--- /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 some Mediastinal Vessels in a thorax CT.
+ Need a set of Anatomical Features (AFDB)
+ */
+ //--------------------------------------------------------------------
+
+ template <class TImageType>
+ class ITK_EXPORT ExtractMediastinalVesselsFilter:
+ 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 ExtractMediastinalVesselsFilter 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(ExtractMediastinalVesselsFilter, ImageToImageFilter);
+
+ /** 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;
+ typedef typename MaskImageType::RegionType MaskImageRegionType;
+ typedef typename MaskImageType::SizeType MaskImageSizeType;
+ typedef typename MaskImageType::IndexType MaskImageIndexType;
+ typedef typename MaskImageType::PointType MaskImagePointType;
+
+ typedef itk::Image<MaskImagePixelType, 2> MaskSliceType;
+ typedef typename MaskSliceType::Pointer MaskSlicePointer;
+ typedef typename MaskSliceType::PointType MaskSlicePointType;
+
+ typedef long LabelType;
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
+ FILTERBASE_INIT;
+
+ itkGetConstMacro(BackgroundValue, MaskImagePixelType);
+ itkSetMacro(BackgroundValue, MaskImagePixelType);
+
+ itkGetConstMacro(ForegroundValue, MaskImagePixelType);
+ itkSetMacro(ForegroundValue, MaskImagePixelType);
+
+ itkGetConstMacro(TemporaryForegroundValue, MaskImagePixelType);
+ itkSetMacro(TemporaryForegroundValue, MaskImagePixelType);
+
+ itkGetConstMacro(OutputFolder, std::string);
+ itkSetMacro(OutputFolder, std::string);
+
+ itkGetConstMacro(Threshold, ImagePixelType);
+ itkSetMacro(Threshold, ImagePixelType);
+
+ protected:
+ ExtractMediastinalVesselsFilter();
+ virtual ~ExtractMediastinalVesselsFilter() {}
+
+ virtual void GenerateOutputInformation();
+ virtual void GenerateInputRequestedRegion();
+ virtual void GenerateData();
+
+ std::string m_OutputFolder;
+ ImagePointer m_Input;
+ MaskImagePointer m_Working_Support;
+ MaskImagePointer m_Mediastinum;
+ MaskImagePointer m_Mask;
+ MaskImagePixelType m_BackgroundValue;
+ MaskImagePixelType m_ForegroundValue;
+ MaskImagePixelType m_TemporaryForegroundValue;
+ ImagePixelType m_Threshold;
+
+ std::vector<MaskSlicePointer> m_slice_recon;
+
+ void CropSupInf();
+ //void SearchBrachioCephalicArtery(int & BCA_first_slice, LabelType & BCA_first_label);
+ void TrackBifurcationFromPoint(MaskImagePointer & recon,
+ std::vector<MaskSlicePointer> & slices_recon,
+ MaskImagePointType BCA_p,
+ LabelType newLabel,
+ std::vector<MaskImagePointType> & bif);
+
+ private:
+ ExtractMediastinalVesselsFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkExtractMediastinalVesselsFilter.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 "clitkExtractMediastinalVesselsFilter.h"
+#include "clitkAutoCropFilter.h"
+#include "clitkSegmentationUtils.h"
+#include "clitkMorphoMathFilter.h"
+
+// itk
+#include <itkBinaryThresholdImageFilter.h>
+#include <itkGrayscaleDilateImageFilter.h>
+#include <itkMinimumMaximumImageCalculator.h>
+
+//--------------------------------------------------------------------
+template <class TImageType>
+clitk::ExtractMediastinalVesselsFilter<TImageType>::
+ExtractMediastinalVesselsFilter():
+ clitk::FilterBase(),
+ clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+ itk::ImageToImageFilter<TImageType, MaskImageType>()
+{
+ this->SetNumberOfRequiredInputs(1);
+ SetBackgroundValue(0);
+ SetForegroundValue(1);
+ SetThreshold(140);
+ SetTemporaryForegroundValue(1);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinalVesselsFilter<TImageType>::
+GenerateOutputInformation() {
+ // Get inputs
+ LoadAFDB();
+ m_Input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+
+ // ------------------------------------------------------------------
+ // Sup-Inf crop -> Carina
+ CropSupInf();
+
+ // ------------------------------------------------------------------
+ // Binarize
+ StartNewStep("Binarize with treshold = "+toString(GetThreshold()));
+ typedef itk::BinaryThresholdImageFilter<ImageType, MaskImageType> BinarizeFilterType;
+ typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
+ binarizeFilter->SetInput(m_Input);
+ binarizeFilter->SetLowerThreshold(GetThreshold());
+ binarizeFilter->SetInsideValue(GetTemporaryForegroundValue());
+ binarizeFilter->SetOutsideValue(GetBackgroundValue());
+ binarizeFilter->Update();
+ m_Mask = binarizeFilter->GetOutput();
+ clitk::writeImage<MaskImageType>(m_Mask, "m.mhd");
+ StopCurrentStep<MaskImageType>(m_Mask);
+
+ // Keep main CCL ?
+ m_Mask = clitk::Labelize<MaskImageType>(m_Mask, GetBackgroundValue(), false, 10);
+ m_Mask = KeepLabels<MaskImageType>(m_Mask, GetBackgroundValue(), GetTemporaryForegroundValue(), 1, 1, true);
+ clitk::writeImage<MaskImageType>(m_Mask, "m2.mhd");
+
+ // ------------------------------------------------------------------
+ // Extract slices
+ StartNewStep("Detect vessels (slice by slice reconstruction)");
+ std::vector<MaskSlicePointer> slices_mask;
+ clitk::ExtractSlices<MaskImageType>(m_Mask, 2, slices_mask);
+
+ DD(slices_mask.size());
+
+ std::vector<MaskSlicePointer> debug_eroded;
+ std::vector<MaskSlicePointer> debug_labeled;
+ std::vector<MaskSlicePointer> debug_slabeled;
+
+ int radius = 3;
+ DD(radius); // TO PUT IN OPTION
+
+ // ------------------------------------------------------------------
+ // Loop Slice by Slice -> erode find CCL and reconstruct
+ clitk::MorphoMathFilter<MaskSliceType>::Pointer f= clitk::MorphoMathFilter<MaskSliceType>::New();
+ for(uint i=0; i<slices_mask.size(); i++) {
+ // Erosion
+ f->SetInput(slices_mask[i]);
+ f->SetBackgroundValue(GetBackgroundValue());
+ f->SetForegroundValue(GetTemporaryForegroundValue());
+ f->SetRadius(radius);
+ f->SetOperationType(0); // Erode
+ f->VerboseFlagOff();
+ f->Update();
+ MaskSlicePointer eroded = f->GetOutput();
+ // writeImage<MaskSliceType>(eroded, "er-"+toString(i)+".mhd");
+ debug_eroded.push_back(eroded);
+
+ // CCL
+ int nb;
+ MaskSlicePointer labeled =
+ clitk::LabelizeAndCountNumberOfObjects<MaskSliceType>(eroded, GetBackgroundValue(), false, 1, nb);
+
+ // Relabel, large CCL with large label number
+ for(int n=nb; n>0; n--) {
+ // DD(n);
+ int li = n;
+ int lo = 2*(nb+1)-li;
+ labeled = clitk::SetBackground<MaskSliceType, MaskSliceType>(labeled, labeled, li, lo, true);
+ }
+ debug_labeled.push_back(labeled);
+
+ // Create kernel for GrayscaleDilateImageFilter
+ typedef itk::BinaryBallStructuringElement<MaskSliceType::PixelType,MaskSliceType::ImageDimension > KernelType;
+ KernelType k;
+ k.SetRadius(radius+1);
+ k.CreateStructuringElement();
+
+ // Keep the MAX -> we prefer the opposite su change the label
+ typedef itk::GrayscaleDilateImageFilter<MaskSliceType, MaskSliceType, KernelType> FilterType;
+ FilterType::Pointer m = FilterType::New();
+ m->SetKernel(k);
+ m->SetInput(labeled);
+ // DD(m->GetAlgorithm());
+ // m->SetAlgorithm(3);
+ m->Update();
+ MaskSlicePointer s = m->GetOutput();
+
+
+ // Remove Initial BG
+ s = clitk::SetBackground<MaskSliceType, MaskSliceType>(s, slices_mask[i],
+ GetBackgroundValue(), GetBackgroundValue(), true);
+
+ m_slice_recon.push_back(s);
+ } // end loop
+ DD("end loop");
+
+ MaskImageType::Pointer eroded = clitk::JoinSlices<MaskImageType>(debug_eroded, m_Mask, 2);
+ clitk::writeImage<MaskImageType>(eroded, "eroded.mhd");
+
+ DD("l");
+ MaskImageType::Pointer l = clitk::JoinSlices<MaskImageType>(debug_labeled, m_Mask, 2);
+ clitk::writeImage<MaskImageType>(l, "labeled.mhd");
+
+ DD("r");
+ MaskImageType::Pointer r = clitk::JoinSlices<MaskImageType>(m_slice_recon, m_Mask, 2);
+ clitk::writeImage<MaskImageType>(r, "recon.mhd");
+
+ // ------------------------------------------------------------------
+ // Loop Slice by Slice -> BCA not found yet
+ /* MaskImagePointType BCA_p;
+ GetAFDB()->GetPoint3D("BrachioCephalicArteryFirstInferiorPoint", BCA_p);
+ DD(BCA_p);
+ MaskImagePointType bif1;
+ MaskImagePointType bif2;
+ TrackBifurcationFromPoint(r, BCA_p, bif1, bif2);
+ DD(bif1);
+ DD(bif2);
+ */
+ // Find max label
+ typedef itk::MinimumMaximumImageCalculator<MaskImageType> MinMaxFilterType;
+ MinMaxFilterType::Pointer ff = MinMaxFilterType::New();
+ ff->SetImage(r);
+ ff->ComputeMaximum();
+ LabelType newLabel = ff->GetMaximum()+1;
+ DD(newLabel);
+
+ // Get all centroids of the first slice
+ std::vector<MaskSlicePointType> centroids2D;
+ clitk::ComputeCentroids<MaskSliceType>(m_slice_recon[0], GetBackgroundValue(), centroids2D);
+ DD(centroids2D.size());
+ std::vector<MaskImagePointType> bifurcations;
+ clitk::PointsUtils<MaskImageType>::Convert2DListTo3DList(centroids2D, 0, r, bifurcations);
+ DD(bifurcations.size());
+ for(uint i=1; i<bifurcations.size()+1; i++) {
+ DD(i);
+ DD(bifurcations.size());
+ TrackBifurcationFromPoint(r, m_slice_recon, bifurcations[i], newLabel+i, bifurcations);
+ DD("end track");
+ DD(bifurcations.size());
+ MaskImageType::Pointer rr = clitk::JoinSlices<MaskImageType>(m_slice_recon, m_Mask, 2);
+ clitk::writeImage<MaskImageType>(rr, "recon"+toString(i)+".mhd");
+ }
+
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinalVesselsFilter<TImageType>::
+GenerateInputRequestedRegion() {
+ //DD("GenerateInputRequestedRegion (nothing?)");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinalVesselsFilter<TImageType>::
+GenerateData() {
+ DD("GenerateData");
+ // Final Step -> graft output (if SetNthOutput => redo)
+ MaskImagePointer BrachioCephalicArtery =
+ GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
+ this->GraftNthOutput(0, BrachioCephalicArtery);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinalVesselsFilter<TImageType>::
+CropSupInf() {
+ StartNewStep("Inf/Sup limits (carina) and crop with mediastinum");
+ // Get Trachea and Carina
+ MaskImagePointer Trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
+
+ // Get or compute Carina
+ double m_CarinaZ;
+ // Get Carina Z position
+ MaskImagePointer Carina = GetAFDB()->template GetImage<MaskImageType>("Carina");
+
+ std::vector<MaskImagePointType> centroids;
+ clitk::ComputeCentroids<MaskImageType>(Carina, GetBackgroundValue(), centroids);
+ m_CarinaZ = centroids[1][2];
+ // DD(m_CarinaZ);
+ // add one slice to include carina ?
+ m_CarinaZ += Carina->GetSpacing()[2];
+ // We dont need Carina structure from now
+ Carina->Delete();
+ GetAFDB()->SetDouble("CarinaZ", m_CarinaZ);
+
+ // Crop
+ m_Input = clitk::CropImageRemoveLowerThan<ImageType>(m_Input, 2,
+ m_CarinaZ, false, GetBackgroundValue());
+
+ // Crop not post to centroid
+ double m_CarinaY = centroids[1][1];
+ DD(m_CarinaY);
+ m_Input = clitk::CropImageRemoveGreaterThan<ImageType>(m_Input, 1, // OLD ABOVE
+ m_CarinaY, false, GetBackgroundValue());
+ // Crop not ant to centroid
+ m_Input = clitk::CropImageRemoveLowerThan<ImageType>(m_Input, 1,
+ m_CarinaY-80, false, GetBackgroundValue());
+
+ // AutoCrop with Mediastinum
+ m_Mediastinum = GetAFDB()->template GetImage<MaskImageType>("Mediastinum");
+ // Resize like input (sup to carina)
+ m_Mediastinum = clitk::ResizeImageLike<MaskImageType>(m_Mediastinum, m_Input, GetBackgroundValue());
+ // Auto crop
+ m_Mediastinum = clitk::AutoCrop<MaskImageType>(m_Mediastinum, GetBackgroundValue());
+ // Resize input
+ m_Input = clitk::ResizeImageLike<ImageType>(m_Input, m_Mediastinum, GetBackgroundValue());
+
+ // End
+ StopCurrentStep<ImageType>(m_Input);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractMediastinalVesselsFilter<TImageType>::
+//SearchBrachioCephalicArtery(int & BCA_first_slice, LabelType & BCA_first_label) {
+TrackBifurcationFromPoint(MaskImagePointer & recon,
+ std::vector<MaskSlicePointer> & slices_recon,
+ MaskImagePointType point3D,
+ LabelType newLabel,
+ std::vector<MaskImagePointType> & bifurcations) {
+ StartNewStep("Search for BCA first slice and label");
+ DD(newLabel);
+
+ // Extract slices
+ // std::vector<MaskSlicePointer> slices_recon;
+ //clitk::ExtractSlices<MaskImageType>(recon, 2, slices_recon);
+
+ // Find first slice
+ MaskImageIndexType index;
+ recon->TransformPhysicalPointToIndex(point3D, index);
+ DD(point3D);
+ DD(index);
+
+ uint i=index[2];
+ bool found = false;
+ LabelType previous_largest_label=recon->GetPixel(index);
+ DD(previous_largest_label);
+ do {
+ DD(i);
+ // Consider current reconstructed slice
+ MaskSlicePointer s = slices_recon[i];
+ MaskSlicePointer previous;
+ if (i==index[2]) previous = s;
+ else previous = slices_recon[i-1];
+
+ // Get centroids of the labels in the current slice
+ typedef typename MaskSliceType::PointType SlicePointType;
+ static const unsigned int Dim = MaskSliceType::ImageDimension;
+ typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
+ typedef itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef itk::LabelImageToLabelMapFilter<MaskSliceType, LabelMapType> ImageToMapFilterType;
+ typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
+ typedef itk::ShapeLabelMapFilter<LabelMapType, MaskSliceType> ShapeFilterType;
+ typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
+ imageToLabelFilter->SetBackgroundValue(GetBackgroundValue());
+ imageToLabelFilter->SetInput(s);
+ statFilter->SetInput(imageToLabelFilter->GetOutput());
+ statFilter->Update();
+ typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
+
+ // Look what centroid inside the previous largest one
+ std::vector<SlicePointType> centroids;
+ std::vector<LabelType> centroids_label;
+ for(uint c=0; c<labelMap->GetNumberOfLabelObjects(); c++) {
+ int label = labelMap->GetLabels()[c];
+ DD(label);
+ SlicePointType center = labelMap->GetLabelObject(label)->GetCentroid();
+ SlicePointType center_previous = center;
+ center_previous[2] -= m_Input->GetSpacing()[2];
+ // Get label into previous slice
+ typename MaskSliceType::IndexType index;
+ previous->TransformPhysicalPointToIndex(center_previous, index);
+ LabelType l = previous->GetPixel(index);
+ DD(l);
+ if (l == previous_largest_label) {
+ centroids.push_back(center);
+ centroids_label.push_back(label);
+ }
+ }
+ DD(centroids.size());
+
+ // If several centroids, we found a bifurcation
+ if (centroids.size() > 1) {
+ found = true;
+ for(uint c=0; c<centroids.size(); c++) {
+ ImagePointType bif;
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[c], m_Mask, i, bif);
+ bifurcations.push_back(bif);
+ s = clitk::SetBackground<MaskSliceType, MaskSliceType>(s, s, centroids_label[c], newLabel+c+1, true);
+ // slices_recon[i] = s; // (useful ?)
+ }
+ DD("FOUND");
+ }
+
+ // if only one centroids, we change the current image with the current label
+ if (centroids.size() == 1) {
+ s = clitk::SetBackground<MaskSliceType, MaskSliceType>(s, s, centroids_label[0], newLabel, true);
+ previous_largest_label = newLabel;
+ /*typedef itk::BinaryThresholdImageFilter<MaskSliceType, MaskSliceType> BinarizeFilterType;
+ typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
+ binarizeFilter->SetInput(s);
+ binarizeFilter->SetLowerThreshold(centroids_label[0]);
+ binarizeFilter->SetUpperThreshold(centroids_label[0]+1);
+ binarizeFilter->SetInsideValue(previous_largest_label);
+ binarizeFilter->SetOutsideValue(GetBackgroundValue());
+ binarizeFilter->Update();
+ s = binarizeFilter->GetOutput();*/
+ slices_recon[i] = s; // (not useful ?)
+ }
+
+ if (centroids.size() == 0) {
+ DD("no centroid, I stop");
+ found = true;
+ }
+
+ if (i == slices_recon.size()-1) found = true;
+
+ // iterate
+ ++i;
+ } while (!found);
+
+
+ //MaskImageType::Pointer rr = clitk::JoinSlices<MaskImageType>(slices_recon, m_Mask, 2);
+ //clitk::writeImage<MaskImageType>(rr, "recon2.mhd");
+
+ // End
+ StopCurrentStep();
+}
+//--------------------------------------------------------------------
+
+
+
+#endif //#define CLITKEXTRACTMEDIASTINALVESSELSFILTER_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 CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
+#define CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
+
+#include "clitkImageCommon.h"
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::ExtractMediastinalVesselsGenericFilter<ArgsInfoType>::ExtractMediastinalVesselsGenericFilter():
+ ImageToImageGenericFilter<Self>("ExtractMediastinalVessels")
+{
+ // Default values
+ cmdline_parser_clitkExtractMediastinalVessels_init(&mArgsInfo);
+ InitializeImageType<3>(); // Only for 3D images
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::ExtractMediastinalVesselsGenericFilter<ArgsInfoType>::InitializeImageType()
+{
+ ADD_IMAGE_TYPE(Dim, short); // Can add float later
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::ExtractMediastinalVesselsGenericFilter<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);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void
+clitk::ExtractMediastinalVesselsGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+ f->SetVerboseOptionFlag(mArgsInfo.verbose_flag);
+ f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
+ f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
+ f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
+ f->SetAFDBFilename(mArgsInfo.afdb_arg);
+ f->SetOutputFolder(mArgsInfo.output_arg);
+
+ f->SetThreshold(mArgsInfo.threshold_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::ExtractMediastinalVesselsGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
+{
+ // Reading input
+ typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
+
+ // Create filter
+ typedef clitk::ExtractMediastinalVesselsFilter<ImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+
+ // Set global Options
+ filter->SetInput(input);
+ SetOptionsFromArgsInfoToFilter<FilterType>(filter);
+
+ // Go !
+ filter->Update();
+
+ // Write/Save results
+ for(uint i=0; i<filter->GetNumberOfOutputs(); i++) {
+ typedef uchar MaskImagePixelType;
+ typedef itk::Image<MaskImagePixelType, 3> OutputImageType;
+ typename OutputImageType::Pointer output = filter->GetOutput(i);
+ this->template SetNextOutput<OutputImageType>(output);
+ }
+}
+//--------------------------------------------------------------------
+
+#endif //#define CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff