/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
  Language:  C++
  Date:      $Date: 2006-03-27 17:01:06 $
  Version:   $Revision: 1.12 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm 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 __itkDiffusionTensor3DReconstructionImageFilter_h_
#define __itkDiffusionTensor3DReconstructionImageFilter_h_

#include "itkImageToImageFilter.h"
#include "itkDiffusionTensor3D.h"
#include "vnl/vnl_matrix.h"
#include "vnl/vnl_vector_fixed.h"
#include "vnl/vnl_matrix_fixed.h"
#include "vnl/algo/vnl_svd.h"
#include "itkVectorContainer.h"
#include "itkVectorImage.h"

namespace itk{
/** \class DiffusionTensor3DReconstructionImageFilter
 * \brief This class takes as input one or more reference image (acquired in the 
 * absence of diffusion sensitizing gradients) and 'n' diffusion
 * weighted images and their gradient directions and computes an image of 
 * tensors. (with DiffusionTensor3D as the pixel type). Once that is done, you 
 * can apply filters on this tensor image to compute FA, ADC, RGB weighted 
 * maps etc. 
 *
 * \par Inputs and Usage
 * There are two ways to use this class. When you have one reference image and \c n
 * gradient images, you would use the class as
 * \code
 *       filter->SetReferenceImage( image0 );
 *       filter->AddGradientImage( direction1, image1 );
 *       filter->AddGradientImage( direction2, image2 );
 *   ...
 * \endcode
 *
 * \par
 * When you have the 'n' gradient and one or more reference images in a single 
 * multi-component image (VectorImage), you can specify the images simply as
 * \code
 *       filter->SetGradientImage( directionsContainer, vectorImage );
 * \endcode
 * Note that this method is used to specify both the reference and gradient images.
 * This is convenient when the DWI images are read in using the 
 * <a href="http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format">NRRD</a> 
 * format. Like the Nrrd format, the reference images are those components of the 
 * vectorImage whose gradient direction is (0,0,0). If more than one reference image
 * is present, they are averaged prior to applying the Stejskal-Tanner equations.
 *
 * \par Outputs
 * The output image is an image of Tensors:
 * \code
 *       Image< DiffusionTensor3D< TTensorPixelType >, 3 >
 * \endcode
 *
 * \par Parameters
 * \li Threshold -  Threshold on the reference image data. The output tensor will 
 * be a null tensor for pixels in the reference image that have a value less 
 * than this.
 * \li BValue - See the documentation of SetBValue().
 * \li At least 6 gradient images must be specified for the filter to be able 
 * to run.
 * 
 * 
 * \par Template parameters
 * The class is templated over the pixel type of the reference and gradient 
 * images (expected to be scalar data types) and the internal representation
 * of the DiffusionTensor3D pixel (double, float etc).
 *  
 * \par References:
 * \li<a href="http://lmi.bwh.harvard.edu/papers/pdfs/2002/westinMEDIA02.pdf">[1]</a> 
 * <em>C.F.Westin, S.E.Maier, H.Mamata, A.Nabavi, F.A.Jolesz, R.Kikinis,
 * "Processing and visualization for Diffusion tensor MRI", Medical image
 * Analysis, 2002, pp 93-108.</em>
 * \li<a href="splweb.bwh.harvard.edu:8000/pages/papers/westin/ISMRM2002.pdf">[2]</a>
 * <em>A Dual Tensor Basis Solution to the Stejskal-Tanner Equations for DT-MRI</em>
 * 
 * \par WARNING:
 * Although this filter has been written to support multiple threads, please 
 * set the number of threads to 1.
 * \code
 *         filter->SetNumberOfThreads(1);
 * \endcode
 * This is due to buggy code in netlib/dsvdc, that is called by vnl_svd. 
 * (used to compute the psudo-inverse to find the dual tensor basis).
 *
 * \author Thanks to Xiaodong Tao, GE, for contributing parts of this class. Also
 * thanks to Casey Goodlet, UNC for patches to support multiple baseline images
 * and other improvements.
 * 
 * \note
 * This work is part of the National Alliance for Medical image Computing 
 * (NAMIC), funded by the National Institutes of Health through the NIH Roadmap
 * for Medical Research, Grant U54 EB005149.
 *
 * \par Examples and Datasets
 * See Examples/Filtering/DiffusionTensor3DReconstructionImageFilter.cxx
 * Sample DTI datasets may be obtained from 
 \begin verbatim
     ftp://public.kitware.com/pub/namic/DTI/Data/dwi.nhdr
     ftp://public.kitware.com/pub/namic/DTI/Data/dwi.img.gz ( gunzip this )
 \end verbatim
 *
 * \sa DiffusionTensor3D SymmetricSecondRankTensor 
 * \ingroup Multithreaded  TensorObjects
 */

template< class TReferenceImagePixelType, 
          class TGradientImagePixelType=TReferenceImagePixelType,
          class TTensorPixelType=double >
class ITK_EXPORT DiffusionTensor3DReconstructionImageFilter :
  public ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, 
                             Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
{

public:

  typedef DiffusionTensor3DReconstructionImageFilter Self;
  typedef SmartPointer<Self>                      Pointer;
  typedef SmartPointer<const Self>                ConstPointer;
  typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3>, 
          Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
                          Superclass;
  
   /** Method for creation through the object factory. */
  itkNewMacro(Self);  

  /** Runtime information support. */
  itkTypeMacro(DiffusionTensor3DReconstructionImageFilter, 
                                                      ImageToImageFilter);
 
  typedef TReferenceImagePixelType                 ReferencePixelType;

  typedef TGradientImagePixelType                  GradientPixelType;

  typedef DiffusionTensor3D< TTensorPixelType >    TensorPixelType;

  /** Reference image data,  This image is aquired in the absence 
   * of a diffusion sensitizing field gradient */
  typedef typename Superclass::InputImageType      ReferenceImageType;
  
  typedef Image< TensorPixelType, 3 >              TensorImageType;
  
  typedef TensorImageType                          OutputImageType;

  typedef typename Superclass::OutputImageRegionType
                                                   OutputImageRegionType;

  /** Typedef defining one (of the many) gradient images.  */
  typedef Image< GradientPixelType, 3 >            GradientImageType;

  /** An alternative typedef defining one (of the many) gradient images. 
   * It will be assumed that the vectorImage has the same dimension as the 
   * Reference image and a vector length parameter of \c n (number of
   * gradient directions)*/
  typedef VectorImage< GradientPixelType, 3 >      GradientImagesType;

  /** Holds the tensor basis coefficients G_k */
  typedef vnl_matrix_fixed< double, 6, 6 >         TensorBasisMatrixType;
  
  typedef vnl_matrix< double >                     CoefficientMatrixType;

  /** Holds each magnetic field gradient used to acquire one DWImage */
  typedef vnl_vector_fixed< double, 3 >            GradientDirectionType;

  /** Container to hold gradient directions of the 'n' DW measurements */
  typedef VectorContainer< unsigned int, 
          GradientDirectionType >                  GradientDirectionContainerType;
  

  /** Set method to add a gradient direction and its corresponding image. */
  void AddGradientImage( const GradientDirectionType &, const GradientImageType *image);

  /** Another set method to add a gradient directions and its corresponding
   * image. The image here is a VectorImage. The user is expected to pass the 
   * gradient directions in a container. The ith element of the container 
   * corresponds to the gradient direction of the ith component image the 
   * VectorImage.  For the baseline image, a vector of all zeros
   * should be set.*/
  void SetGradientImage( GradientDirectionContainerType *, 
                                             const GradientImagesType *image);
  
  /** Set method to set the reference image. */
  void SetReferenceImage( ReferenceImageType *referenceImage )
    {
    if( m_GradientImageTypeEnumeration == GradientIsInASingleImage)
      {
      itkExceptionMacro( << "Cannot call both methods:" 
      << "AddGradientImage and SetGradientImage. Please call only one of them.");
      }
  
    this->ProcessObject::SetNthInput( 0, referenceImage );

    m_GradientImageTypeEnumeration = GradientIsInManyImages;
    }
    
  /** Get reference image */
  virtual ReferenceImageType * GetReferenceImage() 
  { return ( static_cast< ReferenceImageType *>(this->ProcessObject::GetInput(0)) ); }

  /** Return the gradient direction. idx is 0 based */
  virtual GradientDirectionType GetGradientDirection( unsigned int idx) const
    {
    if( idx >= m_NumberOfGradientDirections )
      {
      itkExceptionMacro( << "Gradient direction " << idx << "does not exist" );
      }
    return m_GradientDirectionContainer->ElementAt( idx+1 );
    }

  /** Threshold on the reference image data. The output tensor will be a null
   * tensor for pixels in the reference image that have a value less than this
   * threshold. */
  itkSetMacro( Threshold, ReferencePixelType );
  itkGetMacro( Threshold, ReferencePixelType );

  
  /** 
   * The BValue \f$ (s/mm^2) \f$ value used in normalizing the tensors to 
   * physically meaningful units.  See equation (24) of the first reference for
   * a description of how this is applied to the tensor estimation.
   * Equation (1) of the same reference describes the physical significance.
   */
  itkSetMacro( BValue, TTensorPixelType);
#ifdef GetBValue
#undef GetBValue
#endif
  itkGetConstReferenceMacro( BValue, TTensorPixelType);

#ifdef ITK_USE_CONCEPT_CHECKING
  /** Begin concept checking */
  itkConceptMacro(ReferenceEqualityComparableCheck,
    (Concept::EqualityComparable<ReferencePixelType>));
  itkConceptMacro(TensorEqualityComparableCheck,
    (Concept::EqualityComparable<TensorPixelType>));
  itkConceptMacro(GradientConvertibleToDoubleCheck,
    (Concept::Convertible<GradientPixelType, double>));
  itkConceptMacro(DoubleConvertibleToTensorCheck,
    (Concept::Convertible<double, TensorPixelType>));
  itkConceptMacro(GradientReferenceAdditiveOperatorsCheck,
    (Concept::AdditiveOperators<GradientPixelType, GradientPixelType,
                                ReferencePixelType>));
  itkConceptMacro(ReferenceOStreamWritableCheck,
    (Concept::OStreamWritable<ReferencePixelType>));
  itkConceptMacro(TensorOStreamWritableCheck,
    (Concept::OStreamWritable<TensorPixelType>));
  /** End concept checking */
#endif

protected:
  DiffusionTensor3DReconstructionImageFilter();
  ~DiffusionTensor3DReconstructionImageFilter() {};
  void PrintSelf(std::ostream& os, Indent indent) const;

  void ComputeTensorBasis();
  
  void BeforeThreadedGenerateData();
  void ThreadedGenerateData( const 
      OutputImageRegionType &outputRegionForThread, int);
  
  /** enum to indicate if the gradient image is specified as a single multi-
   * component image or as several separate images */
  typedef enum
    {
    GradientIsInASingleImage = 1,
    GradientIsInManyImages,
    Else
    } GradientImageTypeEnumeration;
    
private:
  
  /* Tensor basis coeffs */
  TensorBasisMatrixType                             m_TensorBasis;
  
  CoefficientMatrixType                             m_BMatrix;

  /** container to hold gradient directions */
  GradientDirectionContainerType::Pointer           m_GradientDirectionContainer;

  /** Number of gradient measurements */
  unsigned int                                      m_NumberOfGradientDirections;

  /** Number of baseline images */
  unsigned int                                      m_NumberOfBaselineImages;

  /** Threshold on the reference image data */
  ReferencePixelType                                m_Threshold;

  /** LeBihan's b-value for normalizing tensors */
  TTensorPixelType                                  m_BValue;

  /** Gradient image was specified in a single image or in multiple images */
  GradientImageTypeEnumeration                      m_GradientImageTypeEnumeration;
};

}

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkDiffusionTensor3DReconstructionImageFilter.txx"
#endif

#endif