itkLabelGeometryImageFilter.h

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/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         https://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkLabelGeometryImageFilter_h
#define itkLabelGeometryImageFilter_h
 
#include "itkImageToImageFilter.h"
#include "itkNumericTraits.h"
#include "itkArray.h"
#include "itkSimpleDataObjectDecorator.h"
#include <map>
#include <vector>
#include "vnl/algo/vnl_symmetric_eigensystem.h"
#include "vnl/vnl_det.h"
#include "itkMath.h"
 
namespace itk
{
template <typename TLabelImage, typename TIntensityImage = TLabelImage>
class ITK_TEMPLATE_EXPORT
#if !defined(ITK_LEGACY_SILENT)
  [[deprecated("This class contains known computational bugs. See class documentation for details.")]]
#endif
  LabelGeometryImageFilter : public ImageToImageFilter<TLabelImage, TIntensityImage>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(LabelGeometryImageFilter);

  using Self = LabelGeometryImageFilter;
  using Superclass = ImageToImageFilter<TLabelImage, TIntensityImage>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(LabelGeometryImageFilter);

  using IntensityImageType = TIntensityImage;
  using InputImagePointer = typename TIntensityImage::Pointer;
  using RegionType = typename TIntensityImage::RegionType;
  using SizeType = typename TIntensityImage::SizeType;
  using IndexType = typename TIntensityImage::IndexType;
  using PixelType = typename TIntensityImage::PixelType;

  using LabelImageType = TLabelImage;
  using LabelImagePointer = typename TLabelImage::Pointer;
  using LabelRegionType = typename TLabelImage::RegionType;
  using LabelSizeType = typename TLabelImage::SizeType;
  using LabelIndexType = typename TLabelImage::IndexType;
  using LabelPixelType = typename TLabelImage::PixelType;
  using LabelPointType = typename TLabelImage::PointType;

  static constexpr unsigned int ImageDimension = TLabelImage::ImageDimension;

  using RealType = typename NumericTraits<PixelType>::RealType;

  using DataObjectPointer = typename DataObject::Pointer;

  using RealObjectType = SimpleDataObjectDecorator<RealType>;

  using BoundingBoxType = itk::FixedArray<typename LabelIndexType::IndexValueType, Self::ImageDimension * 2>;
  using BoundingBoxFloatType = itk::FixedArray<float, Self::ImageDimension * 2>;
 
  // using BoundingBoxVerticesType = itk::FixedArray<
  // LabelPointType,std::pow(2.0,Self::ImageDimension)>;
  using BoundingBoxVerticesType = std::vector<LabelPointType>;

  using AxesLengthType = itk::FixedArray<RealType, Self::ImageDimension>;

  using IndexArrayType = itk::FixedArray<typename LabelIndexType::IndexValueType, Self::ImageDimension>;

  using LabelsType = std::vector<LabelPixelType>;

  using LabelIndicesType = std::vector<LabelIndexType>;

  using VectorType = std::vector<double>;

  using MatrixType = vnl_matrix<double>;

  class LabelGeometry
  {
  public:
    // default constructor
    LabelGeometry()
    {
      // initialized to the default values
      this->m_Label = 0;
      this->m_Sum = RealType{};
 
      const unsigned int imageDimension = Self::ImageDimension;
 
      // m_BoundingBox.resize(imageDimension*2);
      for (unsigned int i = 0; i < imageDimension * 2; i += 2)
      {
        m_BoundingBox[i] = NumericTraits<typename IndexType::IndexValueType>::max();
        m_BoundingBox[i + 1] = NumericTraits<typename IndexType::IndexValueType>::NonpositiveMin();
      }
 
      m_BoundingBoxVolume = 0;
      m_BoundingBoxSize.Fill(0);
      m_PixelIndices.clear();
      m_Centroid.Fill(0);
      m_WeightedCentroid.Fill(0);
      m_ZeroOrderMoment = 0;
      m_FirstOrderRawMoments.Fill(0);
      m_FirstOrderWeightedRawMoments.Fill(0);
      m_Eigenvalues.resize(ImageDimension);
      m_Eigenvalues.clear();
      m_Eigenvectors.set_size(ImageDimension, ImageDimension);
      m_Eigenvectors.fill(0);
      m_AxesLength.Fill(0);
      m_Eccentricity = 1;
      m_Elongation = 1;
      m_Orientation = 0;
      LabelPointType emptyPoint{};
      unsigned int   numberOfVertices = 1 << ImageDimension;
      m_OrientedBoundingBoxVertices.resize(numberOfVertices, emptyPoint);
      m_OrientedBoundingBoxVolume = 0;
      m_OrientedBoundingBoxSize.Fill(0);
      m_OrientedLabelImage = LabelImageType::New();
      m_OrientedIntensityImage = IntensityImageType::New();
      m_OrientedBoundingBoxOrigin.Fill(0);
      m_RotationMatrix.set_size(ImageDimension, ImageDimension);
      m_RotationMatrix.fill(0.0);
 
      m_SecondOrderRawMoments.set_size(ImageDimension, ImageDimension);
      m_SecondOrderCentralMoments.set_size(ImageDimension, ImageDimension);
      for (unsigned int i = 0; i < ImageDimension; ++i)
      {
        for (unsigned int j = 0; j < ImageDimension; ++j)
        {
          m_SecondOrderRawMoments(i, j) = 0;
          m_SecondOrderCentralMoments(i, j) = 0;
        }
      }
    }
 
    LabelPixelType                          m_Label;
    RealType                                m_Sum;
    LabelPointType                          m_Centroid;
    LabelPointType                          m_WeightedCentroid;
    SizeValueType                           m_ZeroOrderMoment;
    IndexArrayType                          m_FirstOrderRawMoments;
    AxesLengthType                          m_FirstOrderWeightedRawMoments;
    SizeValueType                           m_FirstOrderRawCrossMoment;
    RealType                                m_FirstOrderCentralCrossMoment;
    MatrixType                              m_SecondOrderRawMoments;
    MatrixType                              m_SecondOrderCentralMoments;
    VectorType                              m_Eigenvalues;
    MatrixType                              m_Eigenvectors;
    FixedArray<float, Self::ImageDimension> m_AxesLength;
    RealType                                m_Eccentricity;
    RealType                                m_Elongation;
    RealType                                m_Orientation;
    BoundingBoxType                         m_BoundingBox;
    LabelSizeType                           m_BoundingBoxSize;
    RealType                                m_BoundingBoxVolume;
    LabelIndicesType                        m_PixelIndices;
    BoundingBoxVerticesType                 m_OrientedBoundingBoxVertices;
    RealType                                m_OrientedBoundingBoxVolume;
    LabelPointType                          m_OrientedBoundingBoxSize;
    typename LabelImageType::Pointer        m_OrientedLabelImage;
    typename IntensityImageType::Pointer    m_OrientedIntensityImage;
    MatrixType                              m_RotationMatrix;
    LabelPointType                          m_OrientedBoundingBoxOrigin;
  };

  // Map from the label to the class storing all of the geometry information.
  using MapType = std::map<LabelPixelType, LabelGeometry>;
  using MapIterator = typename std::map<LabelPixelType, LabelGeometry>::iterator;
  using MapConstIterator = typename std::map<LabelPixelType, LabelGeometry>::const_iterator;
 
  // Macros for enabling the calculation of additional features.
  itkGetMacro(CalculatePixelIndices, bool);
  itkBooleanMacro(CalculatePixelIndices);
  void
  SetCalculatePixelIndices(const bool value)
  {
    // CalculateOrientedBoundingBox, CalculateOrientedLabelImage, and
    // CalculateOrientedIntensityImage all need CalculatePixelIndices to be
    // turned
    // on if they are turned on.  So, CalculatePixelIndices cannot be
    // turned off if any of these flags are turned on.
    if (value == false)
    {
      if ((this->m_CalculateOrientedBoundingBox) || (this->m_CalculateOrientedLabelRegions) ||
          (this->m_CalculateOrientedIntensityRegions))
      {
        // We cannot change the value, so return.
        return;
      }
    }
 
    if (this->m_CalculatePixelIndices != value)
    {
      this->m_CalculatePixelIndices = value;
      this->Modified();
    }
  }
 
  itkGetMacro(CalculateOrientedBoundingBox, bool);
  itkBooleanMacro(CalculateOrientedBoundingBox);
  void
  SetCalculateOrientedBoundingBox(const bool value)
  {
    if (this->m_CalculateOrientedBoundingBox != value)
    {
      this->m_CalculateOrientedBoundingBox = value;
      this->Modified();
    }
 
    // CalculateOrientedBoundingBox needs
    // CalculatePixelIndices to be turned on.
    if (value)
    {
      this->SetCalculatePixelIndices(true);
    }
  }
 
  itkGetMacro(CalculateOrientedLabelRegions, bool);
  itkBooleanMacro(CalculateOrientedLabelRegions);
  void
  SetCalculateOrientedLabelRegions(const bool value)
  {
    if (this->m_CalculateOrientedLabelRegions != value)
    {
      this->m_CalculateOrientedLabelRegions = value;
      this->Modified();
 
      // CalculateOrientedLabelImage needs
      // CalculateOrientedBoundingBox to be turned on.
      if (value)
      {
        SetCalculateOrientedBoundingBox(true);
      }
    }
  }
 
  itkGetMacro(CalculateOrientedIntensityRegions, bool);
  itkBooleanMacro(CalculateOrientedIntensityRegions);
  void
  SetCalculateOrientedIntensityRegions(const bool value)
  {
    if (this->m_CalculateOrientedIntensityRegions != value)
    {
      this->m_CalculateOrientedIntensityRegions = value;
      this->Modified();
 
      // CalculateOrientedIntensityImage needs
      // CalculateOrientedBoundingBox to be turned on.
      if (value)
      {
        this->SetCalculateOrientedBoundingBox(true);
      }
    }
  }

  void
  SetIntensityInput(const TIntensityImage * input)
  {
    // Process object is not const-correct so the const casting is required.
    this->SetNthInput(1, const_cast<TIntensityImage *>(input));
  }

  const TIntensityImage *
  GetIntensityInput() const
  {
    return static_cast<TIntensityImage *>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
  }

  bool
  HasLabel(LabelPixelType label) const
  {
    return m_LabelGeometryMapper.find(label) != m_LabelGeometryMapper.end();
  }

  SizeValueType
  GetNumberOfObjects() const
  {
    return m_LabelGeometryMapper.size();
  }
 
  SizeValueType
  GetNumberOfLabels() const
  {
    return this->GetNumberOfObjects();
  }

  std::vector<LabelPixelType>
  GetLabels() const
  {
    return m_AllLabels;
  }

  LabelIndicesType
  GetPixelIndices(LabelPixelType label) const;

  SizeValueType
  GetVolume(LabelPixelType label) const;

  RealType
  GetIntegratedIntensity(LabelPixelType label) const;

  LabelPointType
  GetCentroid(LabelPixelType label) const;

  LabelPointType
  GetWeightedCentroid(LabelPixelType label) const;

  VectorType
  GetEigenvalues(LabelPixelType label) const;

  MatrixType
  GetEigenvectors(LabelPixelType label) const;

  AxesLengthType
  GetAxesLength(LabelPixelType label) const;

  RealType
  GetMinorAxisLength(LabelPixelType label) const;

  RealType
  GetMajorAxisLength(LabelPixelType label) const;

  RealType
  GetEccentricity(LabelPixelType label) const;

  RealType
  GetElongation(LabelPixelType label) const;

  RealType
  GetOrientation(LabelPixelType label) const;

  BoundingBoxType
  GetBoundingBox(LabelPixelType label) const;

  RealType
  GetBoundingBoxVolume(LabelPixelType label) const;

  LabelSizeType
  GetBoundingBoxSize(LabelPixelType label) const;

  BoundingBoxVerticesType
  GetOrientedBoundingBoxVertices(LabelPixelType label) const;

  RealType
  GetOrientedBoundingBoxVolume(LabelPixelType label) const;

  LabelPointType
  GetOrientedBoundingBoxSize(LabelPixelType label) const;

  LabelPointType
  GetOrientedBoundingBoxOrigin(LabelPixelType label) const;

  MatrixType
  GetRotationMatrix(LabelPixelType label) const;

  RegionType
  GetRegion(LabelPixelType label) const;

  TLabelImage *
  GetOrientedLabelImage(LabelPixelType label) const;

  TIntensityImage *
  GetOrientedIntensityImage(LabelPixelType label) const;
 
  itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits<PixelType>));
 
protected:
  LabelGeometryImageFilter();
  ~LabelGeometryImageFilter() override = default;
  void
  PrintSelf(std::ostream & os, Indent indent) const override;
 
  void
  GenerateData() override;
 
private:
  bool
  CalculateOrientedBoundingBoxVertices(vnl_symmetric_eigensystem<double> eig, LabelGeometry & m_LabelGeometry);
 
  bool m_CalculatePixelIndices{};
  bool m_CalculateOrientedBoundingBox{};
  bool m_CalculateOrientedLabelRegions{};
  bool m_CalculateOrientedIntensityRegions{};
 
  MapType       m_LabelGeometryMapper{};
  LabelGeometry m_LabelGeometry{};
  LabelsType    m_AllLabels{};
}; // end of class
 
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "itkLabelGeometryImageFilter.hxx"
#endif
 
#endif