
+}
+//--------------------------------------------------------------------
#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff