-/*=========================================================================
- Program: vv http://www.creatis.insa-lyon.fr/rio/vv
-
- Authors belong to:
- - University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://www.centreleonberard.fr
- - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the copyright notices for more information.
-
- It is distributed under dual licence
-
- - BSD See included LICENSE.txt file
- - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================*/
-
-#include <itkBinaryDilateImageFilter.h>
-#include <itkMirrorPadImageFilter.h>
//--------------------------------------------------------------------
template <class ImageType>
//--------------------------------------------------------------------
-template <class ImageType>
+template <class TImageType>
void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3P_SI_Limits()
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_3P()
{
- /*
- Apex of the chest & Carina.
- */
- StartNewStep("[Station 3P] Inf/Sup limits with apex of the chest and carina");
+ if (!CheckForStation("3P")) return;
- // Get Carina position (has been determined in Station8)
- m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
-
- // Get Apex of the Chest. The "lungs" structure is autocroped so we
- // consider the most superior point.
- MaskImagePointer Lungs = GetAFDB()->template GetImage<MaskImageType>("Lungs");
- MaskImageIndexType index = Lungs->GetLargestPossibleRegion().GetIndex();
- index += Lungs->GetLargestPossibleRegion().GetSize();
- MaskImagePointType p;
- Lungs->TransformIndexToPhysicalPoint(index, p);
- p[2] -= 5; // 5 mm below because the autocrop is slightly above the apex
- double m_ApexOfTheChest = p[2];
-
- /* Crop support :
- Superior limit = carina
- Inferior limit = Apex of the chest */
- m_Working_Support =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2,
- m_CarinaZ,
- m_ApexOfTheChest, true,
- GetBackgroundValue());
+ StartNewStep("Station 3P");
+ StartSubStep();
- StopCurrentStep<MaskImageType>(m_Working_Support);
+ // Get the current support
+ StartNewStep("[Station 3P] Get the current 3P suppport");
+ m_Working_Support = m_ListOfSupports["S3P"];
m_ListOfStations["3P"] = m_Working_Support;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3P_Remove_Structures()
-{
- /*
- 3 - (sup) remove Aorta, VB, subcl
- not LR subcl ! -> a séparer LR ?
- (inf) remove Eso, Aorta, Azygousvein
- */
-
- StartNewStep("[Station 3P] Remove some structures.");
-
- Remove_Structures("Aorta");
- Remove_Structures("VertebralBody");
- Remove_Structures("SubclavianArtery");
- Remove_Structures("Esophagus");
- Remove_Structures("Azygousvein");
- Remove_Structures("Thyroid");
- Remove_Structures("VertebralArtery");
-
StopCurrentStep<MaskImageType>(m_Working_Support);
- m_ListOfStations["3P"] = m_Working_Support;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3P_Ant_Limits()
-{
- /*
- Ant Post limit :
-
- Anteriorly, it is in contact with the posterior aspect of Stations
- 1–2 superiorly (Fig. 2A–C) and with Stations 4R and 4L inferiorly
- (Fig. 2D–I and 3A–C). The anterior limit of Station 3P is kept
- posterior to the trachea, which is defined by an imaginary
- horizontal line running along the posterior wall of the trachea
- (Fig. 2B,E, red line). Posteriorly, it is delineated along the
- anterior and lateral borders of the vertebral body until an
- imaginary horizontal line running 1 cm posteriorly to the
- anterior border of the vertebral body (Fig. 2D).
-
- 1 - post to the trachea : define an imaginary line just post the
- Trachea and remove what is anterior.
-
- */
- StartNewStep("[Station 3P] Ant limits with Trachea ");
- // Load Trachea
- MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
-
- // Crop like current support (need by SliceBySliceSetBackgroundFromLineSeparation after)
- Trachea =
- clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
-
- // Slice by slice, determine the most post point of the trachea (A)
- // and consider a second point on the same horizontal line (B)
- std::vector<MaskImagePointType> p_A;
- std::vector<MaskImagePointType> p_B;
- std::vector<typename MaskSliceType::Pointer> slices;
- clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices);
- MaskImagePointType p;
- typename MaskSliceType::PointType sp;
- for(uint i=0; i<slices.size(); i++) {
- // First only consider the main CCL (trachea, not bronchus)
- slices[i] = Labelize<MaskSliceType>(slices[i], 0, true, 100);
- slices[i] = KeepLabels<MaskSliceType>(slices[i], GetBackgroundValue(),
- GetForegroundValue(), 1, 1, true);
- // Find most posterior point
- clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(),
- 1, false, sp);
- clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp, Trachea, i, p);
- p_A.push_back(p);
- p[0] -= 20;
- p_B.push_back(p);
- }
- clitk::WriteListOfLandmarks<MaskImageType>(p_A, "trachea-post.txt");
-
- // Remove Ant part above those lines
- clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support,
- p_A, p_B,
- GetBackgroundValue(),
- 1, 10);
- // End, release memory
- GetAFDB()->template ReleaseImage<MaskImageType>("Trachea");
- StopCurrentStep<MaskImageType>(m_Working_Support);
+ // Generic RelativePosition processes
+ m_ListOfStations["3P"] = this->ApplyRelativePositionList("Station_3P", m_ListOfStations["3P"]);
+ m_Working_Support = m_ListOfStations["3P"];
+ ExtractStation_8_Single_CCL_Limits(); // YES 8 !
+ ExtractStation_3P_Remove_Structures(); // after CCL
m_ListOfStations["3P"] = m_Working_Support;
+
+ // Old stuff
+ // LR limits superiorly => not here for the moment because not clear in the def
+ // ExtractStation_3P_LR_sup_Limits_2(); //TODO
+ // ExtractStation_3P_LR_sup_Limits(); // old version to change
+ // ExtractStation_3P_LR_inf_Limits(); // <-- done in RelPosList
+
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["3P"], "seg/Station3P.mhd");
+ GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd");
+ WriteAFDB();
+ StopSubStep();
}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3P_Post_Limits()
+ExtractStation_3P_Remove_Structures()
{
- /*
- Ant Post limit :
-
- Anteriorly, it is in contact with the posterior aspect of Stations
- 1–2 superiorly (Fig. 2A–C) and with Stations 4R and 4L inferiorly
- (Fig. 2D–I and 3A–C). The anterior limit of Station 3P is kept
- posterior to the trachea, which is defined by an imaginary
- horizontal line running along the posterior wall of the trachea
- (Fig. 2B,E, red line). Posteriorly, it is delineated along the
- anterior and lateral borders of the vertebral body until an
- imaginary horizontal line running 1 cm posteriorly to the
- anterior border of the vertebral body (Fig. 2D).
-
- 2 - post to the trachea : define an imaginary line just post the
- Trachea and remove what is anterior.
-
- */
- StartNewStep("[Station 3P] Post limits with VertebralBody ");
-
- // Load VertebralBody
- MaskImagePointer VertebralBody = GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
-
- // Crop like current support (need by SliceBySliceSetBackgroundFromLineSeparation after)
- VertebralBody = clitk::ResizeImageLike<MaskImageType>(VertebralBody, m_Working_Support, GetBackgroundValue());
-
- writeImage<MaskImageType>(VertebralBody, "vb.mhd");
-
- // Compute VertebralBody most Ant position (again because slices
- // changes). Slice by slice, determine the most post point of the
- // trachea (A) and consider a second point on the same horizontal
- // line (B)
- std::vector<MaskImagePointType> p_A;
- std::vector<MaskImagePointType> p_B;
- std::vector<typename MaskSliceType::Pointer> slices;
- clitk::ExtractSlices<MaskImageType>(VertebralBody, 2, slices);
- MaskImagePointType p;
- typename MaskSliceType::PointType sp;
- for(uint i=0; i<slices.size(); i++) {
- // Find most anterior point
- bool found = clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(),
- 1, true, sp);
-
- // If the VertebralBody stop superiorly before the end of
- // m_Working_Support, we consider the same previous point.
- if (!found) {
- p = p_A.back();
- p[2] += VertebralBody->GetSpacing()[2];
- p_A.push_back(p);
- p = p_B.back();
- p[2] += VertebralBody->GetSpacing()[2];
- p_B.push_back(p);
- }
- else {
- clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp, VertebralBody, i, p);
- p[1] += 10; // Consider 10 mm more post
- p_A.push_back(p);
- p[0] -= 20;
- p_B.push_back(p);
- }
- }
- clitk::WriteListOfLandmarks<MaskImageType>(p_A, "vb-ant.txt");
-
-
- // Remove Ant part above those lines
- clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support,
- p_A, p_B,
- GetBackgroundValue(),
- 1, -10);
- writeImage<MaskImageType>(m_Working_Support, "a.mhd");
-
+ StartNewStep("[Station 3P] Remove some structures.");
+ Remove_Structures("3P", "Esophagus");
+ Remove_Structures("3P", "Thyroid");
+ Remove_Structures("3P", "VertebralArtery"); // (inside the station)
StopCurrentStep<MaskImageType>(m_Working_Support);
m_ListOfStations["3P"] = m_Working_Support;
}
Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
SubclavianArtery = clitk::ResizeImageLike<MaskImageType>(SubclavianArtery, m_Working_Support, GetBackgroundValue());
- writeImage<MaskImageType>(Trachea, "tr.mhd");
- writeImage<MaskImageType>(SubclavianArtery, "sca.mhd");
+ // writeImage<MaskImageType>(Trachea, "tr.mhd");
+ // writeImage<MaskImageType>(SubclavianArtery, "sca.mhd");
// Get list of slices
std::vector<MaskSlicePointer> slices_support;
relPosFilter->SetBackgroundValue(GetBackgroundValue());
relPosFilter->SetInput(slices_support[i]);
relPosFilter->SetInputObject(object);
- relPosFilter->AddOrientationTypeString("R");
+ relPosFilter->AddOrientationTypeString("RightTo");
relPosFilter->SetInverseOrientationFlag(true);
// relPosFilter->SetIntermediateSpacing(3);
relPosFilter->SetIntermediateSpacingFlag(false);
relPosFilter->SetBackgroundValue(GetBackgroundValue());
relPosFilter->SetInput(slices_support[i]);
relPosFilter->SetInputObject(object);
- relPosFilter->AddOrientationTypeString("A");
+ relPosFilter->AddOrientationTypeString("AntTo");
relPosFilter->SetInverseOrientationFlag(true);
// relPosFilter->SetIntermediateSpacing(3);
relPosFilter->SetIntermediateSpacingFlag(false);
void
clitk::ExtractLymphStationsFilter<ImageType>::
ExtractStation_3P_LR_sup_Limits_2()
-{
- /*
- Use VertebralArtery to limit.
-
-
- StartNewStep("[Station 3P] Left/Right limits with VertebralArtery");
-
- // Load structures
- MaskImagePointer VertebralArtery = GetAFDB()->template GetImage<MaskImageType>("VertebralArtery");
-
- clitk::AndNot<MaskImageType>(m_Working_Support, VertebralArtery);
-
- StopCurrentStep<MaskImageType>(m_Working_Support);
- m_ListOfStations["3P"] = m_Working_Support;
- */
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3P_LR_inf_Limits()
{
/*
"On the right side, the limit is defined by the air–soft-tissue
interface superiorly (Fig. 2A–C) and the aorta inferiorly
(Figs. 2D–I and 3A–C)."
- inf : not Right to Azygousvein
+ sup :
+ Resizelike support : Trachea, SubclavianArtery
+ Trachea, slice by slice, get centroid trachea
+ SubclavianArtery, slice by slice, CCL
+ prendre la 1ère à L et R, not at Left
+
*/
- StartNewStep("[Station 3P] Left/Right limits (inferior part) with Azygousvein and Aorta");
-
- // Load structures
- MaskImagePointer AzygousVein = GetAFDB()->template GetImage<MaskImageType>("AzygousVein");
- MaskImagePointer Aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
-
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- relPosFilter->VerboseStepFlagOff();
- relPosFilter->WriteStepFlagOff();
- relPosFilter->SetBackgroundValue(GetBackgroundValue());
- relPosFilter->SetInput(m_Working_Support);
- relPosFilter->SetInputObject(AzygousVein);
- relPosFilter->AddOrientationTypeString("R");
- relPosFilter->SetInverseOrientationFlag(true);
- // relPosFilter->SetIntermediateSpacing(3);
- relPosFilter->SetIntermediateSpacingFlag(false);
- relPosFilter->SetFuzzyThreshold(0.7);
- relPosFilter->AutoCropFlagOn();
- relPosFilter->Update();
- m_Working_Support = relPosFilter->GetOutput();
-
- writeImage<MaskImageType>(m_Working_Support, "before-L-aorta.mhd");
- relPosFilter->SetInput(m_Working_Support);
- relPosFilter->SetInputObject(Aorta);
- relPosFilter->AddOrientationTypeString("L");
- relPosFilter->SetInverseOrientationFlag(true);
- // relPosFilter->SetIntermediateSpacing(3);
- relPosFilter->SetIntermediateSpacingFlag(false);
- relPosFilter->SetFuzzyThreshold(0.7);
- relPosFilter->AutoCropFlagOn();
- relPosFilter->Update();
- m_Working_Support = relPosFilter->GetOutput();
- writeImage<MaskImageType>(m_Working_Support, "after-L-aorta.mhd");
+ // StartNewStep("[Station 3P] Left/Right limits (superior part) ");
+
- StopCurrentStep<MaskImageType>(m_Working_Support);
- m_ListOfStations["3P"] = m_Working_Support;
}
//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff