ADD: HooverConfusionMatrix to compare 2 segmentations

Code/OBIA/otbHooverConfusionMatrix.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 __otbHooverConfusionMatrix_h
+#define __otbHooverConfusionMatrix_h
+
+#include "itkLabelMapFilter.h"
+#include "itkVariableSizeMatrix.h"
+
+namespace otb
+{
+/** \class HooverConfusionMatrix
+ *
+ * \brief This class computes the confusion matrix from two LabelMapObject
+ *
+ * The confusion matrix stores the number of pixel inside the intersection between 
+ * couples of region. These couples are made from a ground truth segmentation and 
+ * a machine segmentation. The line number gives the index of the ground truth region. The 
+ * column number gives the index of the machine segmentation region.
+ */
+
+template< class TLabelMap >
+class ITK_EXPORT HooverConfusionMatrix :
+    public itk::LabelMapFilter< TLabelMap, TLabelMap >
+{
+public:
+  /** Standard class typedefs. */
+  typedef HooverConfusionMatrix   Self;
+  typedef itk::LabelMapFilter< TLabelMap, TLabelMap >      Superclass;
+  typedef itk::SmartPointer<Self>       Pointer;
+  typedef itk::SmartPointer<const Self> ConstPointer;
+
+  /** Standard New method. */
+  itkNewMacro(Self);
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(HooverConfusionMatrix, LabelMapFilter);
+
+  /** Some convenient typedefs. */
+  typedef TLabelMap                                     InputLabelMapType;
+  typedef typename InputLabelMapType::LabelObjectType   LabelObjectType;
+  typedef typename InputLabelMapType::LabelVectorType   LabelVectorType;
+
+  typedef typename LabelObjectType::LineContainerType   LineContainerType;
+  typedef typename LabelObjectType::IndexType           IndexType;
+  typedef typename LabelObjectType::LabelType           LabelType;
+  
+  typedef unsigned long                                 CoefficientType;
+  typedef itk::VariableSizeMatrix<CoefficientType>      MatrixType;
+  
+  /** Set the ground truth label map */
+  void SetGroundTruthLabelMap(const InputLabelMapType *gt);
+  
+  /** Set the machine segmentation label map */
+  void SetMachineSegmentationLabelMap(const InputLabelMapType *ms);
+  
+  /** Get the ground truth label map */
+  const InputLabelMapType* GetGroundTruthLabelMap();
+  
+  /** Get the machine segmentation label map */
+  const InputLabelMapType* GetMachineSegmentationLabelMap();
+
+  /** Get the output Hoover confusion matrix */
+  MatrixType & GetHooverConfusionMatrix()
+  {
+    return m_Matrix;
+  }
+
+protected:
+  /** Constructor */
+  HooverConfusionMatrix();
+  
+  ~HooverConfusionMatrix() {};
+  
+  /** BeforeThreadedGenerateData
+   *  Resize the matrix 
+   */
+  virtual void BeforeThreadedGenerateData();
+
+  /** Real action of the filter : fill the line of the confusion matrix corresponding to 
+   * the given label object 
+   */
+  virtual void ThreadedProcessLabelObject( LabelObjectType * labelObject );
+
+private:
+  
+  /** number of label objects found in the ground truth (GT) label maps */
+  unsigned long     m_NumberOfRegionsGT;
+  
+  /** number of label objects found in the machine segmentation (MS) label maps */
+  unsigned long     m_NumberOfRegionsMS;
+  
+  /** List of labels in GT label map */
+  LabelVectorType   m_LabelsGT;
+  
+  /** Hoover confusion matrix */
+  MatrixType        m_Matrix;
+};
+
+
+}
+
+#ifndef OTB_MANUAL_INSTANTIATION
+#include "otbHooverConfusionMatrix.txx"
+#endif
+
+#endif

Code/OBIA/otbHooverConfusionMatrix.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 __otbHooverConfusionMatrix_txx
+#define __otbHooverConfusionMatrix_txx
+
+#include "otbHooverConfusionMatrix.h"
+
+namespace otb
+{
+
+/** Constructor */
+template <class TLabelMap>
+HooverConfusionMatrix<TLabelMap>
+::HooverConfusionMatrix() : m_NumberOfRegionsGT(0), m_NumberOfRegionsMS(0)
+{
+  this->SetNumberOfRequiredInputs(2);
+  m_Matrix.SetSize(0,0);
+}
+
+/** Set the ground truth label map */
+template <class TLabelMap>
+void HooverConfusionMatrix<TLabelMap>
+::SetGroundTruthLabelMap(const InputLabelMapType *gt)
+{
+  this->SetInput(0,gt);
+}
+
+/** Set the machine segmentation label map */
+template <class TLabelMap>
+void HooverConfusionMatrix<TLabelMap>
+::SetMachineSegmentationLabelMap(const InputLabelMapType *ms)
+{
+  this->SetInput(1,ms);
+}
+
+/** Get the ground truth label map */
+template <class TLabelMap>
+const TLabelMap* HooverConfusionMatrix<TLabelMap>
+::GetGroundTruthLabelMap()
+{
+  return this->GetInput(0);
+}
+
+/** Get the machine segmentation label map */
+template <class TLabelMap>
+const TLabelMap* HooverConfusionMatrix<TLabelMap>
+::GetMachineSegmentationLabelMap()
+{
+  return this->GetInput(1);
+}
+
+template <class TLabelMap>
+void HooverConfusionMatrix<TLabelMap>
+::BeforeThreadedGenerateData()
+{
+  // first : call superclass method
+  Superclass::BeforeThreadedGenerateData();
+  
+  // Set the matrix size
+  m_NumberOfRegionsGT = this->GetGroundTruthLabelMap()->GetNumberOfLabelObjects();
+  m_NumberOfRegionsMS = this->GetMachineSegmentationLabelMap()->GetNumberOfLabelObjects();
+  m_LabelsGT = this->GetGroundTruthLabelMap()->GetLabels();
+  m_Matrix.SetSize(m_NumberOfRegionsGT , m_NumberOfRegionsMS);
+  m_Matrix.Fill(0);
+}
+
+template <class TLabelMap>
+void HooverConfusionMatrix<TLabelMap>
+::ThreadedProcessLabelObject( LabelObjectType * labelObject )
+{
+  typename LineContainerType::const_iterator lit;
+  LineContainerType & lineContainer = labelObject->GetLineContainer();
+  
+  unsigned long currentRegionMS = 0;
+  unsigned long currentRegionGT = 0;
+  // find the index of the current GT region
+  LabelType currentLabelGT = labelObject->GetLabel();
+  for (unsigned long k=0;k<m_NumberOfRegionsGT;k++)
+    {
+    if (currentLabelGT == m_LabelsGT[k])
+      {
+      currentRegionGT = k;
+      break;
+      }
+    }
+    
+  // loop over the given region
+  for (lit = lineContainer.begin();lit != lineContainer.end(); lit++)
+    {
+    IndexType idx = lit->GetIndex();
+    unsigned long length = lit->GetLength();
+    for (unsigned long i=0;i<length;i++)
+      {
+      // find the corresponding label in the ms label map
+      // if found : ++ in the cell [n,p]
+      for (unsigned long j = currentRegionMS;
+           j < (currentRegionMS + m_NumberOfRegionsMS);
+           j++)
+        {
+        // TODO : optimize here : call GetLabelObjet(label) would be faster
+        const LabelObjectType *regionMS = this->GetMachineSegmentationLabelMap()->GetNthLabelObject(j%m_NumberOfRegionsMS);
+        if (regionMS->HasIndex(idx))
+          {
+          currentRegionMS = j%m_NumberOfRegionsMS;
+          m_Matrix(currentRegionGT,currentRegionMS)++;
+          break;
+          }
+        }
+      idx[0]++;
+      }
+    } 
+}
+
+}
+#endif

Testing/Code/OBIA/CMakeLists.txt

@@ -176,7 +176,19 @@ ADD_TEST(obTvLabelImageToLabelMapWithAdjacencyFilter ${OBIA_TESTS3}
   ${TEMP}/obTvLabelImageToLabelMapWithAdjacencyFilterOutput.txt
 )
 
-      
+ADD_TEST(obTuHooverConfusionMatrixNew ${OBIA_TESTS1}
+    otbHooverConfusionMatrixNew)
+
+ADD_TEST(obTvHooverConfusionMatrix ${OBIA_TESTS1}
+    --compare-ascii ${NOTOL}
+    ${BASELINE_FILES}/obTvHooverConfusionMatrix.txt
+    ${TEMP}/obTvHooverConfusionMatrix.txt
+    otbHooverConfusionMatrix
+    ${INPUTDATA}/Seg1InputForRCC8Graph.tif
+    ${INPUTDATA}/Seg2InputForRCC8Graph.tif
+    ${TEMP}/obTvHooverConfusionMatrix.txt
+    )
+
 # OBIATests2 (need PQXX)
 IF(OTB_USE_PQXX)
 ADD_TEST(obTuLabelMapToGISTableFilterNew ${OBIA_TESTS2}
@@ -230,6 +242,8 @@ otbStatisticsAttributesLabelMapFilterNew.cxx
 otbVectorDataToLabelMapFilter.cxx
 otbVectorDataToLabelMapFilterNew.cxx
 otbStreamingConnectedComponentOBIATest.cxx
+otbHooverConfusionMatrixNew.cxx
+otbHooverConfusionMatrix.cxx
 )
 
 IF(OTB_USE_PQXX)

Testing/Code/OBIA/otbHooverConfusionMatrix.cxx

+/*=========================================================================
+
+  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.
+
+=========================================================================*/
+
+#include "otbHooverConfusionMatrix.h"
+
+#include "otbImage.h"
+#include "otbImageFileReader.h"
+#include "itkLabelMap.h"
+#include "itkLabelObject.h"
+#include "itkLabelImageToLabelMapFilter.h"
+
+int otbHooverConfusionMatrix(int argc, char* argv[])
+{
+  typedef itk::LabelObject<unsigned int,2>          LabelObjectType;
+  typedef itk::LabelMap<LabelObjectType>            LabelMapType;
+  typedef otb::HooverConfusionMatrix<LabelMapType>  HooverConfusionMatrixType;
+  typedef otb::Image<unsigned int, 2>               ImageType;
+  typedef itk::LabelImageToLabelMapFilter
+    <ImageType, LabelMapType>                       ImageToLabelMapFilterType;
+  typedef otb::ImageFileReader<ImageType>           ImageReaderType;
+  typedef HooverConfusionMatrixType::MatrixType     MatrixType;
+  
+  if(argc != 4)
+    {
+    std::cerr << "Usage: " << argv[0];
+    std::cerr << " segmentationGT segmentationMS HooverMatrix.txt" << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  ImageReaderType::Pointer gt_reader = ImageReaderType::New();
+  gt_reader->SetFileName(argv[1]);
+  
+  ImageReaderType::Pointer ms_reader = ImageReaderType::New();
+  ms_reader->SetFileName(argv[2]);
+  
+  ImageToLabelMapFilterType::Pointer gt_filter = ImageToLabelMapFilterType::New();
+  gt_filter->SetInput(gt_reader->GetOutput());
+  gt_filter->SetBackgroundValue(0);
+  
+  ImageToLabelMapFilterType::Pointer ms_filter = ImageToLabelMapFilterType::New();
+  ms_filter->SetInput(ms_reader->GetOutput());
+  ms_filter->SetBackgroundValue(0);
+  
+  HooverConfusionMatrixType::Pointer hooverFilter = HooverConfusionMatrixType::New();
+  hooverFilter->SetGroundTruthLabelMap(gt_filter->GetOutput());
+  hooverFilter->SetMachineSegmentationLabelMap(ms_filter->GetOutput());
+  
+  hooverFilter->Update();
+  
+  std::ofstream outputFile;
+  outputFile.open(argv[3]);
+  
+  MatrixType &mat = hooverFilter->GetHooverConfusionMatrix();
+  unsigned int n = mat.Rows(), p = mat.Cols();
+  for (int i=0;i<n;i++)
+    {
+    for (int j=0;j<p;j++)
+      {
+      outputFile << mat(i,j);
+      if (j == (p-1))
+        {
+        outputFile << "\n";
+        }
+      else
+        {
+        outputFile << "\t";
+        }
+      }
+    }
+  
+  return EXIT_SUCCESS;
+}

Testing/Code/OBIA/otbHooverConfusionMatrixNew.cxx

+/*=========================================================================
+
+  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.
+
+=========================================================================*/
+
+#include "otbHooverConfusionMatrix.h"
+
+#include "itkLabelMap.h"
+#include "itkLabelObject.h"
+
+int otbHooverConfusionMatrixNew(int argc, char* argv[])
+{
+  typedef itk::LabelObject<unsigned int,2>          LabelObjectType;
+  typedef itk::LabelMap<LabelObjectType>            LabelMapType;
+  typedef otb::HooverConfusionMatrix<LabelMapType>  HooverConfusionMatrixType;
+
+  // instantiation
+  HooverConfusionMatrixType::Pointer object = HooverConfusionMatrixType::New();
+
+  std::cout << object << std::endl;
+
+  return EXIT_SUCCESS;
+}

Testing/Code/OBIA/otbOBIATests1.cxx

@@ -53,4 +53,6 @@ REGISTER_TEST(otbVectorDataToLabelMapFilterNew);
 REGISTER_TEST(otbVectorDataToLabelMapFilter);
 REGISTER_TEST(otbStreamingConnectedComponentSegmentationOBIAToVectorDataFilterNew);
 REGISTER_TEST(otbStreamingConnectedComponentSegmentationOBIAToVectorDataFilter);
+REGISTER_TEST(otbHooverConfusionMatrixNew);
+REGISTER_TEST(otbHooverConfusionMatrix);
 }