SetBackgroundValue(0);
SetForegroundValue(1);
- // 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");
+ // Default values
+ ExtractStation_8_SetDefaultValues();
+ ExtractStation_3P_SetDefaultValues();
+ ExtractStation_2RL_SetDefaultValues();
+ ExtractStation_3A_SetDefaultValues();
+ ExtractStation_7_SetDefaultValues();
}
//--------------------------------------------------------------------
m_Input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
m_Mediastinum = GetAFDB()->template GetImage <MaskImageType>("Mediastinum");
+ // Global supports for stations
+ StartNewStep("Supports for stations");
+ StartSubStep();
+ ExtractStationSupports();
+ StopSubStep();
+
// Extract Station8
StartNewStep("Station 8");
StartSubStep();
ExtractStation_8();
StopSubStep();
- // Compute some interesting points in trachea
- // ( ALTERNATIVE -> SKELETON ANALYSIS ?
- // Pb : not sufficient for mostXX points ... )
+ // Extract Station3P
+ StartNewStep("Station 3P");
+ StartSubStep();
+ ExtractStation_3P();
+ StopSubStep();
- /* ==> todo (but why ???)
- ComputeTracheaCentroidsAboveCarina();
- ComputeBronchusExtremaPointsBelowCarina();
+ // Extract Station2RL
+ /*
+ StartNewStep("Station 2RL");
+ StartSubStep();
+ ExtractStation_2RL();
+ StopSubStep();
*/
- if (0) { // temporary suppress
- // Extract Station7
- StartNewStep("Station 7");
- StartSubStep();
- ExtractStation_7();
- StopSubStep();
+ // Extract Station3A
+ StartNewStep("Station 3A");
+ StartSubStep();
+ ExtractStation_3A();
+ StopSubStep();
+
+ // Extract Station7
+ StartNewStep("Station 7");
+ StartSubStep();
+ ExtractStation_7();
+ StopSubStep();
+ if (0) { // temporary suppress
// 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();
- */
}
//--------------------------------------------------------------------
void
clitk::ExtractLymphStationsFilter<TImageType>::
GenerateInputRequestedRegion() {
- DD("GenerateInputRequestedRegion (nothing?)");
+ //DD("GenerateInputRequestedRegion (nothing?)");
}
//--------------------------------------------------------------------
void
clitk::ExtractLymphStationsFilter<TImageType>::
GenerateData() {
- DD("GenerateData, graft output");
-
// Final Step -> graft output (if SetNthOutput => redo)
this->GraftOutput(m_ListOfStations["8"]);
}
//--------------------------------------------------------------------
template <class TImageType>
-void
+bool
+clitk::ExtractLymphStationsFilter<TImageType>::
+CheckForStation(std::string station)
+{
+ // Compute Station name
+ std::string s = "Station"+station;
+
+
+ // Check if station already exist in DB
+ bool found = false;
+ if (GetAFDB()->TagExist(s)) {
+ m_ListOfStations[station] = GetAFDB()->template GetImage<MaskImageType>(s);
+ found = true;
+ }
+
+ // Define the starting support
+ if (found && GetComputeStation(station)) {
+ std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
+ }
+ if (!found || GetComputeStation(station)) {
+ m_Working_Support = m_Mediastinum = GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
+ return true;
+ }
+ else {
+ std::cout << "Station " << station << " found. I used it" << std::endl;
+ return false;
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+bool
+clitk::ExtractLymphStationsFilter<TImageType>::
+GetComputeStation(std::string station)
+{
+ return (m_ComputeStationMap.find(station) != m_ComputeStationMap.end());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_8() {
+AddComputeStation(std::string station)
+{
+ m_ComputeStationMap[station] = true;
+}
+//--------------------------------------------------------------------
- // 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"];
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_3P()
+{
+ if (CheckForStation("3P")) {
+ ExtractStation_3P_SI_Limits();
+ ExtractStation_3P_Ant_Limits();
+ ExtractStation_3P_Post_Limits();
+ ExtractStation_3P_LR_sup_Limits();
+ // ExtractStation_3P_LR_sup_Limits_2();
+ ExtractStation_3P_LR_inf_Limits();
+ ExtractStation_8_Single_CCL_Limits(); // YES 8 !
+ ExtractStation_3P_Remove_Structures(); // after CCL
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["3P"], "seg/Station3P.mhd");
+ GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd");
+ WriteAFDB();
}
- else m_Working_Support = m_Mediastinum;
+}
+//--------------------------------------------------------------------
- ExtractStation_8_SI_Limits();
- ExtractStation_8_Post_Limits();
- ExtractStation_8_Ant_Limits();
- ExtractStation_8_LR_Limits();
- // ExtractStation_8_LR_Limits();
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_3A()
+{
+ if (CheckForStation("3A")) {
+ ExtractStation_3A_SI_Limits();
+ ExtractStation_3A_Ant_Limits();
+ ExtractStation_3A_Post_Limits();
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["3A"], "seg/Station3A.mhd");
+ GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd");
+ WriteAFDB();
+ }
}
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_7() {
- if (m_ListOfStations["7"]) {
- DD("Station 7 support already exist -> use it");
- m_Working_Support = m_ListOfStations["7"];
+ExtractStation_2RL()
+{
+ if (CheckForStation("2RL")) {
+ ExtractStation_2RL_SI_Limits();
+ ExtractStation_2RL_Post_Limits();
+ ExtractStation_2RL_Ant_Limits2();
+ ExtractStation_2RL_Ant_Limits();
+ ExtractStation_2RL_LR_Limits();
+ ExtractStation_2RL_Remove_Structures();
+ ExtractStation_2RL_SeparateRL();
+
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["2R"], "seg/Station2R.mhd");
+ writeImage<MaskImageType>(m_ListOfStations["2L"], "seg/Station2L.mhd");
+ GetAFDB()->SetImageFilename("Station2R", "seg/Station2R.mhd");
+ GetAFDB()->SetImageFilename("Station2L", "seg/Station2L.mhd");
+ WriteAFDB();
}
- else m_Working_Support = m_Mediastinum;
- ExtractStation_7_SI_Limits();
- ExtractStation_7_RL_Limits();
- ExtractStation_7_Posterior_Limits();
}
//--------------------------------------------------------------------
void
clitk::ExtractLymphStationsFilter<TImageType>::
ExtractStation_4RL() {
+ DD("TODO");
+ exit(0);
/*
WARNING ONLY 4R FIRST !!! (not same inf limits)
*/
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Remove_Structures(std::string station, std::string s)
+{
+ try {
+ StartNewStep("[Station"+station+"] Remove "+s);
+ MaskImagePointer Structure = GetAFDB()->template GetImage<MaskImageType>(s);
+ clitk::AndNot<MaskImageType>(m_Working_Support, Structure, GetBackgroundValue());
+ }
+ catch(clitk::ExceptionObject e) {
+ std::cout << s << " not found, skip." << std::endl;
+ }
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-FindExtremaPointsInBronchus(MaskImagePointer input,
- int direction,
- double distance_max_from_center_point,
- ListOfPointsType & LR,
- ListOfPointsType & Ant,
- ListOfPointsType & Post)
+SetFuzzyThreshold(std::string station, std::string tag, double value)
{
+ m_FuzzyThreshold[station][tag] = value;
+}
+//--------------------------------------------------------------------
- // 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);
+//--------------------------------------------------------------------
+template <class TImageType>
+double
+clitk::ExtractLymphStationsFilter<TImageType>::
+GetFuzzyThreshold(std::string station, std::string tag)
+{
+ if (m_FuzzyThreshold.find(station) == m_FuzzyThreshold.end()) {
+ clitkExceptionMacro("Could not find options for station "+station+" in the list (while searching for tag "+tag+").");
+ return 0.0;
+ }
+
+ if (m_FuzzyThreshold[station].find(tag) == m_FuzzyThreshold[station].end()) {
+ clitkExceptionMacro("Could not find options "+tag+" in the list of FuzzyThreshold for station "+station+".");
+ return 0.0;
+ }
- // 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);
- */
+ return m_FuzzyThreshold[station][tag];
+}
+//--------------------------------------------------------------------
- // ------- 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],
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B)
+{
+ // Create line from A to B with
+ // A = upper border of LLL at left
+ // B = lower border of bronchus intermedius (BI) or RightMiddleLobeBronchus
+
+ try {
+ GetAFDB()->GetPoint3D("LineForS7S8Separation_Begin", A);
+ GetAFDB()->GetPoint3D("LineForS7S8Separation_End", B);
+ }
+ catch(clitk::ExceptionObject & o) {
+
+ DD("FindLineForS7S8Separation");
+ // Load LeftLowerLobeBronchus and get centroid point
+ MaskImagePointer LeftLowerLobeBronchus =
+ GetAFDB()->template GetImage <MaskImageType>("LeftLowerLobeBronchus");
+ std::vector<MaskImagePointType> c;
+ clitk::ComputeCentroids<MaskImageType>(LeftLowerLobeBronchus, GetBackgroundValue(), c);
+ A = c[1];
+
+ // Load RightMiddleLobeBronchus and get superior point (not centroid here)
+ MaskImagePointer RightMiddleLobeBronchus =
+ GetAFDB()->template GetImage <MaskImageType>("RightMiddleLobeBronchus");
+ bool b = FindExtremaPointInAGivenDirection<MaskImageType>(RightMiddleLobeBronchus,
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);
+ 2, false, B);
+ if (!b) {
+ clitkExceptionMacro("Error while searching most superior point in RightMiddleLobeBronchus. Abort");
+ }
+
+ // Insert into the DB
+ GetAFDB()->SetPoint3D("LineForS7S8Separation_Begin", A);
+ GetAFDB()->SetPoint3D("LineForS7S8Separation_End", B);
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+double
+clitk::ExtractLymphStationsFilter<TImageType>::
+FindCarinaSlicePosition()
+{
+ double z;
+ try {
+ z = GetAFDB()->GetDouble("CarinaZ");
+ }
+ catch(clitk::ExceptionObject e) {
+ DD("FindCarinaSlicePosition");
+ // Get Carina
+ MaskImagePointer Carina = GetAFDB()->template GetImage<MaskImageType>("Carina");
+
+ // Get Centroid and Z value
+ std::vector<MaskImagePointType> centroids;
+ clitk::ComputeCentroids<MaskImageType>(Carina, GetBackgroundValue(), centroids);
+
+ // We dont need Carina structure from now
+ Carina->Delete();
+
+ // Put inside the AFDB
+ GetAFDB()->SetPoint3D("CarinaPoint", centroids[1]);
+ GetAFDB()->SetDouble("CarinaZ", centroids[1][2]);
+ WriteAFDB();
+ z = centroids[1][2];
+ }
+ return z;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+FindLeftAndRightBronchi()
+{
+ try {
+ m_RightBronchus = GetAFDB()->template GetImage <MaskImageType>("RightBronchus");
+ m_LeftBronchus = GetAFDB()->template GetImage <MaskImageType>("LeftBronchus");
+ }
+ catch(clitk::ExceptionObject & o) {
+
+ DD("FindLeftAndRightBronchi");
+ // The goal is to separate the trachea inferiorly to the carina into
+ // a Left and Right bronchus.
+
+ // Get the trachea
+ MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+
+ // Get the Carina position
+ m_CarinaZ = FindCarinaSlicePosition();
+
+ // Consider only inferiorly to the Carina
+ MaskImagePointer m_Working_Trachea =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(Trachea, 2, m_CarinaZ, true, // AutoCrop
+ GetBackgroundValue());
+
+ // Labelize the trachea
+ m_Working_Trachea = Labelize<MaskImageType>(m_Working_Trachea, 0, true, 1);
+
+ // Carina position must at the first slice that separate the two
+ // main bronchus (not superiorly). We thus first check that the
+ // upper slice is composed of at least two labels
+ MaskImagePointer RightBronchus;
+ MaskImagePointer LeftBronchus;
+ typedef itk::ImageSliceIteratorWithIndex<MaskImageType> SliceIteratorType;
+ SliceIteratorType iter(m_Working_Trachea, m_Working_Trachea->GetLargestPossibleRegion());
+ iter.SetFirstDirection(0);
+ iter.SetSecondDirection(1);
+ iter.GoToReverseBegin(); // Start from the end (because image is IS not SI)
+ int maxLabel=0;
+ while (!iter.IsAtReverseEndOfSlice()) {
+ while (!iter.IsAtReverseEndOfLine()) {
+ if (iter.Get() > maxLabel) maxLabel = iter.Get();
+ --iter;
+ }
+ iter.PreviousLine();
}
+ if (maxLabel < 2) {
+ clitkExceptionMacro("First slice from Carina does not seems to seperate the two main bronchus. Abort");
+ }
+
+ // Compute 3D centroids of both parts to identify the left from the
+ // right bronchus
+ std::vector<ImagePointType> c;
+ clitk::ComputeCentroids<MaskImageType>(m_Working_Trachea, GetBackgroundValue(), c);
+ ImagePointType C1 = c[1];
+ ImagePointType C2 = c[2];
+
+ ImagePixelType rightLabel;
+ ImagePixelType leftLabel;
+ if (C1[0] < C2[0]) { rightLabel = 1; leftLabel = 2; }
+ else { rightLabel = 2; leftLabel = 1; }
+
+ // Select LeftLabel (set one label to Backgroundvalue)
+ RightBronchus =
+ clitk::Binarize<MaskImageType>(m_Working_Trachea, rightLabel, rightLabel,
+ GetBackgroundValue(), GetForegroundValue());
+ /*
+ SetBackground<MaskImageType, MaskImageType>(m_Working_Trachea, m_Working_Trachea,
+ leftLabel, GetBackgroundValue(), false);
+ */
+ LeftBronchus = clitk::Binarize<MaskImageType>(m_Working_Trachea, leftLabel, leftLabel,
+ GetBackgroundValue(), GetForegroundValue());
+ /*
+ SetBackground<MaskImageType, MaskImageType>(m_Working_Trachea, m_Working_Trachea,
+ rightLabel, GetBackgroundValue(), false);
+ */
+
+ // Crop images
+ RightBronchus = clitk::AutoCrop<MaskImageType>(RightBronchus, GetBackgroundValue());
+ LeftBronchus = clitk::AutoCrop<MaskImageType>(LeftBronchus, GetBackgroundValue());
+
+ // Insert int AFDB if need after
+ GetAFDB()->template SetImage <MaskImageType>("RightBronchus", "seg/rightBronchus.mhd",
+ RightBronchus, true);
+ GetAFDB()->template SetImage <MaskImageType>("LeftBronchus", "seg/leftBronchus.mhd",
+ LeftBronchus, true);
}
-}
+}
//--------------------------------------------------------------------
#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff