-/*=========================================================================
- 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
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3A_SetDefaultValues()
+{
+ SetFuzzyThreshold("3A", "Sternum", 0.5);
+ SetFuzzyThreshold("3A", "SubclavianArtery", 0.5);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_3A()
+{
+ if (!CheckForStation("3A")) return;
+
+ StartNewStep("Station 3A");
+ StartSubStep();
+
+ // Get the current support
+ StartNewStep("[Station 3A] Get the current 3A suppport");
+ m_Working_Support = m_ListOfSupports["S3A"];
+ m_ListOfStations["3A"] = m_Working_Support;
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+
+ ExtractStation_3A_AntPost_S5();
+ ExtractStation_3A_AntPost_S6();
+ ExtractStation_3A_AntPost_Superiorly();
+ ExtractStation_3A_Remove_Structures();
- 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.
+ Remove_Structures("3A", "Aorta");
+ Remove_Structures("3A", "SubclavianArteryLeft");
+ Remove_Structures("3A", "SubclavianArteryRight");
+ Remove_Structures("3A", "Thyroid");
+ Remove_Structures("3A", "CommonCarotidArteryLeft");
+ Remove_Structures("3A", "CommonCarotidArteryRight");
+ Remove_Structures("3A", "BrachioCephalicArtery");
- It is distributed under dual licence
+ ExtractStation_3A_PostToBones();
+
+ // Keep a single CCL
+ m_ListOfStations["3A"] =
+ clitk::SliceBySliceKeepMainCCL<MaskImageType>(m_ListOfStations["3A"],
+ GetBackgroundValue(),
+ GetForegroundValue());
+
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["3A"], "seg/Station3A.mhd");
+ GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd");
+ WriteAFDB();
+ StopSubStep();
+}
+//--------------------------------------------------------------------
- - 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>
void
clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3A_SetDefaultValues()
+ExtractStation_3A_AntPost_S5()
{
+ StartNewStep("[Station 3A] Post limits around S5");
+
+ // First remove post to SVC
+ MaskImagePointer SVC = GetAFDB()->template GetImage <MaskImageType>("SVC");
+
+ // Trial in 3D -> difficulties superiorly. Stay slice by slice.
+ // Slice by slice not post to SVC. Use initial spacing
+ m_Working_Support =
+ clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, SVC, 2,
+ GetFuzzyThreshold("3A", "SVC"),
+ "NotPostTo", true,
+ SVC->GetSpacing()[0], false, false);
+
+ // Consider Aorta, remove Left/Post part ; only around S5
+ // Get S5 support and Aorta
+ MaskImagePointer S5 = m_ListOfSupports["S5"];
+ MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
+ Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S5, GetBackgroundValue());
+
+ // Inferiorly, Aorta has two CCL that merge into a single one when
+ // S6 appears. Loop on Aorta slices, select the most ant one, detect
+ // the most ant point.
+ std::vector<MaskSlicePointer> slices;
+ clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
+ std::vector<MaskImagePointType> points;
+ for(uint i=0; i<slices.size(); i++) {
+ // Select most ant CCL
+ slices[i] = clitk::Labelize<MaskSliceType>(slices[i], GetBackgroundValue(), false, 1);
+ std::vector<MaskSlicePointType> c;
+ clitk::ComputeCentroids<MaskSliceType>(slices[i], GetBackgroundValue(), c);
+ assert(c.size() == 3); // only 2 CCL
+ typename MaskSliceType::PixelType l;
+ if (c[1][1] > c[2][1]) { // We will remove the label=1
+ l = 1;
+ }
+ else {
+ l = 2;// We will remove the label=2
+ }
+ slices[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices[i], slices[i], l,
+ GetBackgroundValue(), true);
+
+ // Detect the most ant point
+ MaskSlicePointType p;
+ MaskImagePointType pA;
+ clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(), 1, true, p);
+ // Set the X coordinate to the X coordinate of the centroid
+ if (l==1) p[0] = c[2][0];
+ else p[0] = c[1][0];
+
+ // Convert in 3D and store
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Aorta, i, pA);
+ points.push_back(pA);
+ }
+
+ // DEBUG
+ // MaskImagePointer o = clitk::JoinSlices<MaskImageType>(slices, Aorta, 2);
+ // writeImage<MaskImageType>(o, "o.mhd");
+ // clitk::WriteListOfLandmarks<MaskImageType>(points, "Ant-Aorta.txt");
+
+ // Remove Post/Left to this point
+ m_Working_Support =
+ clitk::SliceBySliceSetBackgroundFromPoints<MaskImageType>(m_Working_Support,
+ GetBackgroundValue(), 2,
+ points,
+ true, // Set BG if X greater than point[x], and
+ true); // if Y greater than point[y]
+
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3A"] = m_Working_Support;
}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3A_SI_Limits()
+ExtractStation_3A_AntPost_S6()
{
- // Apex of the chest or Sternum & Carina.
- StartNewStep("[Station 3A] Inf/Sup limits with Sternum and Carina");
+ StartNewStep("[Station 3A] Post limits around S6");
- // Get Carina position (has been determined in Station8)
- m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
+ // Consider Aorta
+ MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
+
+ // Limits the support to S6
+ MaskImagePointer S6 = m_ListOfSupports["S6"];
+ Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S6, GetBackgroundValue());
+
+ // Extend 1cm anteriorly
+ MaskImagePointType radius; // in mm
+ radius[0] = 10;
+ radius[1] = 10;
+ radius[2] = 0; // required
+ Aorta = clitk::Dilate<MaskImageType>(Aorta, radius, GetBackgroundValue(), GetForegroundValue(), false);
- // Get Sternum and search for the upper position
- MaskImagePointer Sternum = GetAFDB()->template GetImage<MaskImageType>("Sternum");
+ // Not Post to
+ m_Working_Support =
+ clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Aorta, 2,
+ GetFuzzyThreshold("3A", "Aorta"),
+ "NotPostTo", true,
+ Aorta->GetSpacing()[0], false, false);
+
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3A"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
- // Search most sup point
- MaskImagePointType ps = Sternum->GetOrigin(); // initialise to avoid warning
- clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Sternum, GetBackgroundValue(), 2, false, ps);
- double m_SternumZ = ps[2]+Sternum->GetSpacing()[2]; // One more slice, because it is below this point
- //* Crop support :
- m_Working_Support =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2,
- m_CarinaZ, m_SternumZ, true,
- GetBackgroundValue());
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3A_AntPost_Superiorly()
+{
+ StartNewStep("[Station 3A] Post limits superiorly");
+ /*
+ MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicVein");
+ MaskImagePointer BrachioCephalicArtery = GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicArtery");
+ MaskImagePointer CommonCarotidArteryLeft = GetAFDB()->template GetImage <MaskImageType>("CommonCarotidArteryLeft");
+ MaskImagePointer CommonCarotidArteryRight = GetAFDB()->template GetImage <MaskImageType>("CommonCarotidArteryRight");
+ MaskImagePointer SubclavianArteryLeft = GetAFDB()->template GetImage <MaskImageType>("SubclavianArteryLeft");
+ MaskImagePointer SubclavianArteryRight = GetAFDB()->template GetImage <MaskImageType>("SubclavianArteryRight");
+
+ // Not Post to
+#define RP(STRUCTURE) \
+ m_Working_Support = \
+ clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, STRUCTURE, 2, \
+ 0.5, \
+ "NotPostTo", true, \
+ STRUCTURE->GetSpacing()[0], false, false);
+
+ // RP(BrachioCephalicVein);
+ RP(BrachioCephalicArtery);
+ RP(CommonCarotidArteryRight);
+ RP(CommonCarotidArteryLeft);
+ RP(SubclavianArteryRight);
+ RP(SubclavianArteryLeft);
+ */
+
+ // 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,
+ GetBackgroundValue());
+
+ // 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::AndNot);
+ boolFilter->Update();
+ m_Working_Support = boolFilter->GetOutput();
+
StopCurrentStep<MaskImageType>(m_Working_Support);
m_ListOfStations["3A"] = m_Working_Support;
}
template <class ImageType>
void
clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3A_Ant_Limits()
+ExtractStation_3A_Remove_Structures()
{
- StartNewStep("[Station 3A] Ant limits with Sternum");
+ Remove_Structures("3A", "Aorta");
+ Remove_Structures("3A", "SubclavianArteryLeft");
+ Remove_Structures("3A", "SubclavianArteryRight");
+ Remove_Structures("3A", "Thyroid");
+ Remove_Structures("3A", "CommonCarotidArteryLeft");
+ Remove_Structures("3A", "CommonCarotidArteryRight");
+ Remove_Structures("3A", "BrachioCephalicArtery");
+ // Remove_Structures("3A", "BrachioCephalicVein"); ?
+
+ StartNewStep("[Station 3A] Remove part of BrachioCephalicVein");
+ // resize like support, extract slices
+ // while single CCL -> remove
+ // when two remove only the most post
+ MaskImagePointer BrachioCephalicVein =
+ GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicVein");
+ BrachioCephalicVein = clitk::ResizeImageLike<MaskImageType>(BrachioCephalicVein,
+ m_Working_Support,
+ GetBackgroundValue());
+ std::vector<MaskSlicePointer> slices;
+ std::vector<MaskSlicePointer> slices_BCV;
+ clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices);
+ clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, slices_BCV);
+ for(uint i=0; i<slices.size(); i++) {
+ // Labelize slices_BCV
+ slices_BCV[i] = Labelize<MaskSliceType>(slices_BCV[i], 0, true, 1);
+
+ // Compute centroids
+ std::vector<typename MaskSliceType::PointType> centroids;
+ ComputeCentroids<MaskSliceType>(slices_BCV[i], GetBackgroundValue(), centroids);
+
+ // If several centroid, select the one most anterior
+ if (centroids.size() > 2) {
+ // Only keep the one most post
+ typename MaskSliceType::PixelType label;
+ if (centroids[1][1] > centroids[2][1]) {
+ label = 2;
+ }
+ else {
+ label = 1;
+ }
+ // "remove" the CCL
+ slices_BCV[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices_BCV[i],
+ slices_BCV[i],
+ label,
+ GetBackgroundValue(),
+ true);
+ }
+
+ // Remove from the support
+ clitk::AndNot<MaskSliceType>(slices[i], slices_BCV[i], GetBackgroundValue());
+ }
+
+ // Joint
+ m_Working_Support = clitk::JoinSlices<MaskImageType>(slices, m_Working_Support, 2);
- // Get Sternum, keep posterior part.
- MaskImagePointer Sternum = GetAFDB()->template GetImage<MaskImageType>("Sternum");
- m_Working_Support =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Sternum, 2,
- 0.5, "PostTo",
- false, 3, true, false);
StopCurrentStep<MaskImageType>(m_Working_Support);
m_ListOfStations["3A"] = m_Working_Support;
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3A_PostToBones()
+{
+ StartNewStep("[Station 3A] Post limits with bones");
+
+ // limits with bones
+ MaskImagePointer Bones = GetAFDB()->template GetImage<MaskImageType>("Bones");
+ m_Working_Support =
+ clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Bones, 2,
+ GetFuzzyThreshold("3A", "Bones"), "NotAntTo",
+ false, 3, true, false);
+
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3A"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff