Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
- ======================================================================-====*/
+ ===========================================================================**/
#ifndef CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
#define CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
{
// Default values
cmdline_parser_clitkExtractLymphStations_init(&mArgsInfo);
- InitializeImageType<3>();
+ InitializeImageType<3>(); // Only for 3D images
}
//--------------------------------------------------------------------
template<unsigned int Dim>
void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::InitializeImageType()
{
- ADD_IMAGE_TYPE(Dim, uchar);
- // ADD_IMAGE_TYPE(Dim, short);
- // ADD_IMAGE_TYPE(Dim, int);
- // ADD_IMAGE_TYPE(Dim, float);
+ ADD_IMAGE_TYPE(Dim, short); // Can add float later
}
//--------------------------------------------------------------------
mArgsInfo=a;
SetIOVerbose(mArgsInfo.verbose_flag);
if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
- if (mArgsInfo.mediastinum_given) AddInputFilename(mArgsInfo.mediastinum_arg);
- if (mArgsInfo.trachea_given) AddInputFilename(mArgsInfo.trachea_arg);
- if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
+ if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
+ if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void
+clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+ f->SetVerboseOptionFlag(mArgsInfo.verbose_flag);
+ f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
+ f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
+ f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
+ f->SetAFDBFilename(mArgsInfo.afdb_arg);
+ f->SetDistanceMaxToAnteriorPartOfTheSpine(mArgsInfo.maxAntSpine_arg);
+ f->SetFuzzyThresholdForS8(mArgsInfo.fuzzyThresholdForS8_arg);
+ f->SetInjectedThresholdForS8(mArgsInfo.injectedThresholdForS8_arg);
+
+ // Check multiple options for radius dilatation
+ /*
+ typename FilterType::MaskImagePointType p;
+ SetMultipleOptionMacro(mArgsInfo, esophagusDilatation, 3, p);
+ default ? = set before
+ exception if fail
+ */
+ typename FilterType::MaskImagePointType p;
+ p[0] = 7; p[1] = 5; p[2] = 0; // default value
+ if (mArgsInfo.esophagusDilatationForAnt_given == 3) {
+ for(uint i=0; i<3; i++)
+ p[i] = mArgsInfo.esophagusDilatationForAnt_arg[i];
+ }
+ else {
+ if (mArgsInfo.esophagusDilatationForAnt_given == 1) {
+ for(uint i=0; i<3; i++)
+ p[i] = mArgsInfo.esophagusDilatationForAnt_arg[0];
+ }
+ }
+ f->SetEsophagusDiltationForAnt(p);
+
+ p[0] = 5; p[1] = 10; p[2] = 1; // default value
+ if (mArgsInfo.esophagusDilatationForRight_given == 3) {
+ for(uint i=0; i<3; i++)
+ p[i] = mArgsInfo.esophagusDilatationForRight_arg[i];
+ }
+ else {
+ if (mArgsInfo.esophagusDilatationForRight_given == 1) {
+ for(uint i=0; i<3; i++)
+ p[i] = mArgsInfo.esophagusDilatationForRight_arg[0];
+ }
+ }
+ f->SetEsophagusDiltationForRight(p);
+
+ for(uint i=0; i<mArgsInfo.station_given; i++)
+ f->AddComputeStation(mArgsInfo.station_arg[i]);
+
+ // Station 7
+ f->SetFuzzyThresholdForS7("Bronchi", mArgsInfo.tS7_Bronchi_arg);
+ f->SetFuzzyThresholdForS7("LeftSuperiorPulmonaryVein", mArgsInfo.tS7_LeftSuperiorPulmonaryVein_arg);
+ f->SetFuzzyThresholdForS7("RightSuperiorPulmonaryVein", mArgsInfo.tS7_RightSuperiorPulmonaryVein_arg);
+ f->SetFuzzyThresholdForS7("RightPulmonaryArtery", mArgsInfo.tS7_RightPulmonaryArtery_arg);
+ f->SetFuzzyThresholdForS7("LeftPulmonaryArtery", mArgsInfo.tS7_LeftPulmonaryArtery_arg);
+ f->SetFuzzyThresholdForS7("SVC", mArgsInfo.tS7_SVC_arg);
}
//--------------------------------------------------------------------
void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
{
// Reading input
- typename ImageType::Pointer mediastinum = this->template GetInput<ImageType>(0);
- typename ImageType::Pointer trachea = this->template GetInput<ImageType>(1);
+ typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
// Create filter
typedef clitk::ExtractLymphStationsFilter<ImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
// Set global Options
- filter->SetInputMediastinumLabelImage(mediastinum, 0); // change 0 with BG
- filter->SetInputTracheaLabelImage(trachea, 0); // change 0 with BG
- filter->SetArgsInfo(mArgsInfo);
+ filter->SetInput(input);
+ SetOptionsFromArgsInfoToFilter<FilterType>(filter);
// Go !
filter->Update();
-
- // Check if error
- if (filter->HasError()) {
- SetLastError(filter->GetLastError());
- // No output
- return;
- }
// Write/Save results
- typename ImageType::Pointer output = filter->GetOutput();
- this->template SetNextOutput<ImageType>(output);
+ typedef uchar MaskImagePixelType;
+ typedef itk::Image<MaskImagePixelType, 3> OutputImageType;
+ typename OutputImageType::Pointer output = filter->GetOutput();
+ this->template SetNextOutput<OutputImageType>(output);
}
//--------------------------------------------------------------------