clitk::ExtractLymphStationsFilter<ImageType>::
ExtractStation_3A_SetDefaultValues()
{
- SetFuzzyThreshold("3A", "Sternum", 0.5);
- SetFuzzyThreshold("3A", "SubclavianArtery", 0.5);
}
//--------------------------------------------------------------------
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_Post_Left_Limits_With_Aorta_S5_Support();
+ ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support();
ExtractStation_3A_AntPost_Superiorly();
-
ExtractStation_3A_Remove_Structures();
+
+ // Generic RelativePosition processes
+ m_ListOfStations["3A"] = this->ApplyRelativePositionList("Station_3A", m_ListOfStations["3A"]);
- 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"); ?
-
-
- // ExtractStation_3A_Ant_Limits(); --> No, already in support; to remove
- // ExtractStation_3A_Post_Limits(); --> No, more complex, see Vessels etc
+ // 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();
}
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3A_Ant_Limits()
-{
- StartNewStep("[Station 3A] Ant limits with Sternum");
-
- // Get Sternum, keep posterior part.
- MaskImagePointer Sternum = GetAFDB()->template GetImage<MaskImageType>("Sternum");
- m_Working_Support =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Sternum, 2,
- GetFuzzyThreshold("3A", "Sternum"), "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_Post_Limits()
-{
- StartNewStep("[Station 3A] Post limits with SubclavianArtery");
-
- // Get Sternum, keep posterior part.
- MaskImagePointer SubclavianArteryLeft =
- GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryLeft");
- MaskImagePointer SubclavianArteryRight =
- GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryRight");
-
- m_Working_Support =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, SubclavianArteryLeft, 2,
- GetFuzzyThreshold("3A", "SubclavianArtery"), "AntTo",
- false, 3, true, false);
- m_Working_Support =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, SubclavianArteryRight, 2,
- GetFuzzyThreshold("3A", "SubclavianArtery"), "AntTo",
- false, 3, true, false);
- StopCurrentStep<MaskImageType>(m_Working_Support);
- m_ListOfStations["3A"] = m_Working_Support;
-}
-//--------------------------------------------------------------------
-
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3A_AntPost_S5()
+ExtractStation_3A_Post_Left_Limits_With_Aorta_S5_Support()
{
- StartNewStep("[Station 3A] Post limits around S5");
-
- // First remove post to SVC
- MaskImagePointer SVC = GetAFDB()->template GetImage <MaskImageType>("SVC");
+ StartNewStep("[Station 3A] Post limits in S5 support according to Aorta");
- // Trial in 3D -> difficulties superiorly. Stay slice by slice.
- /*
- 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(SVC);
- relPosFilter->AddOrientationTypeString("PostTo");
- relPosFilter->SetInverseOrientationFlag(true);
- relPosFilter->SetIntermediateSpacing(4);
- relPosFilter->SetIntermediateSpacingFlag(false);
- relPosFilter->SetFuzzyThreshold(0.5);
- // relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
- relPosFilter->Update();
- m_Working_Support = relPosFilter->GetOutput();
- */
-
- // 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
+ // 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");
// 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.
+
+
+
+ // ====> TO BE CHANGED USING AscendingAorta and DescendingAorta
+
+
+
std::vector<MaskSlicePointer> slices;
clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
std::vector<MaskImagePointType> points;
template <class ImageType>
void
clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3A_AntPost_S6()
+ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support()
{
- StartNewStep("[Station 3A] Post limits around S6");
+ StartNewStep("[Station 3A] Post limits with dilated Aorta");
// Consider Aorta
MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
radius[2] = 0; // required
Aorta = clitk::Dilate<MaskImageType>(Aorta, radius, GetBackgroundValue(), GetForegroundValue(), false);
+ // Now, insert this image in the AFDB (but do not store on disk)
+ GetAFDB()->template SetImage<MaskImageType>("Aorta_Dilated_Anteriorly", "bidon",
+ Aorta, false);
+ /*
// 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;
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
clitk::ExtractLymphStationsFilter<ImageType>::
ExtractStation_3A_Remove_Structures()
{
- 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", "Aorta");
+ Remove_Structures(" 3A", "LeftSubclavianArtery");
+ Remove_Structures(" 3A", "RightSubclavianArtery");
+ Remove_Structures(" 3A", "Thyroid");
+ Remove_Structures(" 3A", "LeftCommonCarotidArtery");
+ Remove_Structures(" 3A", "RightCommonCarotidArtery");
+ Remove_Structures(" 3A", "BrachioCephalicArtery");
+ // Remove_Structures("3A", "Bones"); --> should be in extractmediastinum
// 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());
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 (centroids.size() > 1) {
+
+ // 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 = 1;
- }
- else {
label = 2;
}
-
- HERE
-
- slices_BCV[i] = clitk::SetBackground<MaskSliceType>(slices_BCV[i], slices_BCV[i],
- label,
- GetBackgroundValue(), true);
+ 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
- slices[i] = clitk::AndNot(slices[i], slices_BCV[i], GetBackgroundValue());
+ clitk::AndNot<MaskSliceType>(slices[i], slices_BCV[i], GetBackgroundValue());
}
// Joint
m_ListOfStations["3A"] = m_Working_Support;
}
//--------------------------------------------------------------------
+
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff