// clitk
#include "clitkFilterBase.h"
+#include "clitkCropLikeImageFilter.h"
// itk
#include <itkPasteImageFilter.h>
itkSetMacro(CombineWithOrFlag, bool);
itkBooleanMacro(CombineWithOrFlag);
+ itkGetConstMacro(FuzzyMapOnlyFlag, bool);
+ itkSetMacro(FuzzyMapOnlyFlag, bool);
+ itkBooleanMacro(FuzzyMapOnlyFlag);
+
+ typename FloatImageType::Pointer GetFuzzyMap() { return m_FuzzyMap; }
+
// I dont want to verify inputs information
virtual void VerifyInputInformation() { }
bool m_InverseOrientationFlag;
bool m_RemoveObjectFlag;
bool m_CombineWithOrFlag;
+ bool m_FuzzyMapOnlyFlag;
virtual void GenerateOutputInformation();
virtual void GenerateInputRequestedRegion();
typename ImageType::Pointer working_image;
typename ImageType::Pointer object_resampled;
typename FloatImageType::Pointer relPos;
+ typename FloatImageType::Pointer m_FuzzyMap;
ImagePointer input;
ImagePointer object;
#include "clitkAutoCropFilter.h"
#include "clitkResampleImageWithOptionsFilter.h"
#include "clitkBooleanOperatorLabelImageFilter.h"
+#include "clitkCropLikeImageFilter.h"
// itk
#include <deque>
CombineWithOrFlagOff();
VerboseStepFlagOff();
WriteStepFlagOff();
+ FuzzyMapOnlyFlagOff();
}
//--------------------------------------------------------------------
typedef itk::RelativePositionPropImageFilter<ImageType, FloatImageType> RelPosFilterType;
typename RelPosFilterType::Pointer relPosFilter;
- typename FloatImageType::Pointer m_FuzzyMap;
for(int i=0; i<GetNumberOfAngles(); i++) {
// Compute fuzzy map
relPosFilter = RelPosFilterType::New();
#include "clitkCommon.h"
#include "clitkBooleanOperatorLabelImageFilter.h"
-#include "clitkSegmentationUtils.h"
+#include "clitkBoundingBoxUtils.h"
namespace clitk {
--- /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 CLITKBOUNDINGBOXUTILS_H
+#define CLITKBOUNDINGBOXUTILS_H
+
+// clitk
+#include "clitkCommon.h"
+
+// itk
+#include <itkBoundingBox.h>
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void ComputeBBFromImageRegion(const ImageType * image,
+ typename ImageType::RegionType region,
+ typename itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension>::Pointer bb);
+
+ //--------------------------------------------------------------------
+ template<int Dimension>
+ void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
+ typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
+ typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2);
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void ComputeRegionFromBB(const ImageType * image,
+ const typename itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension>::Pointer bb,
+ typename ImageType::RegionType & region);
+} // end clitk namespace
+
+#include "clitkBoundingBoxUtils.txx"
+
+#endif
--- /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://www.centreleonberard.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
+ ======================================================================-====*/
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void ComputeBBFromImageRegion(const ImageType * image,
+ typename ImageType::RegionType region,
+ typename itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension>::Pointer bb) {
+ typedef typename ImageType::IndexType IndexType;
+ IndexType firstIndex;
+ IndexType lastIndex;
+ for(unsigned int i=0; i<image->GetImageDimension(); i++) {
+ firstIndex[i] = region.GetIndex()[i];
+ lastIndex[i] = firstIndex[i]+region.GetSize()[i];
+ }
+
+ typedef itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension> BBType;
+ typedef typename BBType::PointType PointType;
+ PointType lastPoint;
+ PointType firstPoint;
+ image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
+ image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
+
+ bb->SetMaximum(lastPoint);
+ bb->SetMinimum(firstPoint);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<int Dimension>
+ void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
+ typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
+ typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
+
+ typedef itk::BoundingBox<unsigned long, Dimension> BBType;
+ typedef typename BBType::PointType PointType;
+ PointType lastPoint;
+ PointType firstPoint;
+
+ for(unsigned int i=0; i<Dimension; i++) {
+ firstPoint[i] = std::max(bbi1->GetMinimum()[i],
+ bbi2->GetMinimum()[i]);
+ lastPoint[i] = std::min(bbi1->GetMaximum()[i],
+ bbi2->GetMaximum()[i]);
+ }
+
+ bbo->SetMaximum(lastPoint);
+ bbo->SetMinimum(firstPoint);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ void ComputeRegionFromBB(const ImageType * image,
+ const typename itk::BoundingBox<unsigned long,
+ ImageType::ImageDimension>::Pointer bb,
+ typename ImageType::RegionType & region) {
+ // Types
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::PointType PointType;
+ typedef typename ImageType::RegionType RegionType;
+ typedef typename ImageType::SizeType SizeType;
+
+ // Region starting point
+ IndexType regionStart;
+ PointType start = bb->GetMinimum();
+ image->TransformPhysicalPointToIndex(start, regionStart);
+
+ // Region size
+ SizeType regionSize;
+ PointType maxs = bb->GetMaximum();
+ PointType mins = bb->GetMinimum();
+ for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
+ regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
+ }
+
+ // Create region
+ region.SetIndex(regionStart);
+ region.SetSize(regionSize);
+ }
+ //--------------------------------------------------------------------
+
+
+} // end of namespace
+
}; // end class
//--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ // Convenient function
+ template<class ImageType>
+ typename ImageType::Pointer
+ ResizeImageLike(const ImageType * input,
+ const itk::ImageBase<ImageType::ImageDimension> * like,
+ typename ImageType::PixelType BG);
+
} // end namespace clitk
//--------------------------------------------------------------------
#include "clitkCommon.h"
#include "clitkPasteImageFilter.h"
-// itk
-//#include "itkPasteImageFilter.h"
-
//--------------------------------------------------------------------
template <class ImageType>
clitk::CropLikeImageFilter<ImageType>::
}
//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::ResizeImageLike(const ImageType * input,
+ const itk::ImageBase<ImageType::ImageDimension> * like,
+ typename ImageType::PixelType backgroundValue)
+{
+ typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(input);
+ cropFilter->SetCropLikeImage(like);
+ cropFilter->SetBackgroundValue(backgroundValue);
+ cropFilter->Update();
+ return cropFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
-#endif //#define CLITKAUTOCROPFILTER
+#endif //#define CLITKCROPLIKEIMAGEFILTER_TXX
--- /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://www.centreleonberard.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 CLITKRELATIVEPOSITIONANALYZERFILTER_H
+#define CLITKRELATIVEPOSITIONANALYZERFILTER_H
+
+// clitk
+#include "clitkCommon.h"
+
+// itk
+#include <itkImageToImageFilter.h>
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ /*
+ TODO
+ */
+ //--------------------------------------------------------------------
+
+ template <class ImageType>
+ class ITK_EXPORT RelativePositionAnalyzerFilter:
+ public itk::ImageToImageFilter<ImageType, ImageType>
+ {
+
+ public:
+ /** Standard class typedefs. */
+ typedef itk::ImageToImageFilter<ImageType, ImageType> Superclass;
+ typedef RelativePositionAnalyzerFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(RelativePositionAnalyzerFilter, ImageToImageFilter);
+
+ /** Some convenient typedefs. */
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::RegionType RegionType;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::SpacingType SpacingType;
+ typedef typename ImageType::SizeType SizeType;
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::PointType PointType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
+ typedef itk::Image<float, ImageDimension> FloatImageType;
+
+ /** Input : initial image and object */
+ void SetInputSupport(const ImageType * image);
+ void SetInputObject(const ImageType * image);
+ void SetInputTarget(const ImageType * image);
+
+ // Options
+ itkSetMacro(VerboseFlag, bool);
+ itkGetConstMacro(VerboseFlag, bool);
+ itkBooleanMacro(VerboseFlag);
+
+ itkGetConstMacro(BackgroundValue, PixelType);
+ itkSetMacro(BackgroundValue, PixelType);
+
+ itkGetConstMacro(ForegroundValue, PixelType);
+ itkSetMacro(ForegroundValue, PixelType);
+
+ // For debug
+ void PrintOptions();
+
+ protected:
+ RelativePositionAnalyzerFilter();
+ virtual ~RelativePositionAnalyzerFilter() {}
+
+ bool m_VerboseFlag;
+ PixelType m_BackgroundValue;
+ PixelType m_ForegroundValue;
+ ImagePointer m_Support;
+ ImagePointer m_Object;
+ ImagePointer m_Target;
+
+ virtual void GenerateData();
+
+ private:
+ RelativePositionAnalyzerFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkRelativePositionAnalyzerFilter.txx"
+#endif
+
+#endif
--- /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://www.centreleonberard.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
+ ===========================================================================**/
+
+//--------------------------------------------------------------------
+template <class ImageType>
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+RelativePositionAnalyzerFilter():
+itk::ImageToImageFilter<ImageType, ImageType>()
+{
+ this->SetNumberOfRequiredInputs(3); // support, object, target
+ VerboseFlagOff();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+SetInputSupport(const ImageType * image)
+{
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput(0, const_cast<ImageType *>(image));
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+SetInputObject(const ImageType * image)
+{
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput(1, const_cast<ImageType *>(image));
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+SetInputTarget(const ImageType * image)
+{
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput(1, const_cast<ImageType *>(image));
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+PrintOptions()
+{
+ DD("TODO");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+GenerateData()
+{
+ DD("Update");
+ // Get input pointer
+ m_Support = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+ m_Object = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
+ m_Target = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(2));
+ static const unsigned int dim = ImageType::ImageDimension;
+
+ /*
+ Prerequisite:
+ - target fully inside support ?
+ */
+
+ //for(int i=0; i<m_ListOfOrientation.size(); i++) {
+ //DD(i);
+
+ // Compute Fuzzy map
+
+ // Get minimal value in the target area
+
+ // Or -> analyze floating point values inside the target area (histo ?)
+
+ // Set threshold and compute new support
+
+ // Compute ratio of area before/after
+ // http://www.itk.org/Doxygen/html/classitk_1_1LabelStatisticsImageFilter.html#details
+ /*
+ typedef itk::LabelStatisticsImageFilter<ImageType, ImageType> StatisticsImageFilterType;
+ typename StatisticsImageFilterType::Pointer statisticsFilter = StatisticsImageFilterType::New();
+ statisticsFilter->SetInput(m_Input);
+ statisticsFilter->SetLabelInput(m_Input);
+ statisticsFilter->Update();
+ int n = labelStatisticsImageFilter->GetCount(GetForegroundValue());
+ DD(n);
+ statisticsFilter = StatisticsImageFilterType::New();
+ statisticsFilter->SetInput(m_Output);
+ statisticsFilter->SetLabelInput(m_Output);
+ statisticsFilter->Update();
+ int m = labelStatisticsImageFilter->GetCount(GetForegroundValue());
+ DD(m);
+ */
+
+ // Print results
+
+ //}
+
+
+ // Final Step -> set output TODO
+ // this->SetNthOutput(0, working_image);
+ // this->GraftOutput(working_image);
+}
+//--------------------------------------------------------------------
+
namespace clitk {
//--------------------------------------------------------------------
- template<class ImageType>
- void ComputeBBFromImageRegion(const ImageType * image,
- typename ImageType::RegionType region,
- typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb);
-
- //--------------------------------------------------------------------
- template<int Dimension>
- void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
- typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
- typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2);
-
- //--------------------------------------------------------------------
- template<class ImageType>
- void ComputeRegionFromBB(const ImageType * image,
- const typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb,
- typename ImageType::RegionType & region);
- //--------------------------------------------------------------------
template<class TInternalImageType, class TMaskInternalImageType>
typename TInternalImageType::Pointer
SetBackground(const TInternalImageType * input,
int minimalComponentSize,
LabelizeParameters<typename TImageType::PixelType> * param);
- //--------------------------------------------------------------------
- template<class ImageType>
- typename ImageType::Pointer
- ResizeImageLike(const ImageType * input,
- const itk::ImageBase<ImageType::ImageDimension> * like,
- typename ImageType::PixelType BG);
-
//--------------------------------------------------------------------
template<class MaskImageType>
namespace clitk {
- //--------------------------------------------------------------------
- template<class ImageType>
- void ComputeBBFromImageRegion(const ImageType * image,
- typename ImageType::RegionType region,
- typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb) {
- typedef typename ImageType::IndexType IndexType;
- IndexType firstIndex;
- IndexType lastIndex;
- for(unsigned int i=0; i<image->GetImageDimension(); i++) {
- firstIndex[i] = region.GetIndex()[i];
- lastIndex[i] = firstIndex[i]+region.GetSize()[i];
- }
-
- typedef itk::BoundingBox<unsigned long,
- ImageType::ImageDimension> BBType;
- typedef typename BBType::PointType PointType;
- PointType lastPoint;
- PointType firstPoint;
- image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
- image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
-
- bb->SetMaximum(lastPoint);
- bb->SetMinimum(firstPoint);
- }
- //--------------------------------------------------------------------
-
-
- //--------------------------------------------------------------------
- template<int Dimension>
- void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
- typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
- typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
-
- typedef itk::BoundingBox<unsigned long, Dimension> BBType;
- typedef typename BBType::PointType PointType;
- PointType lastPoint;
- PointType firstPoint;
-
- for(unsigned int i=0; i<Dimension; i++) {
- firstPoint[i] = std::max(bbi1->GetMinimum()[i],
- bbi2->GetMinimum()[i]);
- lastPoint[i] = std::min(bbi1->GetMaximum()[i],
- bbi2->GetMaximum()[i]);
- }
-
- bbo->SetMaximum(lastPoint);
- bbo->SetMinimum(firstPoint);
- }
- //--------------------------------------------------------------------
-
-
- //--------------------------------------------------------------------
- template<class ImageType>
- void ComputeRegionFromBB(const ImageType * image,
- const typename itk::BoundingBox<unsigned long,
- ImageType::ImageDimension>::Pointer bb,
- typename ImageType::RegionType & region) {
- // Types
- typedef typename ImageType::IndexType IndexType;
- typedef typename ImageType::PointType PointType;
- typedef typename ImageType::RegionType RegionType;
- typedef typename ImageType::SizeType SizeType;
-
- // Region starting point
- IndexType regionStart;
- PointType start = bb->GetMinimum();
- image->TransformPhysicalPointToIndex(start, regionStart);
-
- // Region size
- SizeType regionSize;
- PointType maxs = bb->GetMaximum();
- PointType mins = bb->GetMinimum();
- for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
- regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
- }
-
- // Create region
- region.SetIndex(regionStart);
- region.SetSize(regionSize);
- }
- //--------------------------------------------------------------------
-
//--------------------------------------------------------------------
template<class ImageType, class TMaskImageType>
typename ImageType::Pointer
//--------------------------------------------------------------------
- //--------------------------------------------------------------------
- template<class ImageType>
- typename ImageType::Pointer
- ResizeImageLike(const ImageType * input,
- const itk::ImageBase<ImageType::ImageDimension> * like,
- typename ImageType::PixelType backgroundValue)
- {
- typedef CropLikeImageFilter<ImageType> CropFilterType;
- typename CropFilterType::Pointer cropFilter = CropFilterType::New();
- cropFilter->SetInput(input);
- cropFilter->SetCropLikeImage(like);
- cropFilter->SetBackgroundValue(backgroundValue);
- cropFilter->Update();
- return cropFilter->GetOutput();
- }
- //--------------------------------------------------------------------
-
-
//--------------------------------------------------------------------
template<class MaskImageType>
typename MaskImageType::Pointer
bool autocropFlag,
bool singleObjectCCL)
{
- typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
+ typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
sliceRelPosFilter->VerboseStepFlagOff();
sliceRelPosFilter->WriteStepFlagOff();
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);
-
- */
+ GetAFDB()->template SetImage<MaskImageType>("Aorta_Dilated_Anteriorly", "seg/Aorta_Dilated_Anteriorly.mha", Aorta, false);
+ writeImage<MaskImageType>(Aorta, "seg/Aorta_Dilated_Anteriorly.mha");
+ GetAFDB()->Write();
-
StopCurrentStep<MaskImageType>(m_Working_Support);
m_ListOfStations["3A"] = m_Working_Support;
}
MaskImagePointType p;
p[0] = p[1] = p[2] = 0.0; // to avoid warning
clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Sternum, GetBackgroundValue(), 2, false, p);
+ // DD(p);
+ p[2] += Sternum->GetSpacing()[2]; // add one slice: start just superiorly
MaskImagePointer S1RL =
clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2,
p[2], true, GetBackgroundValue());
+++ /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 CLITKEXTRACTLYMPHSTATIONSFILTER_H
-#define CLITKEXTRACTLYMPHSTATIONSFILTER_H
-
-// clitk
-#include "clitkFilterBase.h"
-#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
-
-namespace clitk {
-
- //--------------------------------------------------------------------
- /*
- Try to extract the LymphStations part of a thorax CT.
- Inputs :
- - Patient label image
- - Lungs label image
- - Bones label image
- */
- //--------------------------------------------------------------------
-
- template <class TImageType>
- class ITK_EXPORT ExtractLymphStationsFilter:
- public virtual clitk::FilterBase,
- public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
- public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
- {
-
- public:
- /** Standard class typedefs. */
- typedef itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > Superclass;
- typedef ExtractLymphStationsFilter Self;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(ExtractLymphStationsFilter, InPlaceImageFilter);
-
- /** Some convenient typedefs. */
- typedef TImageType ImageType;
- typedef typename ImageType::ConstPointer ImageConstPointer;
- typedef typename ImageType::Pointer ImagePointer;
- typedef typename ImageType::RegionType ImageRegionType;
- typedef typename ImageType::PixelType ImagePixelType;
- typedef typename ImageType::SizeType ImageSizeType;
- typedef typename ImageType::IndexType ImageIndexType;
- typedef typename ImageType::PointType ImagePointType;
-
- typedef uchar MaskImagePixelType;
- typedef itk::Image<MaskImagePixelType, 3> MaskImageType;
- typedef typename MaskImageType::Pointer MaskImagePointer;
-
- /** Connect inputs */
- // void SetInput(const TImageType * image);
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int, TImageType::ImageDimension);
- FILTERBASE_INIT;
-
- itkGetConstMacro(BackgroundValue, ImagePixelType);
- itkGetConstMacro(ForegroundValue, ImagePixelType);
- itkSetMacro(BackgroundValue, ImagePixelType);
- itkSetMacro(ForegroundValue, ImagePixelType);
-
- itkSetMacro(FuzzyThreshold, double);
- itkGetConstMacro(FuzzyThreshold, double);
-
- protected:
- ExtractLymphStationsFilter();
- virtual ~ExtractLymphStationsFilter() {}
-
- virtual void GenerateOutputInformation();
- virtual void GenerateInputRequestedRegion();
- virtual void GenerateData();
-
- MaskImagePointer m_mediastinum;
- MaskImagePointer m_trachea;
- MaskImagePointer m_working_mediastinum;
- MaskImagePointer m_working_trachea;
- MaskImagePointer m_output;
-
- ImagePixelType m_BackgroundValue;
- ImagePixelType m_ForegroundValue;
- double m_CarinaZPositionInMM;
- bool m_CarinaZPositionInMMIsSet;
- double m_MiddleLobeBronchusZPositionInMM;
-
- double m_IntermediateSpacing;
- double m_FuzzyThreshold;
-
- private:
- ExtractLymphStationsFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- }; // end class
- //--------------------------------------------------------------------
-
-} // end namespace clitk
-//--------------------------------------------------------------------
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkExtractLymphStationsFilter.txx"
-#endif
-
-#endif
+++ /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 CLITKEXTRACTLYMPHSTATIONSFILTER_TXX
-#define CLITKEXTRACTLYMPHSTATIONSFILTER_TXX
-
-// clitk
-#include "clitkCommon.h"
-#include "clitkExtractLymphStationsFilter.h"
-#include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
-#include "clitkSegmentationUtils.h"
-#include "clitkAutoCropFilter.h"
-#include "clitkSegmentationUtils.h"
-#include "clitkSliceBySliceRelativePositionFilter.h"
-
-// itk
-#include <itkStatisticsLabelMapFilter.h>
-#include <itkLabelImageToStatisticsLabelMapFilter.h>
-#include <itkRegionOfInterestImageFilter.h>
-#include <itkBinaryThresholdImageFilter.h>
-#include <itkImageSliceConstIteratorWithIndex.h>
-#include <itkImageSliceIteratorWithIndex.h>
-#include <itkBinaryThinningImageFilter.h>
-
-// itk ENST
-#include "RelativePositionPropImageFilter.h"
-
-//--------------------------------------------------------------------
-template <class TImageType>
-clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractLymphStationsFilter():
- clitk::FilterBase(),
- clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
- itk::ImageToImageFilter<TImageType, MaskImageType>()
-{
- this->SetNumberOfRequiredInputs(1);
- SetBackgroundValue(0);
- SetForegroundValue(1);
- SetFuzzyThreshold(0.5);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateOutputInformation() {
- // Superclass::GenerateOutputInformation();
-
- // Get input
- LoadAFDB();
- m_mediastinum = GetAFDB()->template GetImage <MaskImageType>("mediastinum");
- m_trachea = GetAFDB()->template GetImage <MaskImageType>("trachea");
- ImagePointType carina;
- GetAFDB()->GetPoint3D("carina", carina);
- m_CarinaZPositionInMM = carina[2];
- DD(m_CarinaZPositionInMM);
- ImagePointType mlb;
- GetAFDB()->GetPoint3D("middleLobeBronchus", mlb);
- m_MiddleLobeBronchusZPositionInMM = mlb[2];
- DD(m_MiddleLobeBronchusZPositionInMM);
-
- // ----------------------------------------------------------------
- // ----------------------------------------------------------------
- // Superior limit = carina
- // Inferior limit = origin right middle lobe bronchus
- StartNewStep("Inf/Sup mediastinum limits with carina/bronchus");
- m_working_mediastinum =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_mediastinum, 2,
- m_MiddleLobeBronchusZPositionInMM,
- m_CarinaZPositionInMM, true,
- GetBackgroundValue());
- StopCurrentStep<MaskImageType>(m_working_mediastinum);
- m_output = m_working_mediastinum;
-
- // ----------------------------------------------------------------
- // ----------------------------------------------------------------
- // Superior limit = carina
- // Inferior limit = origin right middle lobe bronchus
- StartNewStep("Inf/Sup trachea limits with carina/bronchus");
- m_working_trachea =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_trachea, 2,
- m_MiddleLobeBronchusZPositionInMM,
- m_CarinaZPositionInMM, true,
- GetBackgroundValue());
- StopCurrentStep<MaskImageType>(m_working_trachea);
-
- // ----------------------------------------------------------------
- // ----------------------------------------------------------------
- // Separate trachea in two CCL
- StartNewStep("Separate trachea under carina");
-
- // Labelize and consider two main labels
- m_working_trachea = Labelize<MaskImageType>(m_working_trachea, 0, true, 1);
-
- // Carina position must at the first slice that separate the two main bronchus (not superiorly)
- // Check that upper slice is composed of at least two labels
- typedef itk::ImageSliceIteratorWithIndex<MaskImageType> SliceIteratorType;
- SliceIteratorType iter(m_working_trachea, m_working_trachea->GetLargestPossibleRegion());
- iter.SetFirstDirection(0);
- iter.SetSecondDirection(1);
- iter.GoToReverseBegin(); // Start from the end (because image is IS not SI)
- int maxLabel=0;
- while (!iter.IsAtReverseEndOfSlice()) {
- while (!iter.IsAtReverseEndOfLine()) {
- // DD(iter.GetIndex());
- if (iter.Get() > maxLabel) maxLabel = iter.Get();
- --iter;
- }
- iter.PreviousLine();
- }
- if (maxLabel < 2) {
- clitkExceptionMacro("First slice form Carina does not seems to seperate the two main bronchus. Abort");
- }
-
- // Compute centroid of both parts to identify the left from the right bronchus
- typedef long LabelType;
- static const unsigned int Dim = ImageType::ImageDimension;
- typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
- typedef itk::LabelMap< LabelObjectType > LabelMapType;
- typedef itk::LabelImageToLabelMapFilter<MaskImageType, LabelMapType> ImageToMapFilterType;
- typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
- typedef itk::ShapeLabelMapFilter<LabelMapType, MaskImageType> ShapeFilterType;
- typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
- imageToLabelFilter->SetBackgroundValue(GetBackgroundValue());
- imageToLabelFilter->SetInput(m_working_trachea);
- statFilter->SetInput(imageToLabelFilter->GetOutput());
- statFilter->Update();
- typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
-
- ImagePointType C1 = labelMap->GetLabelObject(1)->GetCentroid();
- ImagePointType C2 = labelMap->GetLabelObject(2)->GetCentroid();
-
- ImagePixelType leftLabel;
- ImagePixelType rightLabel;
- if (C1[0] < C2[0]) { leftLabel = 1; rightLabel = 2; }
- else { leftLabel = 2; rightLabel = 1; }
- DD(leftLabel);
- DD(rightLabel);
-
- StopCurrentStep<MaskImageType>(m_working_trachea);
-
- //-----------------------------------------------------
- StartNewStep("Left limits with bronchus (slice by slice)");
- // Select LeftLabel (set one label to Backgroundvalue)
- MaskImagePointer leftBronchus =
- SetBackground<MaskImageType, MaskImageType>(m_working_trachea, m_working_trachea,
- rightLabel, GetBackgroundValue());
- MaskImagePointer rightBronchus =
- SetBackground<MaskImageType, MaskImageType>(m_working_trachea, m_working_trachea,
- leftLabel, GetBackgroundValue());
- writeImage<MaskImageType>(leftBronchus, "left.mhd");
- writeImage<MaskImageType>(rightBronchus, "right.mhd");
-
- m_working_mediastinum =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_working_mediastinum,
- leftBronchus, 2,
- GetFuzzyThreshold(), "RightTo",
- true, 4);
- m_working_mediastinum =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_working_mediastinum,
- rightBronchus,
- 2, GetFuzzyThreshold(), "LeftTo",
- true, 4);
- m_working_mediastinum =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_working_mediastinum,
- leftBronchus,
- 2, GetFuzzyThreshold(), "AntTo",
- true, 4, true); // NOT
- m_working_mediastinum =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_working_mediastinum,
- rightBronchus,
- 2, GetFuzzyThreshold(), "AntTo",
- true, 4, true);
- m_working_mediastinum =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_working_mediastinum,
- leftBronchus,
- 2, GetFuzzyThreshold(), "PostTo",
- true, 4, true);
- m_working_mediastinum =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_working_mediastinum,
- rightBronchus,
- 2, GetFuzzyThreshold(), "PostTo",
- true, 4, true);
- m_output = m_working_mediastinum;
- StopCurrentStep<MaskImageType>(m_output);
-
- //-----------------------------------------------------
- //-----------------------------------------------------
- StartNewStep("Posterior limits");
-
- // Left Bronchus slices
- typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
- typedef typename ExtractSliceFilterType::SliceType SliceType;
- typename ExtractSliceFilterType::Pointer
- extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(leftBronchus);
- extractSliceFilter->SetDirection(2);
- extractSliceFilter->Update();
- std::vector<typename SliceType::Pointer> leftBronchusSlices;
- extractSliceFilter->GetOutputSlices(leftBronchusSlices);
-
- // Right Bronchus slices
- extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(rightBronchus);
- extractSliceFilter->SetDirection(2);
- extractSliceFilter->Update();
- std::vector<typename SliceType::Pointer> rightBronchusSlices ;
- extractSliceFilter->GetOutputSlices(rightBronchusSlices);
-
- assert(leftBronchusSlices.size() == rightBronchusSlices.size());
-
- std::vector<MaskImageType::PointType> leftPoints;
- std::vector<MaskImageType::PointType> rightPoints;
- for(uint i=0; i<leftBronchusSlices.size(); i++) {
- // Keep main CCL
- leftBronchusSlices[i] = Labelize<SliceType>(leftBronchusSlices[i], 0, true, 10);
- leftBronchusSlices[i] = KeepLabels<SliceType>(leftBronchusSlices[i],
- GetBackgroundValue(),
- GetForegroundValue(), 1, 1, true);
- rightBronchusSlices[i] = Labelize<SliceType>(rightBronchusSlices[i], 0, true, 10);
- rightBronchusSlices[i] = KeepLabels<SliceType>(rightBronchusSlices[i],
- GetBackgroundValue(),
- GetForegroundValue(), 1, 1, true);
- double distance_max_from_center_point = 15;
-
- // ------- Find point in left Bronchus -------
- // find right most point in left = rightMost
- SliceType::PointType a;
- SliceType::PointType rightMost =
- clitk::FindExtremaPointInAGivenDirection<SliceType>(leftBronchusSlices[i],
- GetBackgroundValue(),
- 0, false, a, 0);
- // find post most point in left, not far away from rightMost
- SliceType::PointType p =
- clitk::FindExtremaPointInAGivenDirection<SliceType>(leftBronchusSlices[i],
- GetBackgroundValue(),
- 1, false, rightMost,
- distance_max_from_center_point);
- MaskImageType::PointType pp;
- pp[0] = p[0]; pp[1] = p[1];
- pp[2] = i*leftBronchus->GetSpacing()[2] + leftBronchus->GetOrigin()[2];
- leftPoints.push_back(pp);
-
- // ------- Find point in right Bronchus -------
- // find left most point in right = leftMost
- SliceType::PointType leftMost =
- clitk::FindExtremaPointInAGivenDirection<SliceType>(rightBronchusSlices[i],
- GetBackgroundValue(),
- 0, true, a, 0);
- // find post most point in left, not far away from leftMost
- p = clitk::FindExtremaPointInAGivenDirection<SliceType>(rightBronchusSlices[i],
- GetBackgroundValue(),
- 1, false, leftMost,
- distance_max_from_center_point);
- pp[0] = p[0]; pp[1] = p[1];
- pp[2] = i*rightBronchus->GetSpacing()[2] + rightBronchus->GetOrigin()[2];
- rightPoints.push_back(pp);
- }
-
- // DEBUG
- std::ofstream osl;
- openFileForWriting(osl, "left.txt");
- osl << "LANDMARKS1" << std::endl;
- std::ofstream osr;
- openFileForWriting(osr, "right.txt");
- osr << "LANDMARKS1" << std::endl;
- for(uint i=0; i<leftBronchusSlices.size(); i++) {
- osl << i << " " << leftPoints[i][0] << " " << leftPoints[i][1]
- << " " << leftPoints[i][2] << " 0 0 " << std::endl;
- osr << i << " " << rightPoints[i][0] << " " << rightPoints[i][1]
- << " " << rightPoints[i][2] << " 0 0 " << std::endl;
- }
- osl.close();
- osr.close();
-
- // Now uses these points to limit, slice by slice
- // http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
- /*
- Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
- (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
- This will equal zero if the point C is on the line formed by points A and B, and will have a different sign depending on the side. Which side this is depends on the orientation of your (x,y) coordinates, but you can plug test values for A,B and C into this formula to determine whether negative values are to the left or to the right.
-
- => to accelerate, start with formula, when change sign -> stop and fill
- */
- // typedef itk::ImageSliceIteratorWithIndex<MaskImageType> SliceIteratorType;
- iter = SliceIteratorType(m_working_mediastinum, m_working_mediastinum->GetLargestPossibleRegion());
- iter.SetFirstDirection(0);
- iter.SetSecondDirection(1);
- iter.GoToBegin();
- int i=0;
- MaskImageType::PointType A;
- MaskImageType::PointType B;
- MaskImageType::PointType C;
- while (!iter.IsAtEnd()) {
- A = leftPoints[i];
- B = rightPoints[i];
- C = A;
- C[1] -= 10; // I know I must keep this point
- double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
- bool isPositive = s<0;
- while (!iter.IsAtEndOfSlice()) {
- while (!iter.IsAtEndOfLine()) {
- // Very slow, I know ... but image should be very small
- m_working_mediastinum->TransformIndexToPhysicalPoint(iter.GetIndex(), C);
- double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
- if (s == 0) iter.Set(2);
- if (isPositive) {
- if (s > 0) iter.Set(GetBackgroundValue());
- }
- else {
- if (s < 0) iter.Set(GetBackgroundValue());
- }
- ++iter;
- }
- iter.NextLine();
- }
- iter.NextSlice();
- ++i;
- }
-
- //-----------------------------------------------------
- //-----------------------------------------------------
- // StartNewStep("Anterior limits");
-
-
- // MISSING FROM NOW
-
- // Station 4R, Station 4L, the right pulmonary artery, and/or the
- // left superior pulmonary vein
-
-
- //-----------------------------------------------------
- //-----------------------------------------------------
- // ALSO SUBSTRACT ARTERY/VEIN (initially in the support)
-
-
- // Set output image information (required)
- MaskImagePointer outputImage = this->GetOutput(0);
- outputImage->SetRegions(m_working_mediastinum->GetLargestPossibleRegion());
- outputImage->SetOrigin(m_working_mediastinum->GetOrigin());
- outputImage->SetRequestedRegion(m_working_mediastinum->GetLargestPossibleRegion());
-
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateInputRequestedRegion() {
- DD("GenerateInputRequestedRegion");
- // Call default
- // Superclass::GenerateInputRequestedRegion();
- // Following needed because output region can be greater than input (trachea)
- //ImagePointer mediastinum = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(0));
- //ImagePointer trachea = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(1));
- DD("set reg");
- m_mediastinum->SetRequestedRegion(m_mediastinum->GetLargestPossibleRegion());
- m_trachea->SetRequestedRegion(m_trachea->GetLargestPossibleRegion());
- DD("end");
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateData() {
- DD("GenerateData");
- // Final Step -> graft output (if SetNthOutput => redo)
- this->GraftOutput(m_output);
-}
-//--------------------------------------------------------------------
-
-
-#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
z = this->GetAFDB()->GetDouble("CarinaZ");
}
catch(clitk::ExceptionObject e) {
- DD("FindCarinaSlicePosition");
+ //DD("FindCarinaSlicePosition");
// Get Carina
MaskImagePointer Carina = this->GetAFDB()->template GetImage<MaskImageType>("Carina");
z = this->GetAFDB()->GetDouble("ApexOfTheChestZ");
}
catch(clitk::ExceptionObject e) {
- DD("FindApexOfTheChestPosition");
+ //DD("FindApexOfTheChestPosition");
MaskImagePointer Lungs = this->GetAFDB()->template GetImage<MaskImageType>("Lungs");
MaskImagePointType p;
p[0] = p[1] = p[2] = 0.0; // to avoid warning
z = this->GetAFDB()->GetDouble("SuperiorBorderOfAorticArchZ");
}
catch(clitk::ExceptionObject e) {
- DD("FindSuperiorBorderOfAorticArch");
+ // DD("FindSuperiorBorderOfAorticArch");
MaskImagePointer Aorta = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
MaskImagePointType p;
p[0] = p[1] = p[2] = 0.0; // to avoid warning
z = this->GetAFDB()->GetDouble("InferiorBorderOfAorticArchZ");
}
catch(clitk::ExceptionObject e) {
- DD("FindInferiorBorderOfAorticArch");
+ //DD("FindInferiorBorderOfAorticArch");
MaskImagePointer Aorta = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
std::vector<MaskSlicePointer> slices;
clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
+++ /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 CLITKEXTRACTLYMPHSTATIONSFILTER_TXX
-#define CLITKEXTRACTLYMPHSTATIONSFILTER_TXX
-
-// clitk
-#include "clitkCommon.h"
-#include "clitkExtractLymphStationsFilter.h"
-#include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
-#include "clitkSegmentationUtils.h"
-#include "clitkAutoCropFilter.h"
-#include "clitkSegmentationUtils.h"
-#include "clitkSliceBySliceRelativePositionFilter.h"
-
-// itk
-#include <itkStatisticsLabelMapFilter.h>
-#include <itkLabelImageToStatisticsLabelMapFilter.h>
-#include <itkRegionOfInterestImageFilter.h>
-#include <itkBinaryThresholdImageFilter.h>
-#include <itkImageSliceConstIteratorWithIndex.h>
-#include <itkBinaryThinningImageFilter.h>
-
-// itk ENST
-#include "RelativePositionPropImageFilter.h"
-
-//--------------------------------------------------------------------
-template <class TImageType>
-clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractLymphStationsFilter():
- clitk::FilterBase(),
- clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
- itk::ImageToImageFilter<TImageType, MaskImageType>()
-{
- this->SetNumberOfRequiredInputs(1);
- SetBackgroundValue(0);
- SetForegroundValue(1);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateOutputInformation() {
- // Superclass::GenerateOutputInformation();
-
- // Get input
- LoadAFDB();
- m_mediastinum = GetAFDB()->template GetImage <MaskImageType>("mediastinum");
- m_trachea = GetAFDB()->template GetImage <MaskImageType>("trachea");
- ImagePointType carina;
- GetAFDB()->GetPoint3D("carina", carina);
- DD(carina);
- m_CarinaZPositionInMM = carina[2];
- DD(m_CarinaZPositionInMM);
- ImagePointType mlb;
- GetAFDB()->GetPoint3D("middleLobeBronchus", mlb);
- m_MiddleLobeBronchusZPositionInMM = mlb[2];
- DD(m_MiddleLobeBronchusZPositionInMM);
-
- // ----------------------------------------------------------------
- // ----------------------------------------------------------------
- // Superior limit = carina
- // Inferior limit = origin right middle lobe bronchus
- StartNewStep("Inf/Sup mediastinum limits with carina/bronchus");
- ImageRegionType region = m_mediastinum->GetLargestPossibleRegion(); DD(region);
- ImageSizeType size = region.GetSize();
- ImageIndexType index = region.GetIndex();
- DD(m_CarinaZPositionInMM);
- DD(m_MiddleLobeBronchusZPositionInMM);
- index[2] = floor((m_MiddleLobeBronchusZPositionInMM - m_mediastinum->GetOrigin()[2]) / m_mediastinum->GetSpacing()[2]);
- size[2] = 1+ceil((m_CarinaZPositionInMM-m_MiddleLobeBronchusZPositionInMM) / m_mediastinum->GetSpacing()[2]); // +1 to
- region.SetSize(size);
- region.SetIndex(index);
- DD(region);
- typedef itk::RegionOfInterestImageFilter<MaskImageType, MaskImageType> CropFilterType;
- typename CropFilterType::Pointer cropFilter = CropFilterType::New();
- cropFilter->SetInput(m_mediastinum);
- cropFilter->SetRegionOfInterest(region);
- cropFilter->Update();
- m_working_image = cropFilter->GetOutput();
- // Auto Crop (because following rel pos is faster)
- m_working_image = clitk::AutoCrop<MaskImageType>(m_working_image, 0);
- StopCurrentStep<MaskImageType>(m_working_image);
- m_output = m_working_image;
-
- // ----------------------------------------------------------------
- // ----------------------------------------------------------------
- // Separate trachea in two CCL
- StartNewStep("Separate trachea under carina");
- // DD(region);
- ImageRegionType trachea_region = m_trachea->GetLargestPossibleRegion();
- for(int i=0; i<3; i++) {
- index[i] = floor(((index[i]*m_mediastinum->GetSpacing()[i])+m_mediastinum->GetOrigin()[i]
- -m_trachea->GetOrigin()[i])/m_trachea->GetSpacing()[i]);
- // DD(index[i]);
- size[i] = ceil((size[i]*m_mediastinum->GetSpacing()[i])/m_trachea->GetSpacing()[i]);
- // DD(size[i]);
- if (index[i] < 0) {
- size[i] += index[i];
- index[i] = 0;
- }
- if (size[i]+index[i] > (trachea_region.GetSize()[i] + trachea_region.GetIndex()[i])) {
- size[i] = trachea_region.GetSize()[i] + trachea_region.GetIndex()[i] - index[i];
- }
- }
- // DD(index);
- // DD(size);
- region.SetIndex(index);
- region.SetSize(size);
- // typedef itk::RegionOfInterestImageFilter<MaskImageType, MaskImageType> CropFilterType;
- // typename CropFilterType::Pointer
- cropFilter = CropFilterType::New();
- // m_trachea.Print(std::cout);
- cropFilter->SetInput(m_trachea);
- cropFilter->SetRegionOfInterest(region);
- cropFilter->Update();
- m_working_trachea = cropFilter->GetOutput();
-
- // Labelize and consider two main labels
- m_working_trachea = Labelize<MaskImageType>(m_working_trachea, 0, true, 1);
-
- // Detect wich label is at Left
- typedef itk::ImageSliceConstIteratorWithIndex<MaskImageType> SliceIteratorType;
- SliceIteratorType iter(m_working_trachea, m_working_trachea->GetLargestPossibleRegion());
- iter.SetFirstDirection(0);
- iter.SetSecondDirection(1);
- iter.GoToBegin();
- bool stop = false;
- ImagePixelType leftLabel;
- ImagePixelType rightLabel;
- while (!stop) {
- if (iter.Get() != GetBackgroundValue()) {
- // DD(iter.GetIndex());
- // DD((int)iter.Get());
- leftLabel = iter.Get();
- stop = true;
- }
- ++iter;
- }
- if (leftLabel == 1) rightLabel = 2;
- else rightLabel = 1;
- DD((int)leftLabel);
- DD((int)rightLabel);
-
- // End step
- StopCurrentStep<MaskImageType>(m_working_trachea);
-
- //-----------------------------------------------------
- /* DD("TEST Skeleton");
- typedef itk::BinaryThinningImageFilter<MaskImageType, MaskImageType> SkeletonFilterType;
- typename SkeletonFilterType::Pointer skeletonFilter = SkeletonFilterType::New();
- skeletonFilter->SetInput(m_working_trachea);
- skeletonFilter->Update();
- writeImage<MaskImageType>(skeletonFilter->GetOutput(), "skel.mhd");
- writeImage<MaskImageType>(skeletonFilter->GetThinning(), "skel2.mhd");
- */
-
- //-----------------------------------------------------
- StartNewStep("Left limits with bronchus (slice by slice)");
- // Select LeftLabel (set right label to 0)
- MaskImagePointer temp = SetBackground<MaskImageType, MaskImageType>(m_working_trachea, m_working_trachea, rightLabel, 0);
- writeImage<MaskImageType>(temp, "temp1.mhd");
-
- m_working_image =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_working_image,
- temp,
- 2, GetFuzzyThreshold(), "RightTo");
- /*
- typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
- typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
- sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- sliceRelPosFilter->VerboseStepOn();
- sliceRelPosFilter->WriteStepOn();
- sliceRelPosFilter->SetInput(m_working_image);
- sliceRelPosFilter->SetInputObject(temp);
- sliceRelPosFilter->SetDirection(2);
- sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThreshold());
- sliceRelPosFilter->SetOrientationTypeString("RightTo");
- sliceRelPosFilter->Update();
- m_working_image = sliceRelPosFilter->GetOutput();*/
- writeImage<MaskImageType>(m_working_image, "afterslicebyslice.mhd");
-
-
- typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
- typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
-
-
- //-----------------------------------------------------
- StartNewStep("Right limits with bronchus (slice by slice)");
- // Select LeftLabel (set right label to 0)
- temp = SetBackground<MaskImageType, MaskImageType>(m_working_trachea, m_working_trachea, leftLabel, 0);
- writeImage<MaskImageType>(temp, "temp2.mhd");
-
- sliceRelPosFilter = SliceRelPosFilterType::New();
- sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- sliceRelPosFilter->VerboseStepOff();
- sliceRelPosFilter->WriteStepOff();
- sliceRelPosFilter->SetInput(m_working_image);
- sliceRelPosFilter->SetInputObject(temp);
- sliceRelPosFilter->SetDirection(2);
- sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThreshold());
- sliceRelPosFilter->SetOrientationTypeString("LeftTo");
- sliceRelPosFilter->Update();
- m_working_image = sliceRelPosFilter->GetOutput();
- writeImage<MaskImageType>(m_working_image, "afterslicebyslice.mhd");
- DD("end");
- m_output = m_working_image;
- StopCurrentStep<MaskImageType>(m_output);
-
- //-----------------------------------------------------
- StartNewStep("Trial Post position according to trachea");
- // Post: do not extend past the post wall of the 2 main bronchi
- sliceRelPosFilter = SliceRelPosFilterType::New();
- sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- sliceRelPosFilter->VerboseStepOn();
- sliceRelPosFilter->WriteStepOn();
- sliceRelPosFilter->SetInput(m_output);
- sliceRelPosFilter->SetInputObject(m_trachea);
- sliceRelPosFilter->SetDirection(2);
- sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThreshold());
- // It means "not PostTo" (different from AntTo)
- sliceRelPosFilter->NotFlagOn();
- //sliceRelPosFilter->SetOrientationType(SliceRelPosFilterType::RelPosFilterType::PostTo);
- sliceRelPosFilter->SetOrientationTypeString("PostTo");
- sliceRelPosFilter->Update();
- m_output = sliceRelPosFilter->GetOutput();
- writeImage<MaskImageType>(m_output, "postrelpos.mhd");
-
-
- // Set output image information (required)
- MaskImagePointer outputImage = this->GetOutput(0);
- outputImage->SetRegions(m_working_image->GetLargestPossibleRegion());
- outputImage->SetOrigin(m_working_image->GetOrigin());
- outputImage->SetRequestedRegion(m_working_image->GetLargestPossibleRegion());
- DD("end2");
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateInputRequestedRegion() {
- DD("GenerateInputRequestedRegion");
- // Call default
- // Superclass::GenerateInputRequestedRegion();
- // Following needed because output region can be greater than input (trachea)
- //ImagePointer mediastinum = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(0));
- //ImagePointer trachea = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(1));
- DD("set reg");
- m_mediastinum->SetRequestedRegion(m_mediastinum->GetLargestPossibleRegion());
- m_trachea->SetRequestedRegion(m_trachea->GetLargestPossibleRegion());
- DD("end");
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
-void
-clitk::ExtractLymphStationsFilter<TImageType>::
-GenerateData() {
- DD("GenerateData");
- // Final Step -> graft output (if SetNthOutput => redo)
- this->GraftOutput(m_output);
-}
-//--------------------------------------------------------------------
-
-
-#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
TARGET_LINK_LIBRARIES(clitkRelativePosition clitkCommon ${ITK_LIBRARIES})
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkRelativePosition)
+ WRAP_GGO(clitkLabelImageOverlapMeasure_GGO_C clitkLabelImageOverlapMeasure.ggo)
+ ADD_EXECUTABLE(clitkLabelImageOverlapMeasure clitkLabelImageOverlapMeasure.cxx ${clitkLabelImageOverlapMeasure_GGO_C})
+ TARGET_LINK_LIBRARIES(clitkLabelImageOverlapMeasure clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES} )
+ SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkLabelImageOverlapMeasure)
+
+ WRAP_GGO(clitkRelativePositionAnalyzer_GGO_C clitkRelativePositionAnalyzer.ggo)
+ ADD_EXECUTABLE(clitkRelativePositionAnalyzer clitkRelativePositionAnalyzer.cxx ${clitkRelativePositionAnalyzer_GGO_C})
+ TARGET_LINK_LIBRARIES(clitkRelativePositionAnalyzer clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES})
+ SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkRelativePositionAnalyzer)
+
WRAP_GGO(clitkTransformLandmarks_GGO_C clitkTransformLandmarks.ggo)
ADD_EXECUTABLE(clitkTransformLandmarks clitkTransformLandmarks.cxx ${clitkTransformLandmarks_GGO_C})
TARGET_LINK_LIBRARIES(clitkTransformLandmarks clitkCommon ${ITK_LIBRARIES})
--- /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://www.centreleonberard.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
+===========================================================================**/
+
+// clitk
+#include "clitkRelativePositionAnalyzer_ggo.h"
+#include "clitkRelativePositionAnalyzerGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkRelativePositionAnalyzer, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::RelativePositionAnalyzerGenericFilter<args_info_clitkRelativePositionAnalyzer> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+
+ try {
+ filter->Update();
+ } catch(std::runtime_error e) {
+ std::cout << e.what() << std::endl;
+ return EXIT_FAILURE;
+ }
+
+ return EXIT_SUCCESS;
+} // This is the end, my friend
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkRelativePositionAnalyzer.ggo
+package "clitkRelativePositionAnalyzer"
+version "1.0"
+purpose "Analyze relative position of a target according to structures"
+
+section "General options"
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
+option "imagetypes" - "Display allowed image types" flag off
+
+section "Input/Output"
+option "support" i "Input mask support" string yes
+option "object" j "Input mask object" string yes
+option "target" t "Input mask target" string yes
+option "output" o "Output image " string yes
+
--- /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://www.centreleonberard.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 CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H
+#define CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H
+
+// clitk
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkRelativePositionAnalyzerFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ template<class ArgsInfoType>
+ class ITK_EXPORT RelativePositionAnalyzerGenericFilter:
+ public ImageToImageGenericFilter<RelativePositionAnalyzerGenericFilter<ArgsInfoType> >
+ {
+ public:
+ //--------------------------------------------------------------------
+ RelativePositionAnalyzerGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageToImageGenericFilter<RelativePositionAnalyzerGenericFilter<ArgsInfoType> > Superclass;
+ typedef RelativePositionAnalyzerGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ itkNewMacro(Self);
+ itkTypeMacro(RelativePositionAnalyzerGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const ArgsInfoType & a);
+ template<class FilterType>
+ void SetOptionsFromArgsInfoToFilter(FilterType * f) ;
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class ImageType>
+ void UpdateWithInputImageType();
+
+ protected:
+ template<unsigned int Dim> void InitializeImageType();
+ ArgsInfoType mArgsInfo;
+
+ private:
+ RelativePositionAnalyzerGenericFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ };// end class
+ //--------------------------------------------------------------------
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkRelativePositionAnalyzerGenericFilter.txx"
+#endif
+
+#endif // #define CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H
--- /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://www.centreleonberard.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
+ ===========================================================================**/
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+RelativePositionAnalyzerGenericFilter():
+ ImageToImageGenericFilter<Self>("RelativePositionAnalyzer")
+{
+ // Default values
+ cmdline_parser_clitkRelativePositionAnalyzer_init(&mArgsInfo);
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+InitializeImageType()
+{
+ ADD_IMAGE_TYPE(Dim, uchar);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+SetArgsInfo(const ArgsInfoType & a)
+{
+ mArgsInfo=a;
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+ if (mArgsInfo.support_given) AddInputFilename(mArgsInfo.support_arg);
+ if (mArgsInfo.object_given) AddInputFilename(mArgsInfo.object_arg);
+ if (mArgsInfo.target_given) AddInputFilename(mArgsInfo.target_arg);
+ if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+
+}
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+UpdateWithInputImageType()
+{
+ // Reading input
+ typename ImageType::Pointer support = this->template GetInput<ImageType>(0);
+ typename ImageType::Pointer object = this->template GetInput<ImageType>(1);
+ typename ImageType::Pointer target = this->template GetInput<ImageType>(2);
+
+ // Create filter
+ typedef clitk::RelativePositionAnalyzerFilter<ImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+
+ // Set global Options
+ filter->SetInputSupport(support);
+ filter->SetInputObject(object);
+ filter->SetInputTarget(target);
+ SetOptionsFromArgsInfoToFilter<FilterType>(filter);
+
+ // Go !
+ filter->Update();
+
+ // Write/Save results
+ // typename ImageType::Pointer output = filter->GetOutput();
+ //this->template SetNextOutput<ImageType>(output);
+
+}
+//--------------------------------------------------------------------
+
+
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================**/
-#ifndef CLITKEXTRACTPATIENTGENERICFILTER_H
-#define CLITKEXTRACTPATIENTGENERICFILTER_H
+#ifndef CLITKRELATIVEPOSITIONGENERICFILTER_H
+#define CLITKRELATIVEPOSITIONGENERICFILTER_H
// clitk
#include "clitkIO.h"
#include "clitkRelativePositionGenericFilter.txx"
#endif
-#endif // #define CLITKEXTRACTPATIENTGENERICFILTER_H
+#endif // #define CLITKRELATIVEPOSITIONGENERICFILTER_H
f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
+ // Must be set before AddOrientationTypeString
+ f->SetInverseOrientationFlag(mArgsInfo.inverse_flag);
+
for(uint i=0; i<mArgsInfo.orientation_given; i++) {
f->AddOrientationTypeString(mArgsInfo.orientation_arg[i]);
}
f->SetRemoveObjectFlag(!mArgsInfo.doNotRemoveObject_flag);
f->SetAutoCropFlag(!mArgsInfo.noAutoCrop_flag);
f->SetCombineWithOrFlag(mArgsInfo.combineWithOr_flag);
- f->SetInverseOrientationFlag(mArgsInfo.inverse_flag);
-
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff