ENH: new code to concatenate MeanShift filter and connected component

Code/OBIA/otbMeanShiftConnectedComponentSegmentationFilter.h

+/*=========================================================================
+
+  Program:   ORFEO Toolbox
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+
+  Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
+  See OTBCopyright.txt for details.
+
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __otbMeanShiftConnectedComponentSegmentationFilter_h
+#define __otbMeanShiftConnectedComponentSegmentationFilter_h
+
+#include "itkMacro.h"
+
+#include "otbConnectedComponentMuParserFunctor.h"
+#include "itkConnectedComponentFunctorImageFilter.h"
+#include "otbMaskMuParserFilter.h"
+#include "itkRelabelComponentImageFilter.h"
+
+#include "otbMeanShiftImageFilter2.h"
+
+namespace otb {
+
+/** \class MeanShiftConnectedComponentSegmentationFilter
+*   \brief [internal] Helper class to perform connected component segmentation on an input image,
+*
+*
+*  The whole chain is described in :
+*  http://wiki.orfeo-toolbox.org/index.php/Connected_component_segmentation_module
+*
+*  This class wraps a processing chain based on meanshift filtering followed by a connected component segmentation,
+*
+*  An optional mask can be applied to segment only the pixels inside the mask.
+*
+*  Parameters of the chain are :
+*  - MaskExpression : mathematical expression to apply on the input image to make a mask
+*  - ConnectedComponentExpression : mathematical expression which connects two pixels
+*  - MinimumObjectSize : minimum object size kept after segmentation
+*
+*/
+
+
+template <class TVInputImage, class TMaskImage,class TLabelImage>
+class MeanShiftConnectedComponentSegmentationFilter : public itk::ImageToImageFilter<TVInputImage, TLabelImage>
+{
+public:
+  /** Standard Self typedef */
+
+  typedef MeanShiftConnectedComponentSegmentationFilter Self;
+  typedef itk::ImageToImageFilter<TVInputImage, TLabelImage> Superclass;
+
+  typedef itk::SmartPointer<Self>       Pointer;
+  typedef itk::SmartPointer<const Self> ConstPointer;
+
+  typedef unsigned int ObjectSizeType;
+
+  /** Some convenient typedefs. */
+  typedef TVInputImage VectorImageType;
+  typedef TMaskImage   MaskImageType;
+  typedef TLabelImage LabelImageType;
+
+  typedef typename VectorImageType::Pointer VectorImagePointerType;
+  typedef typename VectorImageType::PixelType VectorImagePixelType;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Runtime information support. */
+  itkTypeMacro(MeanShiftConnectedComponentSegmentationFilter, ImageToImageFilter);
+
+  /** ImageDimension constants */
+  itkStaticConstMacro(InputImageDimension, unsigned int,TVInputImage::ImageDimension);
+
+  // Mask generation
+  typedef Functor::ConnectedComponentMuParserFunctor<VectorImagePixelType> FunctorType;
+  typedef itk::ConnectedComponentFunctorImageFilter
+      <VectorImageType, LabelImageType, FunctorType, MaskImageType>
+      ConnectedComponentFilterType;
+
+  // mask typedef
+  typedef otb::MaskMuParserFilter<VectorImageType, MaskImageType> MaskMuParserFilterType;
+
+  // Labelization
+  typedef itk::RelabelComponentImageFilter<LabelImageType, LabelImageType>
+  RelabelComponentFilterType;
+
+  typedef double KernelType;
+  typedef otb::MeanShiftImageFilter2
+      <VectorImageType, VectorImageType, VectorImageType, KernelType>
+  MeanShiftFilterType;
+
+  typedef typename MeanShiftFilterType::Pointer MeanShiftFilterPointerType;
+
+  // ** // meanshift filter
+  /* Set/Get mean shift filter */
+  itkSetObjectMacro(MeanShiftFilter, MeanShiftFilterType);
+  itkGetObjectMacro(MeanShiftFilter, MeanShiftFilterType);
+
+  /* Set the mathematical expression used for the mask */
+  itkSetStringMacro(MaskExpression);
+
+  /* Get the mathematical expression used for the mask */
+  itkGetStringMacro(MaskExpression);
+
+  /* Set the mathematical expression used during connected component segmentation */
+  itkSetStringMacro(ConnectedComponentExpression);
+
+  /* Get the mathematical expression used during connected component segmentation */
+  itkGetStringMacro(ConnectedComponentExpression);
+
+  /* Set the minimum object size */
+  itkSetMacro(MinimumObjectSize, ObjectSizeType);
+
+  /* Get the minimum object size */
+  itkGetMacro(MinimumObjectSize, ObjectSizeType);
+
+protected:
+  MeanShiftConnectedComponentSegmentationFilter();
+
+  virtual ~MeanShiftConnectedComponentSegmentationFilter();
+
+  void GenerateInputRequestedRegion();
+  virtual void GenerateData();
+
+private:
+
+  MeanShiftFilterPointerType m_MeanShiftFilter;
+
+  /* CC parameters */
+  ObjectSizeType m_MinimumObjectSize;
+  std::string    m_MaskExpression;
+  std::string    m_ConnectedComponentExpression;
+  /* */
+
+};
+
+
+} // end namespace itk
+
+#ifndef OTB_MANUAL_INSTANTIATION
+#include "otbMeanShiftConnectedComponentSegmentationFilter.txx"
+#endif
+
+#endif

Code/OBIA/otbMeanShiftConnectedComponentSegmentationFilter.txx

+/*=========================================================================
+
+  Program:   ORFEO Toolbox
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+
+  Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
+  See OTBCopyright.txt for details.
+
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __otbMeanShiftConnectedComponentSegmentationFilter_txx
+#define __otbMeanShiftConnectedComponentSegmentationFilter_txx
+
+#include "otbMeanShiftConnectedComponentSegmentationFilter.h"
+#include "itkExtractImageFilter.h"
+
+namespace otb {
+
+template<class TVImage,class TMaskImage, class TLabelImage>
+MeanShiftConnectedComponentSegmentationFilter<TVImage,TMaskImage,  TLabelImage>
+::MeanShiftConnectedComponentSegmentationFilter()
+{
+   m_MinimumObjectSize=2;
+   m_MeanShiftFilter= MeanShiftFilterType::New();
+
+}
+
+template<class TVImage,class TMaskImage, class TLabelImage>
+MeanShiftConnectedComponentSegmentationFilter<TVImage,TMaskImage,  TLabelImage>
+::~MeanShiftConnectedComponentSegmentationFilter()
+{
+}
+
+template<class TVImage,class TMaskImage, class TLabelImage>
+void
+MeanShiftConnectedComponentSegmentationFilter<TVImage,TMaskImage,  TLabelImage>
+::GenerateInputRequestedRegion()
+{
+  Superclass::GenerateInputRequestedRegion();
+}
+
+template<class TVImage,class TMaskImage, class TLabelImage>
+void
+MeanShiftConnectedComponentSegmentationFilter<TVImage,TMaskImage,  TLabelImage>
+::GenerateData()
+{
+  // Apply an ExtractImageFilter to avoid problems with filters asking for the LargestPossibleRegion
+  typedef itk::ExtractImageFilter<TVImage, TVImage> ExtractImageFilterType;
+  typename ExtractImageFilterType::Pointer extract = ExtractImageFilterType::New();
+  extract->SetInput(this->GetInput());
+  extract->SetExtractionRegion(this->GetOutput()->GetRequestedRegion());
+  // WARNING: itk::ExtractImageFilter does not copy the MetadataDictionnary
+
+  // meanshift filtering
+
+  //not necessary
+  /* if (this->m_MeanShiftFilter.IsNotNull())
+   {
+   itkExceptionMacro("MeanShiftFilter is null");
+   }*/
+  this->m_MeanShiftFilter->SetInput(extract->GetOutput());
+
+  //this->m_MeanShiftFilter->SetInput(this->GetInput());
+
+
+  typename MaskImageType::Pointer mask;
+  if (!m_MaskExpression.empty())
+    {
+    // Compute the mask
+    typename MaskMuParserFilterType::Pointer maskFilter;
+    maskFilter = MaskMuParserFilterType::New();
+    maskFilter->SetInput(this->m_MeanShiftFilter->GetOutput());
+    maskFilter->SetExpression(m_MaskExpression);
+    maskFilter->Update();
+    mask = maskFilter->GetOutput();
+    }
+
+  // Perform connected components segmentation
+  typename ConnectedComponentFilterType::Pointer connected = ConnectedComponentFilterType::New();
+  connected->SetInput(this->m_MeanShiftFilter->GetOutput());
+
+  if (mask.IsNotNull()) connected->SetMaskImage(mask);
+  connected->GetFunctor().SetExpression(m_ConnectedComponentExpression);
+  connected->Update();
+
+  // Relabel connected component output
+  typename RelabelComponentFilterType::Pointer relabel = RelabelComponentFilterType::New();
+  relabel->SetInput(connected->GetOutput());
+  relabel->SetMinimumObjectSize(m_MinimumObjectSize);
+  relabel->Update();
+
+  this->GraftOutput(relabel->GetOutput());
+
+}
+
+} // end namespace otb
+#endif