--- /dev/null
+/*=========================================================================
+ 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://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ 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.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ======================================================================-====*/
+
+#ifndef CLITKEXTRACTMEDIASTINUMFILTER_TXX
+#define CLITKEXTRACTMEDIASTINUMFILTER_TXX
+
+// clitk
+#include "clitkCommon.h"
+#include "clitkExtractMediastinumFilter.h"
+#include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
+#include "clitkSegmentationFunctions.h"
+
+// itk
+#include <deque>
+#include "itkStatisticsLabelMapFilter.h"
+#include "itkLabelImageToStatisticsLabelMapFilter.h"
+#include "itkRegionOfInterestImageFilter.h"
+#include "itkBinaryThresholdImageFilter.h"
+
+// itk ENST
+#include "RelativePositionPropImageFilter.h"
+
+//--------------------------------------------------------------------
+template <class TImageType>
+clitk::ExtractMediastinumFilter<TImageType>::
+ExtractMediastinumFilter():
+ clitk::FilterBase(),
+ itk::ImageToImageFilter<TImageType, TImageType>()
+{
+ this->SetNumberOfRequiredInputs(3);
+
+ SetBackgroundValuePatient(0);
+ SetBackgroundValueLung(0);
+ SetBackgroundValueBones(0);
+ SetForegroundValueLeftLung(1);
+ SetForegroundValueRightLung(2);
+ SetBackgroundValue(0);
+ SetForegroundValue(1);
+
+ SetIntermediateSpacing(6);
+ SetFuzzyThreshold1(0.6);
+ SetFuzzyThreshold2(0.7);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinumFilter<TImageType>::
+SetInputPatientLabelImage(const TImageType * image, ImagePixelType bg) {
+ this->SetNthInput(0, const_cast<TImageType *>(image));
+ m_BackgroundValuePatient = bg;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinumFilter<TImageType>::
+SetInputLungLabelImage(const TImageType * image, ImagePixelType bg,
+ ImagePixelType fgLeft, ImagePixelType fgRight) {
+ this->SetNthInput(1, const_cast<TImageType *>(image));
+ m_BackgroundValueLung = bg;
+ m_ForegroundValueLeftLung = fgLeft;
+ m_ForegroundValueRightLung = fgRight;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinumFilter<TImageType>::
+SetInputBonesLabelImage(const TImageType * image, ImagePixelType bg) {
+ this->SetNthInput(2, const_cast<TImageType *>(image));
+ m_BackgroundValueBones = bg;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+template<class ArgsInfoType>
+void
+clitk::ExtractMediastinumFilter<TImageType>::
+SetArgsInfo(ArgsInfoType mArgsInfo)
+{
+ SetVerboseOption_GGO(mArgsInfo);
+ SetVerboseStep_GGO(mArgsInfo);
+ SetWriteStep_GGO(mArgsInfo);
+ SetVerboseWarningOff_GGO(mArgsInfo);
+
+ SetBackgroundValuePatient_GGO(mArgsInfo);
+ SetBackgroundValueLung_GGO(mArgsInfo);
+ SetBackgroundValueBones_GGO(mArgsInfo);
+
+ SetForegroundValueLeftLung_GGO(mArgsInfo);
+ SetForegroundValueRightLung_GGO(mArgsInfo);
+
+ SetIntermediateSpacing_GGO(mArgsInfo);
+ SetFuzzyThreshold1_GGO(mArgsInfo);
+ SetFuzzyThreshold2_GGO(mArgsInfo);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinumFilter<TImageType>::
+GenerateOutputInformation() {
+ ImagePointer input = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(0));
+ ImagePointer outputImage = this->GetOutput(0);
+ outputImage->SetRegions(outputImage->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinumFilter<TImageType>::
+GenerateInputRequestedRegion() {
+ // Call default
+ Superclass::GenerateInputRequestedRegion();
+ // Get input pointers
+ ImagePointer patient = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(0));
+ ImagePointer lung = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(1));
+ ImagePointer bones = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(2));
+
+ patient->SetRequestedRegion(patient->GetLargestPossibleRegion());
+ lung->SetRequestedRegion(lung->GetLargestPossibleRegion());
+ bones->SetRequestedRegion(bones->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinumFilter<TImageType>::
+GenerateData() {
+ // Get input pointers
+ ImageConstPointer patient = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(0));
+ ImageConstPointer lung = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(1));
+ ImageConstPointer bones = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(2));
+
+ // Get output pointer
+ ImagePointer output;
+
+ // Step 1: patient minus lungs, minus bones
+ StartNewStep("Patient contours minus lungs and minus bones");
+ typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+ typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
+ boolFilter->InPlaceOn();
+ boolFilter->SetInput1(patient);
+ boolFilter->SetInput2(lung);
+ boolFilter->SetOperationType(BoolFilterType::AndNot);
+ boolFilter->Update();
+ boolFilter->SetInput1(boolFilter->GetOutput());
+ boolFilter->SetInput2(bones);
+ boolFilter->SetOperationType(BoolFilterType::AndNot);
+ boolFilter->Update();
+ output = boolFilter->GetOutput();
+
+ output = clitk::AutoCrop<ImageType>(output, GetBackgroundValue());
+ ////autoCropFilter->GetOutput(); typedef clitk::AutoCropFilter<ImageType> CropFilterType;
+ //typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ //cropFilter->SetInput(output);
+ //cropFilter->Update();
+ //output = cropFilter->GetOutput();
+
+ this->template StopCurrentStep<TImageType>(output);
+
+ // Step 2: LR limits from lung (need separate lung ?)
+ StartNewStep("Left/Right limits with lungs");
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<TImageType> RelPosFilterType;
+ typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+ relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ relPosFilter->VerboseStepOff();
+ relPosFilter->WriteStepOff();
+ relPosFilter->SetInput(output);
+ relPosFilter->SetInputObject(lung);
+ relPosFilter->SetOrientationType(RelPosFilterType::LeftTo);
+ relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
+ relPosFilter->Update();
+ output = relPosFilter->GetOutput();
+
+ relPosFilter->SetInput(output);
+ relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ relPosFilter->VerboseStepOff();
+ relPosFilter->WriteStepOff();
+ relPosFilter->SetInputObject(lung);
+ relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
+ relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
+ relPosFilter->Update();
+ output = relPosFilter->GetOutput();
+ this->template StopCurrentStep<TImageType>(output);
+
+ // Step 3: AP limits from bones
+ StartNewStep("Ant/Post limits with bones");
+ relPosFilter->SetCurrentStepNumber(0);
+ relPosFilter->ResetPipeline();// = RelPosFilterType::New();
+ relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ relPosFilter->VerboseStepOff();
+ relPosFilter->WriteStepOff();
+ relPosFilter->SetInput(output);
+ relPosFilter->SetInputObject(bones);
+ relPosFilter->SetOrientationType(RelPosFilterType::AntTo);
+ relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
+ relPosFilter->Update();
+
+ relPosFilter->SetInput(relPosFilter->GetOutput());
+ relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ relPosFilter->VerboseStepOff();
+ relPosFilter->WriteStepOff();
+ relPosFilter->SetInputObject(bones);
+ relPosFilter->SetOrientationType(RelPosFilterType::PostTo);
+ relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
+ relPosFilter->Update();
+ output = relPosFilter->GetOutput();
+ this->template StopCurrentStep<TImageType>(output);
+
+ // Get CCL
+ output = clitk::Labelize<TImageType>(output, GetBackgroundValue(), true, 100);
+ // output = RemoveLabels<TImageType>(output, BG, param->GetLabelsToRemove());
+ output = clitk::KeepLabels<TImageType>(output, GetBackgroundValue(),
+ GetForegroundValue(), 1, 1, 0);
+
+ output = clitk::AutoCrop<ImageType>(output, GetBackgroundValue());
+ // cropFilter = CropFilterType::New();
+ //cropFilter->SetInput(output);
+ //cropFilter->Update();
+ //output = cropFilter->GetOutput();
+
+ // Final Step -> set output
+ this->SetNthOutput(0, output);
+}
+//--------------------------------------------------------------------
+
+
+#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff