+++ /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
-======================================================================-====*/
-
-// clitk
-#include "clitkExtractAirwayTreeInfo_ggo.h"
-#include "clitkExtractAirwayTreeInfoGenericFilter.h"
-
-//--------------------------------------------------------------------
-int main(int argc, char * argv[])
-{
-
- // Init command line
- GGO(clitkExtractAirwayTreeInfo, args_info);
- CLITK_INIT;
-
- // Filter
- typedef clitk::ExtractAirwayTreeInfoGenericFilter<args_info_clitkExtractAirwayTreeInfo> 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_SUCCESS;
-} // This is the end, my friend
-//--------------------------------------------------------------------
+++ /dev/null
-#File clitkExtractAirwayTreeInfos.ggo
-package "clitkExtractAirwayTreeInfos"
-version "1.0"
-purpose "From trachea binary image, extract skeleton and carena point."
-
-option "config" - "Config file" string no
-option "imagetypes" - "Display allowed image types" flag off
-option "verbose" v "Verbose" flag off
-option "verboseStep" - "Verbose each step" flag off
-option "writeStep" w "Write image at each step" flag off
-option "verboseOption" - "Display options values" flag off
-option "verboseWarningOff" - "Do not display warning" flag off
-
-section "I/O"
-
-option "input" i "Input trachea mask image filename" string yes
-option "output" o "Output skeleton mask image filename" 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://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 CLITKEXTRACTAIRWAYTREEINFOSFILTER_H
-#define CLITKEXTRACTAIRWAYTREEINFOSFILTER_H
-
-// clitk
-#include "clitkFilterBase.h"
-#include "clitkDecomposeAndReconstructImageFilter.h"
-#include "clitkExplosionControlledThresholdConnectedImageFilter.h"
-#include "clitkSegmentationUtils.h"
-
-// itk
-#include "itkStatisticsImageFilter.h"
-
-namespace clitk {
-
- //--------------------------------------------------------------------
- /*
- From a trachea binary image, compute the skeleton and track the
- path to find the carena.
- */
- //--------------------------------------------------------------------
-
-
- //--------------------------------------------------------------------
- template<class IndexType, class PixelType>
- class Bifurcation
- {
- public:
- Bifurcation(IndexType _index, PixelType _l, PixelType _l1, PixelType _l2) {
- index = _index;
- _l = l;
- _l1 = l1;
- _l2 = l2;
- }
- IndexType index;
- PixelType l;
- PixelType l1;
- PixelType l2;
- };
- //--------------------------------------------------------------------
-
-
- //--------------------------------------------------------------------
- template <class TImageType>
- class ITK_EXPORT ExtractAirwayTreeInfoFilter:
- public clitk::FilterBase,
- public itk::ImageToImageFilter<TImageType, TImageType>
- {
-
- public:
- /** Standard class typedefs. */
- typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
- typedef ExtractAirwayTreeInfoFilter 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(ExtractAirwayTreeInfoFilter, ImageToImageFilter);
- FILTERBASE_INIT;
-
- /** 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;
-
- itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
- typedef int InternalPixelType;
- typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
- typedef typename InternalImageType::Pointer InternalImagePointer;
- typedef typename InternalImageType::IndexType InternalIndexType;
- typedef LabelizeParameters<InternalPixelType> LabelParamType;
-
- /** Connect inputs */
- void SetInput(const ImageType * image);
-
- // Set all options at a time
- template<class ArgsInfoType>
- void SetArgsInfo(ArgsInfoType arg);
-
- // Background / Foreground
- itkGetConstMacro(BackgroundValue, ImagePixelType);
- itkGetConstMacro(ForegroundValue, ImagePixelType);
-
- // Get results
- itkGetConstMacro(FirstTracheaPoint, ImagePointType);
- itkGetConstMacro(CarinaPoint, ImagePointType);
-
- protected:
- ExtractAirwayTreeInfoFilter();
- virtual ~ExtractAirwayTreeInfoFilter() {}
-
- // Main members
- ImageConstPointer input;
- ImagePointer skeleton;
- ImagePointer working_input;
-
- // Global options
- itkSetMacro(BackgroundValue, ImagePixelType);
- itkSetMacro(ForegroundValue, ImagePixelType);
- ImagePixelType m_BackgroundValue;
- ImagePixelType m_ForegroundValue;
-
- // Results
- ImagePointType m_FirstTracheaPoint;
- ImagePointType m_CarinaPoint;
-
- virtual void GenerateOutputInformation();
- virtual void GenerateData();
-
- typedef Bifurcation<ImageIndexType,ImagePixelType> BifurcationType;
- void TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations,
- ImagePointer skeleton,
- ImageIndexType index,
- ImagePixelType label);
- private:
- ExtractAirwayTreeInfoFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- }; // end class
- //--------------------------------------------------------------------
-
-} // end namespace clitk
-//--------------------------------------------------------------------
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkExtractAirwayTreeInfoFilter.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 CLITKEXTRACTAIRWAYTREEINFOSFILTER_TXX
-#define CLITKEXTRACTAIRWAYTREEINFOSFILTER_TXX
-
-// clitk
-#include "clitkImageCommon.h"
-#include "clitkSetBackgroundImageFilter.h"
-#include "clitkSegmentationUtils.h"
-#include "clitkAutoCropFilter.h"
-
-// itk
-#include "itkBinaryThresholdImageFilter.h"
-#include "itkConnectedComponentImageFilter.h"
-#include "itkRelabelComponentImageFilter.h"
-#include "itkOtsuThresholdImageFilter.h"
-#include "itkBinaryThinningImageFilter3D.h"
-#include "itkImageIteratorWithIndex.h"
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-clitk::ExtractAirwayTreeInfoFilter<ImageType>::
-ExtractAirwayTreeInfoFilter():
- clitk::FilterBase(),
- itk::ImageToImageFilter<ImageType, ImageType>()
-{
- // Default global options
- this->SetNumberOfRequiredInputs(1);
- SetBackgroundValue(0);
- SetForegroundValue(1);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractAirwayTreeInfoFilter<ImageType>::
-SetInput(const ImageType * image)
-{
- this->SetNthInput(0, const_cast<ImageType *>(image));
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-template<class ArgsInfoType>
-void
-clitk::ExtractAirwayTreeInfoFilter<ImageType>::
-SetArgsInfo(ArgsInfoType mArgsInfo)
-{
- SetVerboseOption_GGO(mArgsInfo);
- SetVerboseStep_GGO(mArgsInfo);
- SetWriteStep_GGO(mArgsInfo);
- SetVerboseWarningOff_GGO(mArgsInfo);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractAirwayTreeInfoFilter<ImageType>::
-GenerateOutputInformation()
-{
- Superclass::GenerateOutputInformation();
- //this->GetOutput(0)->SetRequestedRegion(this->GetOutput(0)->GetLargestPossibleRegion());
-
- // Get input pointer
- input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
-
- StartNewStep("Find bronchial bifurcations");
- // Step 1 : extract skeleton
- // Define the thinning filter
- typedef itk::BinaryThinningImageFilter3D<ImageType, ImageType> ThinningFilterType;
- typename ThinningFilterType::Pointer thinningFilter = ThinningFilterType::New();
- thinningFilter->SetInput(input);
- thinningFilter->Update();
- skeleton = thinningFilter->GetOutput();
- writeImage<ImageType>(skeleton, "skeleton.mhd");
-
- // Step 2 : tracking
- DD("tracking");
-
- // Step 2.1 : find first point for tracking
- typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
- IteratorType it(skeleton, skeleton->GetLargestPossibleRegion());
- it.GoToReverseBegin();
- while ((!it.IsAtEnd()) && (it.Get() == GetBackgroundValue())) {
- --it;
- }
- if (it.IsAtEnd()) {
- throw clitk::ExceptionObject("ERROR: first point in the skeleton not found ! Abort");
- return;
- }
- DD(skeleton->GetLargestPossibleRegion().GetIndex());
- typename ImageType::IndexType index = it.GetIndex();
- skeleton->TransformIndexToPhysicalPoint(index, m_FirstTracheaPoint);
- DD(index);
- DD(m_FirstTracheaPoint);
-
- // Step 2.2 : initialize neighborhooditerator
- typedef itk::NeighborhoodIterator<ImageType> NeighborhoodIteratorType;
- typename NeighborhoodIteratorType::SizeType radius;
- radius.Fill(1);
- NeighborhoodIteratorType nit(radius, skeleton, skeleton->GetLargestPossibleRegion());
- DD(nit.GetSize());
- DD(nit.Size());
-
- // Find first label number (must be different from BG and FG)
- typename ImageType::PixelType label = GetForegroundValue()+1;
- while ((label == GetBackgroundValue()) || (label == GetForegroundValue())) { label++; }
- DD(label);
-
- // Track from the first point
- std::vector<BifurcationType> listOfBifurcations;
- TrackFromThisIndex(listOfBifurcations, skeleton, index, label);
- DD("end track");
- DD(listOfBifurcations.size());
- writeImage<ImageType>(skeleton, "skeleton2.mhd");
-
- for(unsigned int i=0; i<listOfBifurcations.size(); i++) {
- typename ImageType::PointType p;
- skeleton->TransformIndexToPhysicalPoint(listOfBifurcations[i].index, p);
- DD(p);
- }
-
- // The first bifurcation is supposed to be the carina
- skeleton->TransformIndexToPhysicalPoint(listOfBifurcations[0].index, m_CarinaPoint);
- DD(listOfBifurcations[0].index);
- DD(m_CarinaPoint);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractAirwayTreeInfoFilter<ImageType>::
-GenerateData()
-{
- // If everything goes well, set the output
- this->GraftOutput(skeleton); // not SetNthOutput
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractAirwayTreeInfoFilter<ImageType>::
-TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations,
- ImagePointer skeleton,
- ImageIndexType index,
- ImagePixelType label)
-{
- DD("TrackFromThisIndex");
- DD(index);
- DD((int)label);
- // Create NeighborhoodIterator
- typedef itk::NeighborhoodIterator<ImageType> NeighborhoodIteratorType;
- typename NeighborhoodIteratorType::SizeType radius;
- radius.Fill(1);
- NeighborhoodIteratorType nit(radius, skeleton, skeleton->GetLargestPossibleRegion());
-
- // Track
- std::vector<typename NeighborhoodIteratorType::IndexType> listOfTrackedPoint;
- bool stop = false;
- while (!stop) {
- nit.SetLocation(index);
- // DD((int)nit.GetCenterPixel());
- nit.SetCenterPixel(label);
- listOfTrackedPoint.clear();
- for(unsigned int i=0; i<nit.Size(); i++) {
- if (i != nit.GetCenterNeighborhoodIndex ()) { // Do not observe the current point
- // DD(nit.GetIndex(i));
- if (nit.GetPixel(i) == GetForegroundValue()) { // if this is foreground, we continue the tracking
- // DD(nit.GetIndex(i));
- listOfTrackedPoint.push_back(nit.GetIndex(i));
- }
- }
- }
- // DD(listOfTrackedPoint.size());
- if (listOfTrackedPoint.size() == 1) {
- index = listOfTrackedPoint[0];
- }
- else {
- if (listOfTrackedPoint.size() == 2) {
- BifurcationType bif(index, label, label+1, label+2);
- listOfBifurcations.push_back(bif);
- TrackFromThisIndex(listOfBifurcations, skeleton, listOfTrackedPoint[0], label+1);
- TrackFromThisIndex(listOfBifurcations, skeleton, listOfTrackedPoint[1], label+2);
- }
- else {
- if (listOfTrackedPoint.size() > 2) {
- std::cerr << "too much bifurcation points ... ?" << std::endl;
- exit(0);
- }
- // Else this it the end of the tracking
- }
- stop = true;
- }
- }
-}
-//--------------------------------------------------------------------
-
-
-#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_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://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 CLITKEXTRACTAIRWAYTREEINFOSGENERICFILTER_H
-#define CLITKEXTRACTAIRWAYTREEINFOSGENERICFILTER_H
-
-#include "clitkIO.h"
-#include "clitkImageToImageGenericFilter.h"
-#include "clitkExtractAirwayTreeInfoFilter.h"
-
-//--------------------------------------------------------------------
-namespace clitk
-{
-
- template<class ArgsInfoType>
- class ITK_EXPORT ExtractAirwayTreeInfoGenericFilter:
- public ImageToImageGenericFilter<ExtractAirwayTreeInfoGenericFilter<ArgsInfoType> >
- {
-
- public:
- //--------------------------------------------------------------------
- ExtractAirwayTreeInfoGenericFilter();
-
- //--------------------------------------------------------------------
- typedef ExtractAirwayTreeInfoGenericFilter Self;
- typedef ImageToImageGenericFilter<ExtractAirwayTreeInfoGenericFilter<ArgsInfoType> > Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- //--------------------------------------------------------------------
- itkNewMacro(Self);
- itkTypeMacro(ExtractAirwayTreeInfoGenericFilter, LightObject);
-
- //--------------------------------------------------------------------
- void SetArgsInfo(const ArgsInfoType & a);
-
- //--------------------------------------------------------------------
- // Main function called each time the filter is updated
- template<class ImageType>
- void UpdateWithInputImageType();
-
- protected:
- template<unsigned int Dim> void InitializeImageType();
- ArgsInfoType mArgsInfo;
-
- }; // end class
- //--------------------------------------------------------------------
-
-} // end namespace clitk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkExtractAirwayTreeInfoGenericFilter.txx"
-#endif
-
-#endif // #define CLITKEXTRACTAIRWAYTREEINFOSGENERICFILTER_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://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 CLITKEXTRACTAIRWAYTREEINFOSGENERICFILTER_TXX
-#define CLITKEXTRACTAIRWAYTREEINFOSGENERICFILTER_TXX
-
-#include "clitkImageCommon.h"
-
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-clitk::ExtractAirwayTreeInfoGenericFilter<ArgsInfoType>::ExtractAirwayTreeInfoGenericFilter():
- ImageToImageGenericFilter<Self>("ExtractAirwayTreeInfo")
-{
- this->SetFilterBase(NULL);
- // Default values
- cmdline_parser_clitkExtractAirwayTreeInfo_init(&mArgsInfo);
- InitializeImageType<3>();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-template<unsigned int Dim>
-void clitk::ExtractAirwayTreeInfoGenericFilter<ArgsInfoType>::InitializeImageType()
-{
- ADD_IMAGE_TYPE(Dim, uchar);
- // ADD_IMAGE_TYPE(Dim, int);
- // ADD_IMAGE_TYPE(Dim, float);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-void clitk::ExtractAirwayTreeInfoGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
-{
- mArgsInfo=a;
- SetIOVerbose(mArgsInfo.verbose_flag);
- if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
- if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
- if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-// Update with the number of dimensions and the pixeltype
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-template<class ImageType>
-void clitk::ExtractAirwayTreeInfoGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
-{
- // Reading input
- typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
-
- // Create filter
- typedef clitk::ExtractAirwayTreeInfoFilter<ImageType> FilterType;
- typename FilterType::Pointer filter = FilterType::New();
-
- // Set the filter (needed for example for threaded monitoring)
- this->SetFilterBase(filter);
-
- // Set global Options
- filter->SetArgsInfo(mArgsInfo);
- filter->SetInput(input);
-
- // Go !
- filter->Update();
-
- // Write/Save results
- typename ImageType::Pointer output = filter->GetOutput();
- this->template SetNextOutput<ImageType>(output);
-}
-//--------------------------------------------------------------------
-
-#endif //#define CLITKEXTRACTAIRWAYTREEINFOSGENERICFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff