template <class TImageType>
clitk::ExtractLymphStationsFilter<TImageType>::
ExtractLymphStationsFilter():
- clitk::FilterBase(),
- clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
- itk::ImageToImageFilter<TImageType, MaskImageType>()
+ clitk::StructuresExtractionFilter<ImageType>()
{
this->SetNumberOfRequiredInputs(1);
SetBackgroundValue(0);
SetForegroundValue(1);
- ComputeStationsSupportsFlagOn();
+ ForceSupportsFlagOn();
+ SetSupportLimitsFilename("none");
+ CheckSupportFlagOff();
// Default values
- ExtractStation_8_SetDefaultValues();
ExtractStation_3P_SetDefaultValues();
ExtractStation_2RL_SetDefaultValues();
ExtractStation_3A_SetDefaultValues();
+ ExtractStation_1RL_SetDefaultValues();
+ ExtractStation_4RL_SetDefaultValues();
+ ExtractStation_5_SetDefaultValues();
+ ExtractStation_6_SetDefaultValues();
+
+ // TODO
ExtractStation_7_SetDefaultValues();
+ ExtractStation_8_SetDefaultValues();
}
//--------------------------------------------------------------------
clitk::ExtractLymphStationsFilter<TImageType>::
GenerateOutputInformation() {
// Get inputs
- LoadAFDB();
+ this->LoadAFDB();
m_Input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
- m_Mediastinum = GetAFDB()->template GetImage <MaskImageType>("Mediastinum");
+ m_Mediastinum = this->GetAFDB()->template GetImage <MaskImageType>("Mediastinum");
// Clean some computer landmarks to force the recomputation
- GetAFDB()->RemoveTag("AntPostVesselsSeparation");
-
- // Global supports for stations
- if (GetComputeStationsSupportsFlag()) {
- StartNewStep("Supports for stations");
- StartSubStep();
- GetAFDB()->RemoveTag("CarinaZ");
- GetAFDB()->RemoveTag("ApexOfTheChestZ");
- GetAFDB()->RemoveTag("ApexOfTheChest");
- GetAFDB()->RemoveTag("RightBronchus");
- GetAFDB()->RemoveTag("LeftBronchus");
- GetAFDB()->RemoveTag("SuperiorBorderOfAorticArchZ");
- GetAFDB()->RemoveTag("SuperiorBorderOfAorticArch");
- GetAFDB()->RemoveTag("InferiorBorderOfAorticArchZ");
- GetAFDB()->RemoveTag("InferiorBorderOfAorticArch");
- ExtractStationSupports();
- StopSubStep();
- }
- else {
- m_ListOfSupports["S1R"] = GetAFDB()->template GetImage<MaskImageType>("Support_S1R");
- m_ListOfSupports["S1L"] = GetAFDB()->template GetImage<MaskImageType>("Support_S1L");
- m_ListOfSupports["S2R"] = GetAFDB()->template GetImage<MaskImageType>("Support_S2R");
- m_ListOfSupports["S2L"] = GetAFDB()->template GetImage<MaskImageType>("Support_S2L");
- m_ListOfSupports["S4R"] = GetAFDB()->template GetImage<MaskImageType>("Support_S4R");
- m_ListOfSupports["S4L"] = GetAFDB()->template GetImage<MaskImageType>("Support_S4L");
-
- m_ListOfSupports["S3A"] = GetAFDB()->template GetImage<MaskImageType>("Support_S3A");
- m_ListOfSupports["S3P"] = GetAFDB()->template GetImage<MaskImageType>("Support_S3P");
- m_ListOfSupports["S5"] = GetAFDB()->template GetImage<MaskImageType>("Support_S5");
- m_ListOfSupports["S6"] = GetAFDB()->template GetImage<MaskImageType>("Support_S6");
- m_ListOfSupports["S7"] = GetAFDB()->template GetImage<MaskImageType>("Support_S7");
- m_ListOfSupports["S8"] = GetAFDB()->template GetImage<MaskImageType>("Support_S8");
- m_ListOfSupports["S9"] = GetAFDB()->template GetImage<MaskImageType>("Support_S9");
- m_ListOfSupports["S10"] = GetAFDB()->template GetImage<MaskImageType>("Support_S10");
- m_ListOfSupports["S11"] = GetAFDB()->template GetImage<MaskImageType>("Support_S11");
+ // FIXME -> to put elsewhere ?
+ this->GetAFDB()->RemoveTag("AntPostVesselsSeparation");
+
+ // Must I compute the supports ?
+ bool supportsExist = true;
+ if (!GetForceSupportsFlag()) {
+ try {
+ m_ListOfSupports["S1R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1R");
+ m_ListOfSupports["S1L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1L");
+ m_ListOfSupports["S2R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2R");
+ m_ListOfSupports["S2L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2L");
+ m_ListOfSupports["S4R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4R");
+ m_ListOfSupports["S4L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4L");
+
+ m_ListOfSupports["S3A"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3A");
+ m_ListOfSupports["S3P"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3P");
+ m_ListOfSupports["S5"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S5");
+ m_ListOfSupports["S6"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S6");
+ m_ListOfSupports["S7"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S7");
+ m_ListOfSupports["S8"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S8");
+ m_ListOfSupports["S9"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S9");
+ m_ListOfSupports["S10"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S10");
+ m_ListOfSupports["S11"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S11");
+ } catch(clitk::ExceptionObject o) {
+ supportsExist = false;
+ }
}
- // Extract Station8
- ExtractStation_8();
+ if (!supportsExist || GetForceSupportsFlag()) {
+ this->StartNewStep("Supports for stations");
+ this->StartSubStep();
+
+ // FIXME : why should I remove theses tags ???
+ this->GetAFDB()->RemoveTag("CarinaZ");
+ this->GetAFDB()->RemoveTag("ApexOfTheChestZ");
+ this->GetAFDB()->RemoveTag("ApexOfTheChest");
+ this->GetAFDB()->RemoveTag("RightBronchus");
+ this->GetAFDB()->RemoveTag("LeftBronchus");
+ this->GetAFDB()->RemoveTag("SuperiorBorderOfAorticArchZ");
+ this->GetAFDB()->RemoveTag("SuperiorBorderOfAorticArch");
+ this->GetAFDB()->RemoveTag("InferiorBorderOfAorticArchZ");
+ this->GetAFDB()->RemoveTag("InferiorBorderOfAorticArch");
+ ExtractStationSupports();
+ this->StopSubStep();
+ }
- // Extract Station3P
+ // Extract Stations
+ ExtractStation_1RL();
+ ExtractStation_2RL();
ExtractStation_3P();
-
- // Extract Station3A
ExtractStation_3A();
+ ExtractStation_4R();
+ ExtractStation_4L();
+ ExtractStation_5();
+ ExtractStation_6();
- // HERE
+ // ---------- todo -----------------------
- // Extract Station2RL
- StartNewStep("Station 2RL");
- StartSubStep();
- ExtractStation_2RL();
- StopSubStep();
+ // Extract Station8
+ // ExtractStation_8();
// Extract Station7
- StartNewStep("Station 7");
- StartSubStep();
- ExtractStation_7();
- StopSubStep();
-
- if (0) { // temporary suppress
- // Extract Station4RL
- StartNewStep("Station 4RL");
- StartSubStep();
- //ExtractStation_4RL();
- StopSubStep();
- }
+ //this->StartNewStep("Station 7");
+ //this->StartSubStep();
+ //ExtractStation_7();
+ //this->StopSubStep();
+
}
//--------------------------------------------------------------------
clitk::ExtractLymphStationsFilter<TImageType>::
GenerateData() {
// Final Step -> graft output (if SetNthOutput => redo)
- this->GraftOutput(m_ListOfStations["8"]);
+ // this->GraftOutput(m_ListOfStations["8"]);
}
//--------------------------------------------------------------------
std::string s = "Station"+station;
- // Check if station already exist in DB
- bool found = false;
- if (GetAFDB()->TagExist(s)) {
- m_ListOfStations[station] = GetAFDB()->template GetImage<MaskImageType>(s);
- found = true;
- }
-
// Define the starting support
- if (found && GetComputeStation(station)) {
- std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
- }
- if (!found || GetComputeStation(station)) {
- m_Working_Support = m_Mediastinum = GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
+ // if (GetComputeStation(station)) {
+ // std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
+ // }
+ if (GetComputeStation(station)) {
+ m_Working_Support = m_Mediastinum = this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
return true;
}
- else {
- std::cout << "Station " << station << " found. I used it" << std::endl;
- return false;
+ else return false;
+ // else {
+ // std::cout << "Station " << station << " found. I used it" << std::endl;
+ // return false;
+ // }
+
+ // Check if station already exist in DB
+
+ // FIXME -> do nothing if not on the command line. Is it what I want ?
+ //bool found = false;
+ if (this->GetAFDB()->TagExist(s)) {
+ m_ListOfStations[station] = this->GetAFDB()->template GetImage<MaskImageType>(s);
+ //found = true;
}
+
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-template <class TImageType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_4RL() {
- DD("TODO");
- exit(0);
- /*
- WARNING ONLY 4R FIRST !!! (not same inf limits)
- */
- ExtractStation_4RL_SI_Limits();
- ExtractStation_4RL_LR_Limits();
- ExtractStation_4RL_AP_Limits();
-}
-//--------------------------------------------------------------------
-
-
//--------------------------------------------------------------------
template <class ImageType>
void
Remove_Structures(std::string station, std::string s)
{
try {
- StartNewStep("[Station"+station+"] Remove "+s);
- MaskImagePointer Structure = GetAFDB()->template GetImage<MaskImageType>(s);
+ this->StartNewStep("[Station"+station+"] Remove "+s);
+ MaskImagePointer Structure = this->GetAFDB()->template GetImage<MaskImageType>(s);
clitk::AndNot<MaskImageType>(m_Working_Support, Structure, GetBackgroundValue());
}
catch(clitk::ExceptionObject e) {
// B = lower border of bronchus intermedius (BI) or RightMiddleLobeBronchus
try {
- GetAFDB()->GetPoint3D("LineForS7S8Separation_Begin", A);
- GetAFDB()->GetPoint3D("LineForS7S8Separation_End", B);
+ this->GetAFDB()->GetPoint3D("LineForS7S8Separation_Begin", A);
+ this->GetAFDB()->GetPoint3D("LineForS7S8Separation_End", B);
}
catch(clitk::ExceptionObject & o) {
DD("FindLineForS7S8Separation");
// Load LeftLowerLobeBronchus and get centroid point
MaskImagePointer LeftLowerLobeBronchus =
- GetAFDB()->template GetImage <MaskImageType>("LeftLowerLobeBronchus");
+ this->GetAFDB()->template GetImage <MaskImageType>("LeftLowerLobeBronchus");
std::vector<MaskImagePointType> c;
clitk::ComputeCentroids<MaskImageType>(LeftLowerLobeBronchus, GetBackgroundValue(), c);
A = c[1];
// Load RightMiddleLobeBronchus and get superior point (not centroid here)
MaskImagePointer RightMiddleLobeBronchus =
- GetAFDB()->template GetImage <MaskImageType>("RightMiddleLobeBronchus");
+ this->GetAFDB()->template GetImage <MaskImageType>("RightMiddleLobeBronchus");
bool b = FindExtremaPointInAGivenDirection<MaskImageType>(RightMiddleLobeBronchus,
GetBackgroundValue(),
2, false, B);
}
// Insert into the DB
- GetAFDB()->SetPoint3D("LineForS7S8Separation_Begin", A);
- GetAFDB()->SetPoint3D("LineForS7S8Separation_End", B);
+ this->GetAFDB()->SetPoint3D("LineForS7S8Separation_Begin", A);
+ this->GetAFDB()->SetPoint3D("LineForS7S8Separation_End", B);
}
}
//--------------------------------------------------------------------
{
double z;
try {
- z = GetAFDB()->GetDouble("CarinaZ");
+ z = this->GetAFDB()->GetDouble("CarinaZ");
}
catch(clitk::ExceptionObject e) {
- DD("FindCarinaSlicePosition");
+ //DD("FindCarinaSlicePosition");
// Get Carina
- MaskImagePointer Carina = GetAFDB()->template GetImage<MaskImageType>("Carina");
+ MaskImagePointer Carina = this->GetAFDB()->template GetImage<MaskImageType>("Carina");
// Get Centroid and Z value
std::vector<MaskImagePointType> centroids;
clitk::ComputeCentroids<MaskImageType>(Carina, GetBackgroundValue(), centroids);
// We dont need Carina structure from now
- GetAFDB()->template ReleaseImage<MaskImageType>("Carina");
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("Carina");
// Put inside the AFDB
- GetAFDB()->SetPoint3D("CarinaPoint", centroids[1]);
- GetAFDB()->SetDouble("CarinaZ", centroids[1][2]);
- WriteAFDB();
+ this->GetAFDB()->SetPoint3D("CarinaPoint", centroids[1]);
+ this->GetAFDB()->SetDouble("CarinaZ", centroids[1][2]);
+ this->WriteAFDB();
z = centroids[1][2];
}
return z;
{
double z;
try {
- z = GetAFDB()->GetDouble("ApexOfTheChestZ");
+ z = this->GetAFDB()->GetDouble("ApexOfTheChestZ");
}
catch(clitk::ExceptionObject e) {
- DD("FindApexOfTheChestPosition");
- MaskImagePointer Lungs = GetAFDB()->template GetImage<MaskImageType>("Lungs");
+
+ /*
+ //DD("FindApexOfTheChestPosition");
+ MaskImagePointer Lungs = this->GetAFDB()->template GetImage<MaskImageType>("Lungs");
MaskImagePointType p;
p[0] = p[1] = p[2] = 0.0; // to avoid warning
clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Lungs, GetBackgroundValue(), 2, false, p);
// We dont need Lungs structure from now
- GetAFDB()->template ReleaseImage<MaskImageType>("Lungs");
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("Lungs");
// Put inside the AFDB
- GetAFDB()->SetPoint3D("ApexOfTheChest", p);
+ this->GetAFDB()->SetPoint3D("ApexOfTheChest", p);
p[2] -= 5; // We consider 5 mm lower
- GetAFDB()->SetDouble("ApexOfTheChestZ", p[2]);
- WriteAFDB();
+ this->GetAFDB()->SetDouble("ApexOfTheChestZ", p[2]);
+ this->WriteAFDB();
z = p[2];
+ */
+
+ // the superior border becomes the more inferior of the two apices
+ MaskImagePointer RightLung = this->GetAFDB()->template GetImage<MaskImageType>("RightLung");
+ MaskImagePointer LeftLung = this->GetAFDB()->template GetImage<MaskImageType>("LeftLung");
+ MaskImagePointType pr;
+ MaskImagePointType pl;
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(RightLung, GetBackgroundValue(), 2, false, pr);
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(LeftLung, GetBackgroundValue(), 2, false, pl);
+ // We dont need Lungs structure from now
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("RightLung");
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("LeftLung");
+ // Put inside the AFDB
+ if (pr[2] < pl[2]) z = pr[2];
+ else z = pl[2];
+ this->GetAFDB()->SetDouble("ApexOfTheChestZ", z);
+ this->WriteAFDB();
}
return z;
}
FindLeftAndRightBronchi()
{
try {
- m_RightBronchus = GetAFDB()->template GetImage <MaskImageType>("RightBronchus");
- m_LeftBronchus = GetAFDB()->template GetImage <MaskImageType>("LeftBronchus");
+ m_RightBronchus = this->GetAFDB()->template GetImage <MaskImageType>("RightBronchus");
+ m_LeftBronchus = this->GetAFDB()->template GetImage <MaskImageType>("LeftBronchus");
}
catch(clitk::ExceptionObject & o) {
// a Left and Right bronchus.
// Get the trachea
- MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+ MaskImagePointer Trachea = this->GetAFDB()->template GetImage<MaskImageType>("Trachea");
// Get the Carina position
double m_CarinaZ = FindCarina();
LeftBronchus = clitk::AutoCrop<MaskImageType>(LeftBronchus, GetBackgroundValue());
// Insert int AFDB if need after
- GetAFDB()->template SetImage <MaskImageType>("RightBronchus", "seg/rightBronchus.mhd",
+ this->GetAFDB()->template SetImage <MaskImageType>("RightBronchus", "seg/rightBronchus.mhd",
RightBronchus, true);
- GetAFDB()->template SetImage <MaskImageType>("LeftBronchus", "seg/leftBronchus.mhd",
+ this->GetAFDB()->template SetImage <MaskImageType>("LeftBronchus", "seg/leftBronchus.mhd",
LeftBronchus, true);
}
}
{
double z;
try {
- z = GetAFDB()->GetDouble("SuperiorBorderOfAorticArchZ");
+ z = this->GetAFDB()->GetDouble("SuperiorBorderOfAorticArchZ");
}
catch(clitk::ExceptionObject e) {
- DD("FindSuperiorBorderOfAorticArch");
- MaskImagePointer Aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
+ // DD("FindSuperiorBorderOfAorticArch");
+ MaskImagePointer Aorta = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
MaskImagePointType p;
p[0] = p[1] = p[2] = 0.0; // to avoid warning
clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Aorta, GetBackgroundValue(), 2, false, p);
p[2] += Aorta->GetSpacing()[2]; // the slice above
// We dont need Lungs structure from now
- GetAFDB()->template ReleaseImage<MaskImageType>("Aorta");
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("Aorta");
// Put inside the AFDB
- GetAFDB()->SetPoint3D("SuperiorBorderOfAorticArch", p);
- GetAFDB()->SetDouble("SuperiorBorderOfAorticArchZ", p[2]);
- WriteAFDB();
+ this->GetAFDB()->SetPoint3D("SuperiorBorderOfAorticArch", p);
+ this->GetAFDB()->SetDouble("SuperiorBorderOfAorticArchZ", p[2]);
+ this->WriteAFDB();
z = p[2];
}
return z;
{
double z;
try {
- z = GetAFDB()->GetDouble("InferiorBorderOfAorticArchZ");
+ z = this->GetAFDB()->GetDouble("InferiorBorderOfAorticArchZ");
}
catch(clitk::ExceptionObject e) {
- DD("FindInferiorBorderOfAorticArch");
- MaskImagePointer Aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
+ //DD("FindInferiorBorderOfAorticArch");
+ MaskImagePointer Aorta = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
std::vector<MaskSlicePointer> slices;
clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
bool found=false;
Aorta->TransformIndexToPhysicalPoint(index, lower);
// We dont need Lungs structure from now
- GetAFDB()->template ReleaseImage<MaskImageType>("Aorta");
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("Aorta");
// Put inside the AFDB
- GetAFDB()->SetPoint3D("InferiorBorderOfAorticArch", lower);
- GetAFDB()->SetDouble("InferiorBorderOfAorticArchZ", lower[2]);
- WriteAFDB();
+ this->GetAFDB()->SetPoint3D("InferiorBorderOfAorticArch", lower);
+ this->GetAFDB()->SetDouble("InferiorBorderOfAorticArchZ", lower[2]);
+ this->WriteAFDB();
z = lower[2];
}
return z;
template <class ImageType>
typename clitk::ExtractLymphStationsFilter<ImageType>::MaskImagePointer
clitk::ExtractLymphStationsFilter<ImageType>::
-FindAntPostVessels()
+FindAntPostVesselsOLD()
{
// -----------------------------------------------------
/* Rod says: "The anterior border, as with the Atlas – UM, is
bool found = true;
MaskImagePointer binarizedContour;
try {
- DD("FindAntPostVessels try to get");
- binarizedContour = GetAFDB()->template GetImage <MaskImageType>("AntPostVesselsSeparation");
+ binarizedContour = this->GetAFDB()->template GetImage <MaskImageType>("AntPostVesselsSeparation");
}
catch(clitk::ExceptionObject e) {
- DD("not found");
found = false;
}
if (found) {
*/
// Read structures
- MaskImagePointer BrachioCephalicArtery = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
- MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
- MaskImagePointer CommonCarotidArtery = GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArtery");
- MaskImagePointer SubclavianArtery = GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
- MaskImagePointer Thyroid = GetAFDB()->template GetImage<MaskImageType>("Thyroid");
- MaskImagePointer Aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
- MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+ MaskImagePointer BrachioCephalicArtery = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
+ MaskImagePointer BrachioCephalicVein = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
+ MaskImagePointer CommonCarotidArtery = this->GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArtery");
+ MaskImagePointer SubclavianArtery = this->GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
+ MaskImagePointer Thyroid = this->GetAFDB()->template GetImage<MaskImageType>("Thyroid");
+ MaskImagePointer Aorta = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
+ MaskImagePointer Trachea = this->GetAFDB()->template GetImage<MaskImageType>("Trachea");
// Create a temporay support
// From first slice of BrachioCephalicVein to end of 3A
- MaskImagePointer support = GetAFDB()->template GetImage<MaskImageType>("Support_Sup_Carina");
+ MaskImagePointer support = this->GetAFDB()->template GetImage<MaskImageType>("Support_Sup_Carina");
MaskImagePointType p;
p[0] = p[1] = p[2] = 0.0; // to avoid warning
clitk::FindExtremaPointInAGivenDirection<MaskImageType>(BrachioCephalicVein, GetBackgroundValue(), 2, true, p);
double inf = p [2];
- clitk::FindExtremaPointInAGivenDirection<MaskImageType>(GetAFDB()->template GetImage<MaskImageType>("Support_S3A"),
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(this->GetAFDB()->template GetImage<MaskImageType>("Support_S3A"),
GetBackgroundValue(), 2, false, p);
double sup = p [2];
support = clitk::CropImageAlongOneAxis<MaskImageType>(support, 2, inf, sup,
binarizedContour = clitk::CropImageAlongOneAxis<MaskImageType>(binarizedContour, 2, inf, sup,
false, GetBackgroundValue());
// Update the AFDB
- writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mhd");
- GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mhd");
- WriteAFDB();
+ writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mha");
+ this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mha");
+ this->WriteAFDB();
return binarizedContour;
/*
//--------------------------------------------------------------------
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
//--------------------------------------------------------------------
template <class ImageType>
typename clitk::ExtractLymphStationsFilter<ImageType>::MaskImagePointer
bool found = true;
MaskImagePointer binarizedContour;
try {
- DD("FindAntPostVessels try to get");
- binarizedContour = GetAFDB()->template GetImage <MaskImageType>("AntPostVesselsSeparation");
+ binarizedContour = this->GetAFDB()->template GetImage <MaskImageType>("AntPostVesselsSeparation");
}
catch(clitk::ExceptionObject e) {
- DD("not found");
found = false;
}
if (found) {
// Read structures
std::map<std::string, MaskImagePointer> MapOfStructures;
typedef std::map<std::string, MaskImagePointer>::iterator MapIter;
- MapOfStructures["BrachioCephalicArtery"] = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
- MapOfStructures["BrachioCephalicVein"] = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
- MapOfStructures["CommonCarotidArteryLeft"] = GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArteryLeft");
- MapOfStructures["CommonCarotidArteryRight"] = GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArteryRight");
- MapOfStructures["SubclavianArteryLeft"] = GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryLeft");
- MapOfStructures["SubclavianArteryRight"] = GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryRight");
- MapOfStructures["Thyroid"] = GetAFDB()->template GetImage<MaskImageType>("Thyroid");
- MapOfStructures["Aorta"] = GetAFDB()->template GetImage<MaskImageType>("Aorta");
- MapOfStructures["Trachea"] = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+ MapOfStructures["BrachioCephalicArtery"] = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
+ MapOfStructures["BrachioCephalicVein"] = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
+ MapOfStructures["CommonCarotidArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("LeftCommonCarotidArtery");
+ MapOfStructures["CommonCarotidArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("RightCommonCarotidArtery");
+ MapOfStructures["SubclavianArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("LeftSubclavianArtery");
+ MapOfStructures["SubclavianArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("RightSubclavianArtery");
+ MapOfStructures["Thyroid"] = this->GetAFDB()->template GetImage<MaskImageType>("Thyroid");
+ MapOfStructures["Aorta"] = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
+ MapOfStructures["Trachea"] = this->GetAFDB()->template GetImage<MaskImageType>("Trachea");
std::vector<std::string> ListOfStructuresNames;
// Create a temporay support
- // From first slice of BrachioCephalicVein to end of 3A
- MaskImagePointer support = GetAFDB()->template GetImage<MaskImageType>("Support_Sup_Carina");
+ // From first slice of BrachioCephalicVein to end of 3A or end of 2RL
+ MaskImagePointer support = this->GetAFDB()->template GetImage<MaskImageType>("Support_Sup_Carina");
MaskImagePointType p;
p[0] = p[1] = p[2] = 0.0; // to avoid warning
clitk::FindExtremaPointInAGivenDirection<MaskImageType>(MapOfStructures["BrachioCephalicVein"],
GetBackgroundValue(), 2, true, p);
double inf = p[2];
- clitk::FindExtremaPointInAGivenDirection<MaskImageType>(GetAFDB()->template GetImage<MaskImageType>("Support_S3A"),
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(this->GetAFDB()->template GetImage<MaskImageType>("Support_S3A"),
GetBackgroundValue(), 2, false, p);
+ MaskImagePointType p2;
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(this->GetAFDB()->template GetImage<MaskImageType>("Support_S2L"),
+ GetBackgroundValue(), 2, false, p2);
+ if (p2[2] > p[2]) p = p2;
+
double sup = p[2]+support->GetSpacing()[2];//one slice more ?
support = clitk::CropImageAlongOneAxis<MaskImageType>(support, 2, inf, sup,
false, GetBackgroundValue());
false, GetBackgroundValue());
// Update the AFDB
- writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mhd");
- GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mhd");
- WriteAFDB();
+ writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mha");
+ this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mha");
+ this->WriteAFDB();
return binarizedContour;
/*
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+WriteImageSupport(std::string support)
+{
+ writeImage<MaskImageType>(m_ListOfSupports[support], this->GetAFDBPath()+"/"+"seg/Support_"+support+".mha");
+ this->GetAFDB()->SetImageFilename("Support_"+support, "seg/Support_"+support+".mha");
+}
+//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+WriteImageStation(std::string station)
+{
+ writeImage<MaskImageType>(m_ListOfStations[station], GetAFDB()->GetPath()+"/seg/Station"+station+".mha");
+ GetAFDB()->SetImageFilename("Station"+station, "seg/Station"+station+".mha");
+ WriteAFDB();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ComputeOverlapWithRef(std::string station)
+{
+ if (GetComputeStation(station)) {
+ MaskImagePointer ref = this->GetAFDB()->template GetImage <MaskImageType>("Station"+station+"_Ref");
+ typedef clitk::LabelImageOverlapMeasureFilter<MaskImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetInput(0, m_ListOfStations[station]);
+ filter->SetInput(1, ref);
+ filter->Update();
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ReadSupportLimits(std::string filename)
+{
+ m_ListOfSupportLimits.clear();
+ ifstream is;
+ openFileForReading(is, filename);
+ while (is) {
+ skipComment(is);
+ SupportLimitsType s;
+ s.Read(is);
+ if (is) m_ListOfSupportLimits.push_back(s);
+ }
+}
+//--------------------------------------------------------------------
+
#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff