X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.txx;h=1823e998c40cf228444cb29439c5adc760d5cd0e;hb=431fea9a7c825943b07fc4b4f3423355a5fee501;hp=7b2fd2ff91346aa16e10e96de0844af056ff999a;hpb=5e2af376544fce0c6dc46bb3c3227d35b501c1f1;p=clitk.git diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx index 7b2fd2f..1823e99 100644 --- a/segmentation/clitkExtractLymphStationsFilter.txx +++ b/segmentation/clitkExtractLymphStationsFilter.txx @@ -52,20 +52,12 @@ ExtractLymphStationsFilter(): SetBackgroundValue(0); SetForegroundValue(1); - // Station 7 - SetFuzzyThreshold(0.5); - SetStation7Filename("station7.mhd"); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -template -void -clitk::ExtractLymphStationsFilter:: -SetArgsInfo(ArgsInfoType & argsinfo) { - DD("SetArgsInfo"); + // Default values + ExtractStation_8_SetDefaultValues(); + ExtractStation_3P_SetDefaultValues(); + ExtractStation_2RL_SetDefaultValues(); + ExtractStation_3A_SetDefaultValues(); + ExtractStation_7_SetDefaultValues(); } //-------------------------------------------------------------------- @@ -78,29 +70,45 @@ GenerateOutputInformation() { // Get inputs LoadAFDB(); m_Input = dynamic_cast(itk::ProcessObject::GetInput(0)); - m_Support = GetAFDB()->template GetImage ("mediastinum"); - - // - typedef clitk::BooleanOperatorLabelImageFilter BFilter; - BFilter::Pointer merge = BFilter::New(); + m_Mediastinum = GetAFDB()->template GetImage ("Mediastinum"); + + // Extract Station8 + StartNewStep("Station 8"); + StartSubStep(); + ExtractStation_8(); + StopSubStep(); + + // Extract Station3P + StartNewStep("Station 3P"); + StartSubStep(); + ExtractStation_3P(); + StopSubStep(); + + // Extract Station2RL + StartNewStep("Station 2RL"); + StartSubStep(); + ExtractStation_2RL(); + StopSubStep(); + + // Extract Station3A + StartNewStep("Station 3A"); + StartSubStep(); + ExtractStation_3A(); + StopSubStep(); // Extract Station7 + StartNewStep("Station 7"); + StartSubStep(); ExtractStation_7(); - m_Output = m_Station7; - - // Extract Station4RL - ExtractStation_4RL(); + StopSubStep(); - writeImage(m_Station4RL, "s4rl.mhd"); - // writeImage(m_Output, "ouput.mhd"); - //writeImage(m_Working_Support, "ws.mhd"); - /*merge->SetInput1(m_Station7); - merge->SetInput2(m_Station4RL); // support - merge->SetOperationType(BFilter::AndNot); CHANGE OPERATOR - merge->SetForegroundValue(4); - merge->Update(); - m_Output = merge->GetOutput(); - */ + if (0) { // temporary suppress + // Extract Station4RL + StartNewStep("Station 4RL"); + StartSubStep(); + //ExtractStation_4RL(); + StopSubStep(); + } } //-------------------------------------------------------------------- @@ -110,7 +118,7 @@ template void clitk::ExtractLymphStationsFilter:: GenerateInputRequestedRegion() { - DD("GenerateInputRequestedRegion (nothing?)"); + //DD("GenerateInputRequestedRegion (nothing?)"); } //-------------------------------------------------------------------- @@ -120,23 +128,133 @@ template void clitk::ExtractLymphStationsFilter:: GenerateData() { - DD("GenerateData, graft output"); - // Final Step -> graft output (if SetNthOutput => redo) - this->GraftOutput(m_Output); + this->GraftOutput(m_ListOfStations["8"]); } //-------------------------------------------------------------------- +//-------------------------------------------------------------------- +template +bool +clitk::ExtractLymphStationsFilter:: +CheckForStation(std::string station) +{ + // Compute Station name + 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(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("Mediastinum", true); + return true; + } + else { + std::cout << "Station " << station << " found. I used it" << std::endl; + return false; + } +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +bool +clitk::ExtractLymphStationsFilter:: +GetComputeStation(std::string station) +{ + return (m_ComputeStationMap.find(station) != m_ComputeStationMap.end()); +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +AddComputeStation(std::string station) +{ + m_ComputeStationMap[station] = true; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8() +{ + if (CheckForStation("8")) { + ExtractStation_8_SI_Limits(); + ExtractStation_8_Post_Limits(); + ExtractStation_8_Ant_Sup_Limits(); + ExtractStation_8_Ant_Inf_Limits(); + ExtractStation_8_LR_1_Limits(); + ExtractStation_8_LR_2_Limits(); + ExtractStation_8_LR_Limits(); + ExtractStation_8_Ant_Injected_Limits(); + ExtractStation_8_Single_CCL_Limits(); + ExtractStation_8_Remove_Structures(); + // Store image filenames into AFDB + writeImage(m_ListOfStations["8"], "seg/Station8.mhd"); + GetAFDB()->SetImageFilename("Station8", "seg/Station8.mhd"); + WriteAFDB(); + } +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_3P() +{ + if (CheckForStation("3P")) { + ExtractStation_3P_SI_Limits(); + ExtractStation_3P_Ant_Limits(); + ExtractStation_3P_Post_Limits(); + ExtractStation_3P_LR_sup_Limits(); + // ExtractStation_3P_LR_sup_Limits_2(); + ExtractStation_3P_LR_inf_Limits(); + ExtractStation_8_Single_CCL_Limits(); // YES 8 ! + ExtractStation_3P_Remove_Structures(); // after CCL + // Store image filenames into AFDB + writeImage(m_ListOfStations["3P"], "seg/Station3P.mhd"); + GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd"); + WriteAFDB(); + } +} +//-------------------------------------------------------------------- + + //-------------------------------------------------------------------- template void clitk::ExtractLymphStationsFilter:: ExtractStation_7() { - DD("ExtractStation_7"); + if (CheckForStation("7")) { ExtractStation_7_SI_Limits(); ExtractStation_7_RL_Limits(); ExtractStation_7_Posterior_Limits(); + // ExtractStation_8_Single_CCL_Limits(); // Yes the same than 8 + ExtractStation_7_Remove_Structures(); + // Store image filenames into AFDB + writeImage(m_ListOfStations["7"], "seg/Station7.mhd"); + GetAFDB()->SetImageFilename("Station7", "seg/Station7.mhd"); + WriteAFDB(); + } } //-------------------------------------------------------------------- @@ -145,20 +263,114 @@ ExtractStation_7() { template void clitk::ExtractLymphStationsFilter:: -ExtractStation_4RL() { - DD("ExtractStation_4RL"); - writeImage(m_Support, "essai.mhd"); // OK +ExtractStation_3A() +{ + if (CheckForStation("3A")) { + ExtractStation_3A_SI_Limits(); + ExtractStation_3A_Ant_Limits(); + ExtractStation_3A_Post_Limits(); + // Store image filenames into AFDB + writeImage(m_ListOfStations["3A"], "seg/Station3A.mhd"); + GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd"); + WriteAFDB(); + } +} +//-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_2RL() +{ + if (CheckForStation("2RL")) { + ExtractStation_2RL_SI_Limits(); + ExtractStation_2RL_Post_Limits(); + ExtractStation_2RL_Ant_Limits2(); + ExtractStation_2RL_Ant_Limits(); + ExtractStation_2RL_LR_Limits(); + ExtractStation_2RL_Remove_Structures(); + ExtractStation_2RL_SeparateRL(); + + // Store image filenames into AFDB + writeImage(m_ListOfStations["2R"], "seg/Station2R.mhd"); + writeImage(m_ListOfStations["2L"], "seg/Station2L.mhd"); + GetAFDB()->SetImageFilename("Station2R", "seg/Station2R.mhd"); + GetAFDB()->SetImageFilename("Station2L", "seg/Station2L.mhd"); + WriteAFDB(); + } +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +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 +void +clitk::ExtractLymphStationsFilter:: +Remove_Structures(std::string station, std::string s) +{ + try { + StartNewStep("[Station"+station+"] Remove "+s); + MaskImagePointer Structure = GetAFDB()->template GetImage(s); + clitk::AndNot(m_Working_Support, Structure, GetBackgroundValue()); + } + catch(clitk::ExceptionObject e) { + std::cout << s << " not found, skip." << std::endl; + } +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +SetFuzzyThreshold(std::string station, std::string tag, double value) +{ + m_FuzzyThreshold[station][tag] = value; +} +//-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +template +double +clitk::ExtractLymphStationsFilter:: +GetFuzzyThreshold(std::string station, std::string tag) +{ + if (m_FuzzyThreshold.find(station) == m_FuzzyThreshold.end()) { + clitkExceptionMacro("Could not find options for station "+station+" in the list (while searching for tag "+tag+")."); + return 0.0; + } + + if (m_FuzzyThreshold[station].find(tag) == m_FuzzyThreshold[station].end()) { + clitkExceptionMacro("Could not find options "+tag+" in the list of FuzzyThreshold for station "+station+"."); + return 0.0; + } + + return m_FuzzyThreshold[station][tag]; } //-------------------------------------------------------------------- + #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX