+++ /dev/null
-
-
-// vtk
-#include <vtkAppendPolyData.h>
-#include <vtkPolyDataWriter.h>
-#include <vtkCellArray.h>
-
-// clitk
-#include "clitkMeshToBinaryImageFilter.h"
-
-// itk
-#include <itkImageDuplicator.h>
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_2RL_SetDefaultValues()
-{
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_2RL()
-{
- if ((!CheckForStation("2R")) && (!CheckForStation("2L"))) return;
-
- StartNewStep("Stations 2RL");
- StartSubStep();
-
- // Get the current support
- StartNewStep("[Station 2RL] Get the current 2RL suppport");
- m_ListOfStations["2R"] = m_ListOfSupports["S2R"];
- m_ListOfStations["2L"] = m_ListOfSupports["S2L"];
- StopCurrentStep<MaskImageType>(m_ListOfStations["2R"]);
-
- // Do the same limits for R & L
- m_Working_Support = m_ListOfStations["2R"];
- ExtractStation_2RL_Ant_Limits("2R");
- ExtractStation_2RL_Remove_Structures(" 2R");
- m_ListOfStations["2R"] = m_Working_Support;
-
- m_Working_Support = m_ListOfStations["2L"];
- ExtractStation_2RL_Ant_Limits("2L");
- ExtractStation_2RL_Remove_Structures(" 2L");
- m_ListOfStations["2L"] = m_Working_Support;
-
- // Remove superior part to BrachioCephalicVein (used then by RelPos)
- ExtractStation_2RL_Cut_BrachioCephalicVein_superiorly_when_it_split();
-
- // Generic RelativePosition processes
- m_ListOfStations["2R"] = this->ApplyRelativePositionList("Station_2R", m_ListOfStations["2R"]);
- m_ListOfStations["2L"] = this->ApplyRelativePositionList("Station_2L", m_ListOfStations["2L"]);
-
- // 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();
- StopSubStep();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_2RL_Ant_Limits(std::string s)
-{
- // -----------------------------------------------------
- StartNewStep("[Station "+s+"] Ant limits with vessels centroids");
-
- // WARNING, as I used "And" after, empty slice in binarizedContour
- // lead to remove part of the support, although we want to keep
- // unchanged. So we decide to ResizeImageLike but pad with
- // ForegroundValue instead of BG
-
- // Get or compute the binary mask that separate Ant/Post part
- // according to vessels
- MaskImagePointer binarizedContour = FindAntPostVessels2();
- binarizedContour = clitk::ResizeImageLike<MaskImageType>(binarizedContour,
- m_Working_Support,
- GetForegroundValue());
- // remove from support
- typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
- typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
- boolFilter->InPlaceOn();
- boolFilter->SetInput1(m_Working_Support);
- boolFilter->SetInput2(binarizedContour);
- boolFilter->SetBackgroundValue1(GetBackgroundValue());
- boolFilter->SetBackgroundValue2(GetBackgroundValue());
- boolFilter->SetOperationType(BoolFilterType::And);
- boolFilter->Update();
- m_Working_Support = boolFilter->GetOutput();
-
- // End
- StopCurrentStep<MaskImageType>(m_Working_Support);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_2RL_Cut_BrachioCephalicVein_superiorly_when_it_split()
-{
- // -----------------------------------------------------
- StartNewStep("[Station 2RL] Cut BrachioCephalicVein superiorly (when it split)");
-
- // Get BrachioCephalicVein
- MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
-
- // Remove the part superior to the slice where BrachioCephalicVein
- // divide in two CCL
- std::vector<MaskSlicePointer> BCV_slices;
- clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, BCV_slices);
- bool stop = false;
- uint i=0;
- while (!stop) {
- // Count the number of CCL
- int nb;
- clitk::LabelizeAndCountNumberOfObjects<MaskSliceType>(BCV_slices[i], GetBackgroundValue(), true, 1, nb);
- if (nb>1) stop = true;
- i++;
- }
- // Convert slice into coordinate
- MaskImagePointType p;
- MaskImageIndexType index;
- index[0] = index[1] = 0;
- index[2] = i;
- BrachioCephalicVein->TransformIndexToPhysicalPoint(index, p);
- BrachioCephalicVein =
- clitk::CropImageRemoveGreaterThan<MaskImageType>(BrachioCephalicVein, 2,
- p[2], true,
- GetBackgroundValue());
-
- // Now, insert this image in the AFDB (but do not store on disk)
- GetAFDB()->template SetImage<MaskImageType>("BrachioCephalicVein_ForS2RL", "bidon",
- BrachioCephalicVein, false);
- // End
- StopCurrentStep<MaskImageType>(BrachioCephalicVein);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-// Build a vtk mesh from a list of slice number/closed-contours
-template <class ImageType>
-vtkSmartPointer<vtkPolyData>
-clitk::ExtractLymphStationsFilter<ImageType>::
-Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points)
-{
- // create a contour, polydata.
- vtkSmartPointer<vtkPolyData> mesh = vtkSmartPointer<vtkPolyData>::New();
- mesh->Allocate(); //for cell structures
- mesh->SetPoints(vtkPoints::New());
- vtkIdType ids[2];
- int point_number = points.size();
- for (unsigned int i=0; i<points.size(); i++) {
- mesh->GetPoints()->InsertNextPoint(points[i][0],points[i][1],points[i][2]);
- ids[0]=i;
- ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
- mesh->GetLines()->InsertNextCell(2,ids);
- }
- // Return
- return mesh;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_2RL_Remove_Structures(std::string s)
-{
- // m_Working_Support must be set
- Remove_Structures(s, "BrachioCephalicVein");
- Remove_Structures(s, "BrachioCephalicArtery");
- Remove_Structures(s, "LeftCommonCarotidArtery");
- Remove_Structures(s, "RightCommonCarotidArtery");
- Remove_Structures(s, "LeftSubclavianArtery");
- Remove_Structures(s, "RightSubclavianArtery");
- Remove_Structures(s, "Thyroid");
- Remove_Structures(s, "Aorta");
-}
-//--------------------------------------------------------------------
-
-
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff