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 "vnl/vnl_math.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 ImagePCAShapeModelEstimator:
  public ImageShapeModelEstimatorBase< TInputImage, TOutputImage >
{
public:
  typedef ImagePCAShapeModelEstimator                               Self;
  typedef ImageShapeModelEstimatorBase< TInputImage, TOutputImage > Superclass;
  typedef SmartPointer< Self >                                      Pointer;
  typedef SmartPointer< const Self >                                ConstPointer;

  itkNewMacro(Self);

  itkTypeMacro(ImagePCAShapeModelEstimator, ImageShapeModelEstimatorBase);

  typedef TInputImage                        InputImageType;
  typedef typename TInputImage::Pointer      InputImagePointer;
  typedef typename TInputImage::ConstPointer InputImageConstPointer;

  typedef typename TInputImage::PixelType InputImagePixelType;

  typedef ImageRegionIterator< TInputImage >      InputImageIterator;
  typedef ImageRegionConstIterator< TInputImage > InputImageConstIterator;

  itkStaticConstMacro(InputImageDimension, unsigned int,
                      TInputImage::ImageDimension);

  typedef TOutputImage                   OutputImageType;
  typedef typename TOutputImage::Pointer OutputImagePointer;

  typedef ImageRegionIterator< TOutputImage > OutputImageIterator;

  typedef vnl_matrix< double > MatrixOfDoubleType;

  typedef vnl_matrix< int > MatrixOfIntegerType;

  typedef vnl_vector< double > VectorOfDoubleType;

  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();
  virtual void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

  virtual void EnlargeOutputRequestedRegion(DataObject *) ITK_OVERRIDE;

  virtual void GenerateInputRequestedRegion() ITK_OVERRIDE;

  void GenerateData() ITK_OVERRIDE;

private:

  ImagePCAShapeModelEstimator(const Self &); //purposely not implemented
  void operator=(const Self &);              //purposely not implemented

  typedef std::vector< InputImageConstPointer >  InputImagePointerArray;
  typedef std::vector< InputImageConstIterator > InputImageIteratorArray;

  typedef typename TInputImage::SizeType ImageSizeType;

  typedef typename TInputImage::PixelType InputPixelType;

  virtual void EstimateShapeModels() ITK_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;

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

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

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

#endif