itkImagePCAShapeModelEstimator.h

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/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  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
 *
 *         http://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 itkImagePCAShapeModelEstimator_h
#define itkImagePCAShapeModelEstimator_h

#include <ctime>
#include <cmath>
#include <cfloat>

#include "vnl/vnl_vector.h"
#include "vnl/vnl_matrix.h"
#include "itkMath.h"
#include "vnl/algo/vnl_matrix_inverse.h"

#include "itkImageRegionIterator.h"
#include "itkMacro.h"

#include "itkImageShapeModelEstimatorBase.h"
#include "itkConceptChecking.h"
#include "itkImage.h"
#include "vnl/algo/vnl_generalized_eigensystem.h"
#include "vnl/algo/vnl_symmetric_eigensystem.h"

namespace itk
{
template< typename TInputImage,
          typename TOutputImage = Image< double, TInputImage::ImageDimension > >
class ITK_TEMPLATE_EXPORT ImagePCAShapeModelEstimator:
  public ImageShapeModelEstimatorBase< TInputImage, TOutputImage >
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(ImagePCAShapeModelEstimator);

  using Self = ImagePCAShapeModelEstimator;
  using Superclass = ImageShapeModelEstimatorBase< TInputImage, TOutputImage >;
  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;

  itkNewMacro(Self);

  itkTypeMacro(ImagePCAShapeModelEstimator, ImageShapeModelEstimatorBase);

  using InputImageType = TInputImage;
  using InputImagePointer = typename TInputImage::Pointer;
  using InputImageConstPointer = typename TInputImage::ConstPointer;

  using InputImagePixelType = typename TInputImage::PixelType;

  using InputImageIterator = ImageRegionIterator< TInputImage >;
  using InputImageConstIterator = ImageRegionConstIterator< TInputImage >;

  static constexpr unsigned int InputImageDimension = TInputImage::ImageDimension;

  using OutputImageType = TOutputImage;
  using OutputImagePointer = typename TOutputImage::Pointer;

  using OutputImageIterator = ImageRegionIterator< TOutputImage >;

  using MatrixOfDoubleType = vnl_matrix< double >;

  using MatrixOfIntegerType = vnl_matrix< int >;

  using VectorOfDoubleType = vnl_vector< double >;

  virtual void SetNumberOfPrincipalComponentsRequired(unsigned int n);

  itkGetConstMacro(NumberOfPrincipalComponentsRequired, unsigned int);

  virtual void SetNumberOfTrainingImages(unsigned int n);

  itkGetConstMacro(NumberOfTrainingImages, unsigned int);

  itkGetConstMacro(EigenValues, VectorOfDoubleType);

protected:
  ImagePCAShapeModelEstimator();
  ~ImagePCAShapeModelEstimator() override = default;
  void PrintSelf(std::ostream & os, Indent indent) const override;

  void EnlargeOutputRequestedRegion(DataObject *) override;

  void GenerateInputRequestedRegion() override;

  void GenerateData() override;

private:

  using InputImagePointerArray = std::vector< InputImageConstPointer >;
  using InputImageIteratorArray = std::vector< InputImageConstIterator >;

  using ImageSizeType = typename TInputImage::SizeType;

  using InputPixelType = typename TInputImage::PixelType;

  void EstimateShapeModels() override;

  void EstimatePCAShapeModelParameters();

  void CalculateInnerProduct();

  InputImageIteratorArray m_InputImageIteratorArray;

  VectorOfDoubleType m_Means;

  MatrixOfDoubleType m_InnerProduct;

  MatrixOfDoubleType m_EigenVectors;

  VectorOfDoubleType m_EigenValues;

  VectorOfDoubleType m_EigenVectorNormalizedEnergy;

  ImageSizeType m_InputImageSize;

  unsigned int m_NumberOfPixels{0};

  // The number of input images for PCA
  unsigned int m_NumberOfTrainingImages{0};

  // The number of output Principal Components
  unsigned int m_NumberOfPrincipalComponentsRequired;
}; // class ImagePCAShapeModelEstimator
} // namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkImagePCAShapeModelEstimator.hxx"
#endif

#endif