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();
}
//--------------------------------------------------------------------
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>::
-ExtractStation_8() {
+CheckForStation(std::string station)
+{
+ // Compute Station name
+ std::string s = "Station"+station;
+
- // 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"];
+ // Check if station already exist in DB
+ bool found = false;
+ if (GetAFDB()->TagExist(s)) {
+ m_ListOfStations[station] = GetAFDB()->template GetImage<MaskImageType>(s);
+ found = true;
}
- else m_Working_Support = m_Mediastinum;
- ExtractStation_8_SI_Limits();
- ExtractStation_8_AP_Limits();
- // ExtractStation_8_LR_Limits();
+ // 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>::
+AddComputeStation(std::string station)
+{
+ m_ComputeStationMap[station] = true;
}
//--------------------------------------------------------------------
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_8()
+{
+ if (CheckForStation("8")) {
+ ExtractStation_8_SI_Limits();
+ ExtractStation_8_Post_Limits();
+ ExtractStation_8_Ant_Sup_Limits();
+ ExtractStation_8_Ant_Inf_Limits();
+ ExtractStation_8_LR_1_Limits();
+ ExtractStation_8_LR_2_Limits();
+ ExtractStation_8_LR_Limits();
+ ExtractStation_8_Ant_Injected_Limits();
+ ExtractStation_8_Single_CCL_Limits();
+ ExtractStation_8_Remove_Structures();
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["8"], "seg/Station8.mhd");
+ GetAFDB()->SetImageFilename("Station8", "seg/Station8.mhd");
+ WriteAFDB();
}
- else m_Working_Support = m_Mediastinum;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+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();
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_7() {
+ if (CheckForStation("7")) {
ExtractStation_7_SI_Limits();
ExtractStation_7_RL_Limits();
ExtractStation_7_Posterior_Limits();
+ // ExtractStation_8_Single_CCL_Limits(); // Yes the same than 8
+ ExtractStation_7_Remove_Structures();
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["7"], "seg/Station7.mhd");
+ GetAFDB()->SetImageFilename("Station7", "seg/Station7.mhd");
+ WriteAFDB();
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+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_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();
+ }
}
//--------------------------------------------------------------------
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);
-
- // 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);
- }
+//--------------------------------------------------------------------
+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;
}
-}
+
+ return m_FuzzyThreshold[station][tag];
+}
//--------------------------------------------------------------------
+
+
+
#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff