itkMultiGaussianImageSource.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.
 *
 *=========================================================================*/
/*=========================================================================
 *
 *  Portions of this file are subject to the VTK Toolkit Version 3 copyright.
 *
 *  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
 *
 *  For complete copyright, license and disclaimer of warranty information
 *  please refer to the NOTICE file at the top of the ITK source tree.
 *
 *=========================================================================*/
#ifndef __itkMultiGaussianImageSource_h
#define __itkMultiGaussianImageSource_h

#include "itkImageSource.h"
#include "itkNumericTraits.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkImageFileWriter.h"
#include <itkMapContainer.h>


namespace itk
{
template< typename TOutputImage >
class ITK_EXPORT MultiGaussianImageSource:public ImageSource< TOutputImage >
{
public:
  typedef MultiGaussianImageSource           Self;
  typedef ImageSource< TOutputImage > Superclass;
  typedef SmartPointer< Self >        Pointer;
  typedef SmartPointer< const Self >  ConstPointer;

  typedef typename TOutputImage::PixelType OutputImagePixelType;

  typedef typename TOutputImage::RegionType OutputImageRegionType;

  itkNewMacro(Self);

  typedef typename TOutputImage::SizeType                     SizeType;
  typedef typename TOutputImage::IndexType                    IndexType;
  typedef typename TOutputImage::SpacingType                  SpacingType;
  typedef typename TOutputImage::PointType                    PointType;
  typedef typename SizeType::SizeValueType                    SizeValueType;
  typedef SizeValueType                                       SizeValueArrayType[TOutputImage::ImageDimension];
  typedef typename TOutputImage::SpacingValueType             SpacingValueType;
  typedef SpacingValueType                                    SpacingValueArrayType[TOutputImage::ImageDimension];
  typedef typename TOutputImage::PointValueType               PointValueType;
  typedef PointValueType                                      PointValueArrayType[TOutputImage::ImageDimension];
  typedef typename itk::ImageRegion<3> ::SizeValueType        SizeRegionType;
  typedef double                                              RadiusType;
  typedef std::vector<double>                                 VectorType;
  typedef Vector<double, TOutputImage::ImageDimension>        ItkVectorType;
  typedef ImageRegionIteratorWithIndex<TOutputImage>          IteratorType;
  typedef typename TOutputImage::Pointer                      ImageType;

  typedef  MapContainer<unsigned int, PointType>              MapContainerPoints;
   typedef  MapContainer<unsigned int, double>                MapContainerRadius;


  itkSetMacro(Size, SizeType);
  virtual void SetSize(SizeValueArrayType sizeArray);
  virtual const SizeValueType * GetSize() const;
  itkSetMacro(Spacing, SpacingType);
  virtual void SetSpacing(SpacingValueArrayType spacingArray);
  virtual const SpacingValueType * GetSpacing() const;
  itkSetMacro(Origin, PointType);
  virtual void SetOrigin(PointValueArrayType originArray);
  virtual const PointValueType * GetOrigin() const;
  virtual unsigned int GetNumberOfGaussians() const;
  virtual void SetNumberOfGausssians( unsigned int );
  virtual RadiusType GetRadius() const;
  virtual void  SetRadius( RadiusType  radius );
  virtual const OutputImagePixelType GetMaxMeanValue() const;
  virtual const IndexType GetSphereMidpoint() const;
  virtual double MultiGaussianFunctionValueAtPoint(double , double, double);
  virtual void AddGaussian( VectorType centerX, VectorType centerY, VectorType centerZ, VectorType sigmaX, VectorType sigmaY, VectorType sigmaZ, VectorType altitude);
  virtual void CalculateTheMidpointAndTheMeanValueWithOctree();
  virtual void CalculateMaxAndMinInSphere();
  virtual const IndexType GetMaxValueIndexInSphere() const;
  virtual const OutputImagePixelType GetMaxValueInSphere() const;
  virtual const IndexType GetMinValueIndexInSphere() const;
  virtual const OutputImagePixelType GetMinValueInSphere() const;
  virtual void SetRegionOfInterest(ItkVectorType, ItkVectorType);
  virtual void WriteXMLToTestTheCuboidInsideTheSphere();
  virtual void CalculateEdgesInSphere( PointType globalCoordinateMidpointCuboid, PointType globalCoordinateMidpointSphere, double cuboidRadius, int level);
  virtual double MultiGaussianFunctionValueAtCuboid(double xMin, double xMax, double yMin, double yMax, double zMin, double zMax);
  virtual void InsertPoints( PointType globalCoordinateMidpointCuboid, double cuboidRadius);
  virtual void GenerateCuboidSegmentationInSphere( PointType globalCoordinateMidpointSphere );
  virtual double FunctionPhi(double value);
  virtual  unsigned int IntersectTheSphere( PointType globalCoordinateMidpointCuboid, PointType globalCoordinateMidpointSphere, double sideLength);
  void SetNormalDistributionValues();


  itkSetClampMacro( Min, OutputImagePixelType,
                    NumericTraits< OutputImagePixelType >::NonpositiveMin(),
                    NumericTraits< OutputImagePixelType >::max() );
  bool IsInImage(IndexType index);

  itkGetConstMacro(Min, OutputImagePixelType);

  itkSetClampMacro( Max, OutputImagePixelType,
                    NumericTraits< OutputImagePixelType >::NonpositiveMin(),
                    NumericTraits< OutputImagePixelType >::max() );

  itkGetConstMacro(Max, OutputImagePixelType);

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

  virtual void GenerateData();
  virtual void GenerateOutputInformation();

private:
  MultiGaussianImageSource(const MultiGaussianImageSource &); //purposely not implemented
  void operator=(const MultiGaussianImageSource &);    //purposely not implemented

  SizeType                                  m_Size;                  //size of the output image
  SpacingType                               m_Spacing;               //spacing
  PointType                                 m_Origin;                //origin
  OutputImagePixelType                      m_MaxValueInSphere;      //maximal value in the wanted sphere
  IndexType                                 m_MaxValueIndexInSphere; //index of the maximal value in the wanted sphere
  OutputImagePixelType                      m_MinValueInSphere;      //minimal value in the wanted sphere
  IndexType                                 m_MinValueIndexInSphere; //index of the minimal value in the wanted sphere
  unsigned int                              m_NumberOfGaussians;     //number of Gaussians
  RadiusType                                m_Radius;                //radius of the sphere
  unsigned int                              m_RadiusStepNumber;      //number of steps to traverse the sphere radius
  OutputImagePixelType                      m_MeanValue;             //mean value in the wanted sphere
  OutputImagePixelType                      m_ValueAtMidpoint;       //value at the midpoint of the wanted sphere
  IndexType                                 m_SphereMidpoint;        //midpoint of the wanted sphere
  VectorType                                m_SigmaX;                //deviation in the x-axis
  VectorType                                m_SigmaY;                //deviation in the y-axis
  VectorType                                m_SigmaZ;                //deviation in the z-axis
  VectorType                                m_CenterX;               //x-coordinate of the mean value of Gaussians
  VectorType                                m_CenterY;               //y-coordinate of the mean value of Gaussians
  VectorType                                m_CenterZ;               //z-coordinate of the mean value of Gaussians
  VectorType                                m_Altitude;              //amplitude
  ItkVectorType                             m_RegionOfInterestMax;   //maximal values for the coordinates in the region of interest
  ItkVectorType                             m_RegionOfInterestMin;   //minimal values for the coordinates in the region of interest
  typename TOutputImage::PixelType          m_Min;                   //minimum possible value
  typename TOutputImage::PixelType          m_Max;                   //maximum possible value
  PointType                                 m_GlobalCoordinate;      //physical coordiante of the sphere midpoint
  bool                                      m_WriteMPS;              //1 = write a MPS File to visualise the cuboid midpoints of one approximation of the sphere
  MapContainerPoints                        m_Midpoints;             //the midpoints of the cuboids
  MapContainerRadius                        m_RadiusCuboid;          //the radius ( = 0.5 * side length) of the cuboids (in the same order as the midpoints in m_Midpoints)
  double                                    m_Volume;                //the volume of the body, that approximize the sphere
  double                                    m_NormalDistValues [410];//normal distribution values
  double                                    m_meanValueTemp;         //= m_Volume * meanValue in each sphere
  // The following variables are deprecated, and provided here just for
  // backward compatibility. It use is discouraged.
  mutable PointValueArrayType               m_OriginArray;
  mutable SpacingValueArrayType             m_SpacingArray;
};

} // end namespace itk

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

#endif