--- /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 "clitkExtractAirwaysTreeInfo_ggo.h"
+#include "clitkExtractAirwaysTreeInfoGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkExtractAirwaysTreeInfo, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::ExtractAirwaysTreeInfoGenericFilter<args_info_clitkExtractAirwaysTreeInfo> 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 clitkExtractAirwaysTreeInfos.ggo
+package "clitkExtractAirwaysTreeInfos"
+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 "afdb" a "Output Anatomical Feature DB (Carina position)" string no
+option "output" o "Output skeleton mask image filename" string yes
+
+section "Main options"
+
+option "writeSkeleton" - "Write skeleton" flag off
+option "skeletonFilename" - "Skeleton filename" string no
--- /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"
+#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
+#include "tree.hh"
+
+// itk
+#include "itkStatisticsImageFilter.h"
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ /*
+ From a trachea binary image, compute the skeleton and track the
+ path to find the carena.
+ */
+ //--------------------------------------------------------------------
+
+
+
+ class Bifurcation
+ {
+ public:
+ typedef itk::Index<3> IndexType;
+ typedef itk::Point<double, 3> PointType;
+ typedef double PixelType;
+ Bifurcation(IndexType _index, PixelType _l, PixelType _l1, PixelType _l2) {
+ index = _index;
+ _l = l;
+ _l1 = l1;
+ _l2 = l2;
+ }
+ IndexType index;
+ PointType point;
+ PixelType l;
+ PixelType l1;
+ PixelType l2;
+ typedef itk::Index<3> NodeType;
+ typedef tree<NodeType> TreeType;
+ typedef TreeType::iterator TreeIterator;
+ TreeIterator treeIter;
+ };
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template <class TImageType>
+ class ITK_EXPORT ExtractAirwaysTreeInfoFilter:
+ public virtual clitk::FilterBase,
+ public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
+ public itk::ImageToImageFilter<TImageType, TImageType>
+ {
+
+ public:
+ /** Standard class typedefs. */
+ typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
+ typedef ExtractAirwaysTreeInfoFilter 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(ExtractAirwaysTreeInfoFilter, 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;
+
+ typedef Bifurcation BifurcationType;
+ typedef ImageIndexType NodeType;
+ typedef tree<NodeType> TreeType;
+ typedef typename TreeType::iterator TreeIterator;
+
+ 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:
+ ExtractAirwaysTreeInfoFilter();
+ virtual ~ExtractAirwaysTreeInfoFilter() {}
+
+ // 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();
+
+ TreeType m_SkeletonTree;
+ void TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations,
+ ImagePointer skeleton,
+ ImageIndexType index,
+ ImagePixelType label,
+ TreeIterator currentNode);
+ private:
+ ExtractAirwaysTreeInfoFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkExtractAirwaysTreeInfoFilter.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 CLITKEXTRACTAIRWAYSTREEINFOSFILTER_TXX
+#define CLITKEXTRACTAIRWAYSTREEINFOSFILTER_TXX
+
+// clitk
+#include "clitkImageCommon.h"
+#include "clitkSetBackgroundImageFilter.h"
+#include "clitkSegmentationUtils.h"
+#include "clitkAutoCropFilter.h"
+#include "clitkExtractSliceFilter.h"
+
+// itk
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkConnectedComponentImageFilter.h"
+#include "itkRelabelComponentImageFilter.h"
+#include "itkOtsuThresholdImageFilter.h"
+#include "itkBinaryThinningImageFilter3D.h"
+#include "itkImageIteratorWithIndex.h"
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+clitk::ExtractAirwaysTreeInfoFilter<ImageType>::
+ExtractAirwaysTreeInfoFilter():
+ clitk::FilterBase(),
+ clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+ itk::ImageToImageFilter<ImageType, ImageType>()
+{
+ // Default global options
+ this->SetNumberOfRequiredInputs(1);
+ SetBackgroundValue(0);
+ SetForegroundValue(1);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractAirwaysTreeInfoFilter<ImageType>::
+SetInput(const ImageType * image)
+{
+ this->SetNthInput(0, const_cast<ImageType *>(image));
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+template<class ArgsInfoType>
+void
+clitk::ExtractAirwaysTreeInfoFilter<ImageType>::
+SetArgsInfo(ArgsInfoType mArgsInfo)
+{
+ SetVerboseOption_GGO(mArgsInfo);
+ SetVerboseStep_GGO(mArgsInfo);
+ SetWriteStep_GGO(mArgsInfo);
+ SetVerboseWarningOff_GGO(mArgsInfo);
+ SetAFDBFilename_GGO(mArgsInfo);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractAirwaysTreeInfoFilter<ImageType>::
+GenerateOutputInformation()
+{
+ Superclass::GenerateOutputInformation();
+ //this->GetOutput(0)->SetRequestedRegion(this->GetOutput(0)->GetLargestPossibleRegion());
+
+ // Get input pointer
+ input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
+
+ // Try to load the DB
+ try {
+ LoadAFDB();
+ } catch (clitk::ExceptionObject e) {
+ // Do nothing if not found, it will be used anyway to write the result
+ }
+
+
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractAirwaysTreeInfoFilter<ImageType>::
+GenerateData()
+{
+ StartNewStep("Thinning filter (skeleton)");
+ // Extract skeleton
+ typedef itk::BinaryThinningImageFilter3D<ImageType, ImageType> ThinningFilterType;
+ typename ThinningFilterType::Pointer thinningFilter = ThinningFilterType::New();
+ thinningFilter->SetInput(input); // input = trachea
+ thinningFilter->Update();
+ skeleton = thinningFilter->GetOutput();
+ StopCurrentStep<ImageType>(skeleton);
+
+ // Find first point for tracking
+ StartNewStep("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()) {
+ clitkExceptionMacro("first point in the trachea skeleton not found.");
+ }
+ typename ImageType::IndexType index = it.GetIndex();
+ DD(index);
+
+ // Initialize neighborhooditerator
+ typedef itk::NeighborhoodIterator<ImageType> NeighborhoodIteratorType;
+ typename NeighborhoodIteratorType::SizeType radius;
+ radius.Fill(1);
+ NeighborhoodIteratorType nit(radius, skeleton, skeleton->GetLargestPossibleRegion());
+
+ // 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);
+
+ /*
+ Tracking ?
+ Goal : find position of C, RUL, RML, RLL, LUL, LLL bronchus
+ Carina : ok "easy", track, slice by slice until 2 path into different label
+ -> follow at Right
+ -
+ -> follow at Left
+ */
+
+
+ // Track from the first point
+ StartNewStep("Start tracking");
+ std::vector<BifurcationType> listOfBifurcations;
+ m_SkeletonTree.set_head(index);
+ TrackFromThisIndex(listOfBifurcations, skeleton, index, label, m_SkeletonTree.begin());
+ DD("end track");
+
+ // Convert index into physical point coordinates
+ for(unsigned int i=0; i<listOfBifurcations.size(); i++) {
+ skeleton->TransformIndexToPhysicalPoint(listOfBifurcations[i].index,
+ listOfBifurcations[i].point);
+ }
+
+ // Search for the first slice that separate the bronchus
+ // (carina). Labelize slice by slice, stop when the two points of
+ // the skeleton ar not in the same connected component
+ StartNewStep("Search for carina position");
+ typedef clitk::ExtractSliceFilter<ImageType> ExtractSliceFilterType;
+ typename ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
+ extractSliceFilter->SetInput(input);
+ extractSliceFilter->SetDirection(2);
+ extractSliceFilter->Update();
+ typedef typename ExtractSliceFilterType::SliceType SliceType;
+ std::vector<typename SliceType::Pointer> mInputSlices;
+ extractSliceFilter->GetOutputSlices(mInputSlices);
+ DD(mInputSlices.size());
+
+ bool stop = false;
+ int slice_index = listOfBifurcations[0].index[2]; // first slice from carina in skeleton
+ int i=0;
+ TreeIterator firstIter = m_SkeletonTree.child(listOfBifurcations[0].treeIter, 0);
+ TreeIterator secondIter = m_SkeletonTree.child(listOfBifurcations[0].treeIter, 1);
+ typename SliceType::IndexType in1;
+ typename SliceType::IndexType in2;
+ while (!stop) {
+ // Labelize the current slice
+ typename SliceType::Pointer temp = Labelize<SliceType>(mInputSlices[slice_index],
+ GetBackgroundValue(),
+ true,
+ 0); // min component size=0
+ // Check the value of the two skeleton points;
+ in1[0] = (*firstIter)[0];
+ in1[1] = (*firstIter)[1];
+ typename SliceType::PixelType v1 = temp->GetPixel(in1);
+ in2[0] = (*secondIter)[0];
+ in2[1] = (*secondIter)[1];
+ typename SliceType::PixelType v2 = temp->GetPixel(in2);
+
+ // Check the label value of the two points
+ DD(slice_index);
+ if (v1 != v2) {
+ stop = true; // We found it !
+ }
+ else {
+ // Check error
+ if (slice_index == (int)(mInputSlices.size()-1)) {
+ clitkExceptionMacro("Error while searching for carina, the two skeleton points are always in the same CC ... ???");
+ }
+ // Iterate
+ i++;
+ --slice_index;
+ ++firstIter;
+ ++secondIter;
+ }
+ }
+ ImageIndexType carina_index; // middle position in X/Y
+ carina_index[0] = lrint(in2[0] + in1[0])/2.0;
+ carina_index[1] = lrint(in2[1] + in1[1])/2.0;
+ carina_index[2] = slice_index;
+ // Get physical coordinates
+ ImagePointType carina_position;
+ skeleton->TransformIndexToPhysicalPoint(carina_index,
+ carina_position);
+
+ // Set and save Carina position
+ if (GetVerboseStep()) {
+ std::cout << "\t Found carina at " << carina_position << " mm" << std::endl;
+ }
+ GetAFDB()->SetPoint3D("Carina", carina_position);
+
+ // Write bifurcation (debug)
+ for(uint i=0; i<listOfBifurcations.size(); i++) {
+ GetAFDB()->SetPoint3D("Bif"+toString(i), listOfBifurcations[i].point);
+ }
+
+ // Set the output (skeleton);
+ this->GraftOutput(skeleton); // not SetNthOutput
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractAirwaysTreeInfoFilter<ImageType>::
+TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations,
+ ImagePointer skeleton,
+ ImageIndexType index,
+ ImagePixelType label,
+ TreeIterator currentNode)
+{
+ // 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);
+ nit.SetCenterPixel(label);
+ listOfTrackedPoint.clear();
+ for(unsigned int i=0; i<nit.Size(); i++) {
+ if (i != nit.GetCenterNeighborhoodIndex ()) { // Do not observe the current point
+ if (nit.GetPixel(i) == GetForegroundValue()) { // if this is foreground, we continue the tracking
+ listOfTrackedPoint.push_back(nit.GetIndex(i));
+ }
+ }
+ }
+ if (listOfTrackedPoint.size() == 1) {
+ // Add this point to the current path
+ currentNode = m_SkeletonTree.append_child(currentNode, listOfTrackedPoint[0]);
+ index = listOfTrackedPoint[0];
+ skeleton->SetPixel(index, label); // change label in skeleton image
+ }
+ else {
+ if (listOfTrackedPoint.size() == 2) {
+ // m_SkeletonTree->Add(listOfTrackedPoint[0], index); // the parent is 'index'
+ // m_SkeletonTree->Add(listOfTrackedPoint[1], index); // the parent is 'index'
+ BifurcationType bif(index, label, label+1, label+2);
+ bif.treeIter = currentNode;
+ listOfBifurcations.push_back(bif);
+ TreeIterator firstNode = m_SkeletonTree.append_child(currentNode, listOfTrackedPoint[0]);
+ TreeIterator secondNode = m_SkeletonTree.append_child(currentNode, listOfTrackedPoint[1]);
+ TrackFromThisIndex(listOfBifurcations, skeleton, listOfTrackedPoint[0], label+1, firstNode);
+ TrackFromThisIndex(listOfBifurcations, skeleton, listOfTrackedPoint[1], label+2, secondNode);
+ }
+ else {
+ //DD(listOfTrackedPoint.size());
+ if (listOfTrackedPoint.size() > 2) {
+ //clitkExceptionMacro("error while tracking trachea bifurcation. Too much bifurcation points ... ?");
+ stop = true; // this it the end of the tracking
+ }
+ // Else this it the end of the tracking
+ }
+ stop = true;
+ }
+ }
+}
+//--------------------------------------------------------------------
+
+/*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 "clitkExtractAirwaysTreeInfoFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ template<class ArgsInfoType>
+ class ITK_EXPORT ExtractAirwaysTreeInfoGenericFilter:
+ public ImageToImageGenericFilter<ExtractAirwaysTreeInfoGenericFilter<ArgsInfoType> >
+ {
+
+ public:
+ //--------------------------------------------------------------------
+ ExtractAirwaysTreeInfoGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ExtractAirwaysTreeInfoGenericFilter Self;
+ typedef ImageToImageGenericFilter<ExtractAirwaysTreeInfoGenericFilter<ArgsInfoType> > Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ itkNewMacro(Self);
+ itkTypeMacro(ExtractAirwaysTreeInfoGenericFilter, 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 "clitkExtractAirwaysTreeInfoGenericFilter.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::ExtractAirwaysTreeInfoGenericFilter<ArgsInfoType>::ExtractAirwaysTreeInfoGenericFilter():
+ ImageToImageGenericFilter<Self>("ExtractAirwaysTreeInfo")
+{
+ this->SetFilterBase(NULL);
+ // Default values
+ cmdline_parser_clitkExtractAirwaysTreeInfo_init(&mArgsInfo);
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::ExtractAirwaysTreeInfoGenericFilter<ArgsInfoType>::InitializeImageType()
+{
+ ADD_IMAGE_TYPE(Dim, uchar);
+ // ADD_IMAGE_TYPE(Dim, int);
+ // ADD_IMAGE_TYPE(Dim, float);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::ExtractAirwaysTreeInfoGenericFilter<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::ExtractAirwaysTreeInfoGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
+{
+ // Reading input
+ typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
+
+ // Create filter
+ typedef clitk::ExtractAirwaysTreeInfoFilter<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);
+ filter->WriteAFDB();
+}
+//--------------------------------------------------------------------
+
+#endif //#define CLITKEXTRACTAIRWAYTREEINFOSGENERICFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff