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");
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-template <class TImageType>
-template <class ArgsInfoType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-SetArgsInfo(ArgsInfoType & argsinfo) {
- DD("SetArgsInfo");
-}
-//--------------------------------------------------------------------
-
-
//--------------------------------------------------------------------
template <class TImageType>
void
// Get inputs
LoadAFDB();
m_Input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
- m_Support = GetAFDB()->template GetImage <MaskImageType>("mediastinum");
-
- //
- typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BFilter;
- BFilter::Pointer merge = BFilter::New();
+ 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();
+ */
- // Extract Station7
- ExtractStation_7();
- m_Output = m_Station7;
+ if (0) { // temporary suppress
+ // Extract Station7
+ StartNewStep("Station 7");
+ StartSubStep();
+ ExtractStation_7();
+ StopSubStep();
- // Extract Station4RL
- ExtractStation_4RL();
+ // Extract Station4RL
+ StartNewStep("Station 4RL");
+ StartSubStep();
+ //ExtractStation_4RL();
+ StopSubStep();
+ }
- writeImage<MaskImageType>(m_Station4RL, "s4rl.mhd");
+
+ //
+ // 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();
+ merge->SetInput2(m_Station4RL); // support
+ merge->SetOperationType(BFilter::AndNot); CHANGE OPERATOR
+ merge->SetForegroundValue(4);
+ merge->Update();
+ m_Output = merge->GetOutput();
*/
}
//--------------------------------------------------------------------
DD("GenerateData, graft output");
// Final Step -> graft output (if SetNthOutput => redo)
- this->GraftOutput(m_Output);
+ this->GraftOutput(m_ListOfStations["8"]);
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_8() {
+
+ // 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;
+
+ ExtractStation_8_SI_Limits();
+ ExtractStation_8_AP_Limits();
+ // ExtractStation_8_LR_Limits();
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
ExtractStation_7() {
- DD("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();
void
clitk::ExtractLymphStationsFilter<TImageType>::
ExtractStation_4RL() {
- DD("ExtractStation_4RL");
- writeImage<MaskImageType>(m_Support, "essai.mhd"); // OK
-
/*
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